The Microbiology of Cocoa Fermentation and its Role in Chocolate Quality

Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects

Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.

Counts of mesophilic aerobic, mesophilic anaerobic, thermophilic aerobic sporeforming bacteria and persistence of Bacillus cereus spores throughout cocoa powder processing chain

Sporeforming bacteria are a concern in some food raw materials, such as cocoa powder. Samples (n = 618) were collected on two farms and at several stages during cocoa powder manufacture in three commercial processing lines to determine the impact of each stage on bacterial spore populations. Mesophilic aerobic, mesophilic anaerobic, thermophilic aerobic, and Bacillus cereus spore populations were enumerated in all the samples. Genetic diversity in B. cereus strains (n = 110) isolated from the samples was examined by M13 sequence-based PCR typing, partial sequencing of the panC gene, and the presence/absence of ces and cspA genes. The counts of different groups of sporeforming bacteria varied amongst farms and processing lines. For example, the counts of mesophilic aerobic spore-forming (MAS) populations of cocoa bean fermentation were lower than 1 log spore/g in Farm 1 but higher than 4 log spore/g in Farm 2. B. cereus isolated from cocoa powder was also recovered from cocoa beans, nibs, and samples after roasting, refining, and pressing, which indicated that B. cereus spores persist throughout cocoa processing. Phylogenetic group IV was the most frequent (73%), along with processing. Strains from phylogenetic group III (14 %) did not show the ces gene's presence.

High temperature and nib acidification during cacao-controlled fermentation improve cadmium transfer from nibs to testa and the liquor's flavor

Migration of nib Cd to the testa during fermentation can be achieved with high temperatures (> 45 °C) and low nib pH values (< 5.0) using spontaneous fermentation. However, this low pH can lead to low flavor quality. This study used three controlled temperature fermentation treatments on three cacao genotypes (CCN 51, ICS 95, and TCS 01) to test its effects on the nib pH, the migration of nib Cd to the testa, and the liquor flavor quality. All treatments were effective in reducing the total nib Cd concentration. Nevertheless, the treatment with the higher mean temperature (44.25 °C) and acidification (pH 4.66) reached the highest mean nib Cd reductions throughout fermentation, a 1.37 factor in TCS 01, promoting the development of fine-flavor cocoa sensorial notes. In unfermented beans, the Cd concentration of nibs was higher than that of the testa, and the Cd migration proceeded down the total concentration gradient. However, Cd migration was observed against the concentration gradient (testa Cd > nib Cd) from the fourth day. Cd migration could increase by extensive fermentation until the sixth day in high temperatures and probably by the adsorbent capacity of the testa. Genotype-by-treatment interactions were present for the nib Cd reduction, and a universal percentage of decrease of Cd for each genotype with fermentation cannot be expected. Selecting genotypes with highly adsorbent testa combined with controlled temperatures would help reduce the Cd concentration in the cacao raw material, improving its safety and quality.

Effect of Pod Storage and Drying Temperature on Fermentation Dynamics and Final Bean Quality of Cacao Nacional in Ecuador

The impact of pod storage (PS) and two drying temperatures of fermented cocoa beans was investigated in Ecuador. Therefore, four variations were simultaneously carried out three times at two locations, independently: 0, 3, and 5 days of PS, dried at 60 °C and 0 days of PS, dried at 80 °C. Pod weight during storage, pulp content, pH, temperature, microbial counts, total free amino acids, protein profiles, sugars, organic acids, cut-test, fermentation index, and sensory profiles were analyzed. Minor differences in fermentation dynamics and bean quality were found between variations with and without PS. A rather accelerated fermentation with pod-stored beans was observed (e.g., faster color change, slightly lower pH in cotyledon after 48 h), along with a significantly higher maximal temperature during 24-42 h (43.1 ± 3.2 °C compared to 39.2 ± 2.0 °C without PS). More well-fermented beans were reached with PS (52.3 ± 22.6%) than without (62.7 ± 9.2%). Differences during fermentation were observed between the locations (e.g., pH, acids, sugars), but sensory evaluation indicated that the impact of location was mitigated with PS. Drying at 80 °C showed no adverse effects, as evidenced by the results of the cut-test and fermentation index. However, sensory evaluations revealed significant differences between 80 °C and 60 °C, with the former exhibiting more bitter and astringent cocoa liquor.

The rate of adaptive molecular evolution in wild and domesticated Saccharomyces cerevisiae populations

Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilisation during the Neolithic period, and the yeast remains of importance in industry and biotechnology, giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distributions of fitness effects to infer the rate of adaptive (ω a ) and non-adaptive (ω na ) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated withω na and positively correlated withω a . However, the effect of recombination onω a was found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation withω na , suggesting that it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population's demography. Together, our results provide a detailed characterisation of adaptive mutations in protein-coding genes across S. cerevisiae populations.

Integrating shotgun metagenomics and metabolomics to elucidate the dynamics of microbial communities and metabolites in fine flavor cocoa fermentation in Hainan

The aim of this study was to investigate the dynamic profile of microorganisms and metabolites in Hainan Trinitario cocoa during a six-day spontaneous box fermentation process. Shotgun metagenomic and metabolomic approaches were employed for this investigation. The potential metabolic functions of microorganisms in cocoa fermentation were revealed through a joint analysis of microbes, functional genes, and metabolites. During the anaerobic fermentation phase, Hanseniaspora emerged as the most prevalent yeast genus, implicated in pectin decomposition and potentially involved in glycolysis and starch and sucrose metabolism. Tatumella, possessing potential for pyruvate kinase, and Fructobacillus with a preference for fructose, constituted the primary bacteria during the pre-turning fermentation stage. Upon the introduction of oxygen into the fermentation mass, acetic acid bacteria ascended to dominant within the microflora. The exponential proliferation of Acetobacter resulted in a decline in taxonomic richness and abundance. Moreover, the identification of novel species within the Komagataeibacter genus suggests that Hainan cocoa may serve as a valuable reservoir for the discovery of unique cocoa fermentation bacteria. The KEGG annotation of metabolites and enzymes also highlighted the significant involvement of phenylalanine metabolism in cocoa fermentation. This research will offer a new perspective for the selection of starter strains and the formulation of mixed starter cultures.

Exploring future applications of the apiculate yeast Hanseniaspora

As a metaphor, lemons get a bad rap; however the proverb 'if life gives you lemons, make lemonade' is often used in a motivational context. The same could be said of Hanseniaspora in winemaking. Despite its predominance in vineyards and grape must, this lemon-shaped yeast is underappreciated in terms of its contribution to the overall sensory profile of fine wine. Species belonging to this apiculate yeast are known for being common isolates not just on grape berries, but on many other fruits. They play a critical role in the early stages of a fermentation and can influence the quality of the final product. Their deliberate addition within mixed-culture fermentations shows promise in adding to the complexity of a wine and thus provide sensorial benefits. Hanseniaspora species are also key participants in the fermentations of a variety of other foodstuffs ranging from chocolate to apple cider. Outside of their role in fermentation, Hanseniaspora species have attractive biotechnological possibilities as revealed through studies on biocontrol potential, use as a whole-cell biocatalyst and important interactions with Drosophila flies. The growing amount of 'omics data on Hanseniaspora is revealing interesting features of the genus that sets it apart from the other Ascomycetes. This review collates the fields of research conducted on this apiculate yeast genus.

Variations in Ecuadorian Cocoa Fermentation and Drying at Two Locations: Implications for Quality and Sensory

In Ecuador, various processes are applied during cocoa post-harvesting. This study, therefore, explored fermentation parameters across two locations with 2-7 independent runs, focusing on temperature, microbial counts, pH during fermentation and drying, and their impact on cocoa bean quality. Factors including fermentation devices (jute bags, plastic bags, and wooden boxes), pre-drying, turning during fermentation, fermentation duration, and drying temperature were investigated. Fermenting in plastic bags without pre-drying or turning and fermenting in jute bags for only 40 ± 2.0 h yielded low maximal fermentation temperatures Tmax (31.1 ± 0.4 °C and 37.6 ± 1.8 °C), leading to bitter, astringent, woody, and earthy cocoa liquor. Longer fermentation (63 ± 6 h) in wooden boxes with turning (Wt) and in jute bags with pre-drying and turning (Jpt) achieved the highest Tmax of 46.5 ± 2.0 °C, and a more acidic cocoa liquor, particularly in Wt (both locations) and Jpt (location E). Therefore, it is recommended to ferment for a minimum duration from day 1 to 4 (63 ± 6 h), whether using plastic bags (with mandatory pre-drying) or jute bags (with or without pre-drying or turning). Furthermore, this study underscores the risks associated with excessively high drying temperatures (up to 95.2 ± 13.7 °C) and specific dryer types, which can falsify cut-tests and introduce unwanted burnt-roasted off-flavors in the cocoa liquor.

Pulped natural/honey robusta coffee fermentation metabolites, physico-chemical and sensory profiles

The pulped natural/honey coffee (HC) of Coffea canephora (Robusta) is an innovative modified semi-dry technique. Studies have focused on HC and washed coffee (WC) fermentation, microbial metabolites, quality of green and roasted, using 1H NMR, GC-MS, and sensory investigation. Pipecolate and 3-hydroxy-3-methyglutarate have been identified for the first time. Principal Component Analysis (PCA) variability of the roasted beans, with PC 1 depicting 87.4 % and 12.6 % PC 2 respectively highlights the impact of major sugars and secondary metabolites acquired through HC. The HC fermentation (192 h) influenced carbohydrates, organic acids, and secondary metabolites besides flavor precursors compared to WC (72 h). Although HC and WC beans share similar physical qualities, enhanced volatile compounds, enriched concentration, organoleptics with pleasant, sweet, tea rose and chocolaty flavors attributes were embodied in HC than WC. The pulped natural post-harvest technique in robusta is a value addition with quality that can fetch a better premium.

Effect of Solar Pre-Drying and Yeast Starter Inoculation Treatments on the Chemical Composition of Cocoa (Theobroma cacao L.) Beans from Southwestern Colombia

In Southwestern Colombia, cocoa clones are cultivated in which productivity characteristics predominate over bean quality. In this study, cocoa beans of the CCN-51 clone harvested in the Tumaco region (Nariño, Colombia) were fermented following four different treatments: (1) spontaneously (at room temperature for 120 h) in traditional conditions (Control); (2) traditional processing with a pre-drying (sun-dried for 24 h) treatment (PD); (3) with fermentation (for 120 h) after inoculation of a yeast starter culture (YS); and (4) including both treatments, pre-drying and yeast inoculation (PD + YS). Chemical composition, fatty acids, total polyphenol, methylxanthines (theobromine and caffeine) and lactic acid content of cocoa beans were determined. Chemical and fatty acid composition and theobromine content were not affected by the different fermentation treatments applied (p > 0.05). When analyzing total polyphenol content, YS (16.62 mg/g) and PD + YS (17.74) treatments significantly decreased (p < 0.05) the content of these compounds at the end of the fermentation process, affecting cocoa flavour, while PD treatment decreased (p < 0.05) the caffeine content (0.68 mg/g) of cocoa beans. Finally, lactic acid content decreased because of both inoculation of yeast starter (1.11 mg/g) and mainly the pre-drying treatment (0.60). In conclusion, solar pre-drying in the open air and the inoculation of yeast starter treatments could improve the final quality of cocoa beans.

Monitoring Changes in the Volatile Profile of Ecuadorian Cocoa during Different Steps in Traditional On-Farm Processing

The present work was conducted to evaluate the volatile profile of Ecuadorian Forastero, CCN-51, ETT103 and LR14 cocoa beans during traditional fermentation in laurel wood boxes followed by a sun-drying process. Fifty-six volatiles were identified with HS-SPME-GC-MS. Aldehydes, alcohols and ketones were the compounds that mainly characterized the fresh cocoa. The main compounds formed during the anaerobic fermentation step were esters and acids, while in the aerobic fermentation step, an increase in ester-, aldehyde- and acid-type compounds was observed. Finally, after the drying step, a notable increase in the acid (i.e., acetic acid) content was the predominant trend. According to the genotypes, ETT103 presented high contents of terpenes, alcohols, aldehydes and ketones and low contents of unfavorable acid compounds. The CCN-51 and LR14 (Trinitarian) varieties stood out for their highest amounts in acids (i.e., acetic acid) at the end of primary processing. Finally, the Forastero cocoa beans were highlighted for their low acid and high trimethylpyrazine contents. According to the chemometric and Venn diagram analyses, ETT-103 was an interestingly high-aromatic-quality variety for cocoa gourmet preparations. The results also showed the need for good control of the processing steps (using prefermentative treatments, starter cultures, etc.) on Ecuadorian genotypes of Trinitarian origin.

Cocoa quality: Chemical relationship of cocoa beans and liquors in origin identitation

In this study, HS-SPME-GC-MS was applied in combination with machine learning tools to the identitation of a set of cocoa samples of different origins. Untargeted fingerprinting and profiling approaches were tested for their informative, discriminative and classification ability provided by the volatilome of the raw beans and liquors inbound at the factory in search of robust tools exploitable for long-time studies. The ability to distinguish the country of origin on both beans and liquors is not so obvious due to processing steps accompanying the transformation of the beans, but this capacity is of particular interest to the chocolate industry as both beans and liquors can enter indifferently into the processing of chocolate. Both fingerprinting (untargeted) and profiling (targeted) strategies enable to decipher of the information contained in the complex dataset and the cross-validation of the results, affording to discriminate between the origins with effective classification models.

Exploration of probiotic attributes in lactic acid bacteria isolated from fermented Theobroma cacao L. fruit using in vitro techniques

Probiotics are known for their health-promoting properties and are recognized as beneficial microorganisms. The current investigation delves into the isolation and comprehensive in vitro characterization of lactic acid bacteria (LAB) obtained from the Indian-origin Theobroma cacao L. Forastero variety to assess their potential as probiotic candidates. Eleven LAB isolates were obtained, and among them, five exhibited classical LAB traits. These five isolates underwent rigorous in vitro characterization to evaluate their suitability as probiotics. The assessments included resilience against acid and bile salts, which are crucial for probiotic viability. Additionally, the isolates were subjected to simulated gastric and pancreatic fluids and lysozyme exposure to assess their survival rates. Auto- aggregation, co-aggregation, hydrophobicity, and exopolysaccharide production were also examined. The inhibitory potential of α-glucosidase, an enzyme related to glucose metabolism, was measured, and antioxidant activity was evaluated using DPPH and ABTS assays. A safety assessment was conducted to confirm the non-pathogenic nature of the isolates. Among the five isolates, CR2 emerged as a standout candidate with maximal bile salt hydrolase activity, phenol resistance, and lysozyme resistance. CR2 and CYF3 exhibited notable survival rates under simulated conditions. The isolates displayed variable degrees of auto-aggregation, co-aggregation, and hydrophobicity. CR2 exhibited the highest exopolysaccharide production (0.66 mg/mL), suggesting diverse applications in the food industry. CR2 also demonstrated the highest inhibition rate against α-glucosidase (56.55%) and substantial antioxidant activity (79.62% DPPH, 83.45% ABTS). Safety assessment confirmed the non- pathogenic nature of the isolates. Molecular characterization identified CR2 as Lactococcus lactis subsp. lactis and CYF3 as Limnosilactobacillus fermentum. Both strains exhibited commendable probiotic and technological attributes, positioning them as promising candidates for functional foods and beyond. This study provides valuable insights into the in vitro characterization of LAB isolated from Indian Theobroma cacao L., highlighting their potential as probiotic candidates with advantageous traits, including survival in hostile conditions, beneficial enzymatic activities, bioactivity, and other essential attributes.

Microbial composition and metabolic profiles during machine-controlled intra-factory fermentation of cocoa beans harvested in semitropical area of Japan

Cocoa bean fermentation is typically performed in a spontaneous manner on farms in tropical countries or areas and involves several microbial groups. Metabolism by microbes markedly affects the quality of cocoa beans fermented and the chocolate produced thereof. The present study characterized the microbiota and their metabolic profiles in temperature- and humidity-controlled intra-factory cocoa fermentation in a semitropical area of Japan. Although environmental factors were uniform, the microbiota of cocoa beans subjected to intra-factory fermentation was not stable between tests, particularly in terms of the cell count levels and species observed. Fermentation was sometimes delayed, and fermenting microbes were present at very low levels after 24 hr of fermentation. Due to the unstable microbiota, the profiles of water-soluble compounds differed between tests, indicating the unstable qualities of the fermented cocoa beans. These results suggest the necessity of starter cultures not only in on-farm fermentation but also in machine-controlled intra-factory cocoa fermentation.

Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof

The microbiological and metabolic outcomes of good cocoa fermentation practices can be standardized and influenced through the addition of starter culture mixtures composed of yeast and bacterial strains. The present study performed two spontaneous and 10 starter culture-initiated (SCI) cocoa fermentation processes (CFPs) in Costa Rica with local Trinitario cocoa. The yeast strains Saccharomyces cerevisiae IMDO 050523, Hanseniaspora opuntiae IMDO 020003, and Pichia kudriavzevii IMDO 060005 were used to compose starter culture mixtures in combination with the lactic acid bacterium strain Limosilactobacillus fermentum IMDO 0611222 and the acetic acid bacterium strain Acetobacter pasteurianus IMDO 0506386. The microbial community and metabolite dynamics of the cocoa pulp-bean mass fermentation, the metabolite dynamics of the drying cocoa beans, and the volatile organic compound (VOC) profiles of the chocolate production were assessed. An amplicon sequence variant approach based on full-length 16S rRNA gene sequencing instead of targeting the V4 region led to a highly accurate monitoring of the starter culture strains added, in particular the Liml. fermentum IMDO 0611222 strain. The latter strain always prevailed over the background lactic acid bacteria. A similar approach, based on the internal transcribed spacer (ITS1) region of the fungal rRNA transcribed unit, was used for yeast strain monitoring. The SCI CFPs evolved faster when compared to the spontaneous ones. Moreover, the yeast strains applied did have an impact. The presence of S. cerevisiae IMDO 050523 was necessary for successful fermentation of the cocoa pulp-bean mass, which was characterized by the production of higher alcohols and esters. In contrast, the inoculation of H. opuntiae IMDO 020003 as the sole yeast strain led to underfermentation and a poor VOC profile, mainly due to its low competitiveness. The P. kudriavzevii IMDO 060005 strain tested in the present study did not contribute to a richer VOC profile. Although differences in VOCs could be revealed in the cocoa liquors, no significant effect on the final chocolates could be obtained, mainly due to a great impact of cocoa liquor processing during chocolate-making. Hence, optimization of the starter culture mixture and cocoa liquor processing seem to be of pivotal importance.

Identification of Important Aroma Components and Sensory Profiles of Minimally Processed (Unroasted) and Conventionally Roasted Dark Chocolates

Roasting is an important unit operation for the development of characteristic chocolate aroma during manufacturing. However, there is an increase in interest in minimally processed chocolate products due to their potential positive health benefits. The odor-important compounds and sensory characteristics of minimally processed (unroasted) and conventionally roasted dark chocolates were determined by gas chromatography-olfactometry, aroma extract dilution analysis (AEDA), and stable isotope dilution analysis (SIDA). Except for acetic acid, all odorants had higher odor-activity values (OAVs) in roasted chocolate. Acetic acid, developed during fermentation and drying, had the highest OAV in both chocolates but was better preserved in unroasted chocolate. Compounds making a greater aroma impact on roasted chocolate compared with unroasted chocolate included dimethyl trisulfide, 2-ethyl-3,5-dimethylpyrazine, and 3-methylbutanal. Nine significant sensory attributes in unroasted and roasted chocolates were identified. Vinegar (aroma) and roasted (aroma and aroma by mouth), sweet (taste), and hardness (texture) attributes differed between unroasted and roasted chocolates. The results of this study enforce the embracement of low thermal processes to showcase the inherent flavor potential of cacao beans but also to support the concept of chocolate "terroir" by potentially preserving important aroma compounds developed during fermentation.

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.

Bacterial and Fungal Communities Are Specifically Modulated by the Cocoa Bean Fermentation Method

Cocoa bean fermentation is carried out in different production areas following various methods. This study aimed to assess how the bacterial and fungal communities were affected by box, ground or jute fermentation methods, using high-throughput sequencing (HTS) of phylogenetic amplicons. Moreover, an evaluation of the preferable fermentation method was carried out based on the microbial dynamics observed. Box fermentation resulted in higher bacterial species diversity, while beans processed on the ground had a wider fungal community. Lactobacillus fermentum and Pichia kudriavzevii were observed in all three fermentation methods studied. Moreover, Acetobacter tropicalis dominated box fermentation and Pseudomonas fluorescens abounded in ground-fermented samples. Hanseniaspora opuntiae was the most important yeast in jute and box, while Saccharomyces cerevisiae prevailed in the box and ground fermentation. PICRUST analysis was performed to identify potential interesting pathways. In conclusion, there were noticeable differences between the three different fermentation methods. Due to its limited microbial diversity and the presence of microorganisms that guarantee good fermentation, the box method was found to be preferable. Moreover, the present study allowed us to thoroughly explore the microbiota of differently treated cocoa beans and to better understand the technological processes useful to obtain a standardized end-product.

Rapid determination of the shell content in cocoa products using FT-NIR spectroscopy and chemometrics

The determination of the cocoa shell content is of interest because a high shell content causes a reduction in the quality of cocoa products. Consequently, the aim of the present study was the development of a routinely applicable method for the quantitation of shell material in cocoa nibs. For this, 51 fermented cocoa samples of different varieties from 14 cocoa growing countries covering the crop years 2012-2017 were acquired. Admixtures of cocoa nibs with shell material were prepared in a range of 0-20% cocoa shell and subsequently analysed by Fourier transform near-infrared spectroscopy (FT-NIRS). Support vector machine regression models were created, which enabled the prediction of the cocoa shell content in a mixing ratio range of 0-20% with an RMSE of 2.05% and a R² of 0.88 and in a range of 0-10% with an RMSE of 1.70% and a R² of 0.72. This predictive capability suggests that the presented method is suitable for rapid determination of cocoa shell content in cocoa nibs. In addition, it was demonstrated that the method is applicable to other relevant cocoa matrices, as the prediction of the shell content of several industrial cocoa masses by the FT-NIRS-based model showed good consistency with the prediction by liquid chromatography-mass spectrometry. This emphasizes that FT-NIRS combined with chemometrics has great potential for the determination of cocoa shell content in cocoa nibs and cocoa masses in routine analysis, such as incoming inspection.

Forastero and Criollo cocoa beans, differences on the profile of volatile and non-volatile compounds in the process from fermentation to liquor

Cocoa bean fermentation is an important process because during this process, aroma compounds are produced, the astringency decreases, and the embryo dies. The fermentation processes of the Criollo and Forastero types have been studied separately without comparing them at the same time and in the same place. The aim of this work was to determine differences in the profile of volatile and nonvolatile compounds of Criollo and Forastero cocoa from the fermentation process to the final stage of obtaining the liquor. The experiments were carried out at the same time in the Maya region. Volatile compounds were determined by HS-SPME GC-MS (headspace solid phase-microextraction with gas chromatography-mass spectrometry). Sugars, organic acids, and alkaloids were determined by ultrahigh-performance liquid chromatography (UHPLC-PDA/UV). Criollo cocoa liquor was defined by the volatile and nonvolatile compounds such as acetic acid, phenylethyl alcohol, benzaldehyde, 2-phenylethyl acetate, acetophenone and 3-methylbutanal., which are associated with sour, honey, almond, flowery and chocolate aroma. Forastero cocoa liquor was represented with a significant difference by acetic acid, isobutyl acetate, 2,3-diethyl-5-methylpyrazine and ethyl octanoate and these could provide aroma descriptors such as sour, fruity and nutty. This study characterized for the first time the dynamics of volatile compounds during the fermentation, drying, and roasting stages and in the final cocoa liquor of Criollo and Forastero from cocoa beans of the same origin.

Changes in bioactive compounds during fermentation of cocoa (Theobroma cacao) harvested in Amazonas-Peru

Cocoa (Theobroma cacao) is the main raw material for the production of chocolate; it is considered the food of the gods, as it possesses a diversity of bioactive compounds beneficial to human health. The abundance of bioactive compounds, among others, is conditioned by the post-harvest processing of cocoa beans, and fermentation is a major step in this regard. Consequently, this research evaluated the changes in phenolic compounds and methylxanthines occurred in the fermentation of Criollo and CCN-51 cocoa beans, varieties of great commercial interest for the cocoa-growing areas of Peru. For this purpose, samples were taken every 12 h of cocoa beans under fermentation for 204 h in which phenols (gallic acid, caffeic acid, catechin, and epicatechin) and methylxanthines (theobromine, caffeine and theophylline) were quantified by ultra-high performance liquid chromatography (UHPLC); total polyphenols by Folin Ciocalteu; antioxidant capacity by DPPH free radical capture method; total anthocyanins; pH; titratable acidity; and fermentation rate of beans. We found that during fermentation, phenolic content, antioxidant activity, and methylxanthines of cocoa beans decreased; on the other hand, the anthocyanin content increased slightly. Indeed, at distinctly degree, fermentation influences bioactive compounds in cocoa beans, depending on the variety cultivated.

Soybean fermentation: Microbial ecology and starter culture technology

Fermented soybean products, including Soya sauce, Tempeh, Miso, and Natto have been consumed for decades, mainly in Asian countries. Beans are processed using either solid-state fermentation, submerged fermentation, or a sequential of both methods. Traditional ways are still used to conduct the fermentation processes, which, depending on the fermented products, might take a few days or even years to complete. Diverse microorganisms were detected during fermentation in various processes with Bacillus species or filamentous fungi being the two main dominant functional groups. Microbial activities were essential to increase the bean's digestibility, nutritional value, and sensory quality, as well as lower its antinutritive factors. The scientific understanding of fermentation microbial communities, their enzymes, and their metabolic activities, however, still requires further development. The use of a starter culture is crucial, to control the fermentation process and ensure product consistency. A broad understanding of the spontaneous fermentation ecology, biochemistry, and the current starter culture technology is essential to facilitate further improvement and meet the needs of the current extending and sustainable economy. This review covers what is currently known about these aspects and reveals the limited available information, along with the possible directions for future starter culture design in soybean fermentation.

Chemical Composition and Sensory Profiles of Fermented Cocoa Beans Obtained from Various Regions of Indonesia

The chemical composition and sensory profile of cocoa beans are essential factors determining the quality of cocoa-based products. In this study, cocoa bean samples were collected from various regions of Indonesia, including Aceh, Banten, Bali, East Java, West Sumatra, West Sulawesi, East Kalimantan, and Yogyakarta. The cocoa beans were fermented and sun-dried according to the producers' protocols and local practices. The sensory profile, fat content, total phenolic content, and the composition of sugars, organic acids, and amino acids of the cocoa bean samples were analyzed. The results revealed that the chemical composition and sensory profiles of the samples were diverse. The sensory profiles of cocoa liquor samples were described by low intensities of cocoa notes with the occurrence of fruity, floral, spicy, and sweet notes. The concentration of acetic acid, lactic acid, and some amino acids (glutamic acid, proline, and methionine) was associated with fresh fruit, browned fruit, and roasted note of the cocoa liquor, respectively. The variation in the environmental conditions and postharvest practices contributed to the diversity of cocoa beans' chemical and sensory characteristics.

Influence of Aerobic and Anaerobic Moist Incubation on Selected Nonvolatile Constituents─Comparison to Traditionally Fermented Cocoa Beans

Recently, moist incubation has been proposed as an alternative postharvest processing method for cocoa beans. During this treatment, unfermented and dried cocoa nibs are rehydrated with a lactic acid solution containing ethanol and subsequently incubated for 72 h at 45 °C before drying. Previous studies focused on the aroma formation during this treatment and the further processing of chocolate. The current study focused on the influence of aerobic and anaerobic moist incubation on selected nonvolatile components in comparison with the unfermented raw material and traditionally fermented cocoa. Total phenolic content and total flavan-3-ol content, contents of (+)-catechin, (-)-epicatechin, procyanidins B2 and C1, cinnamtannin A2, methylxanthines (theobromine and caffeine), contents of sugars (sucrose, d-glucose, and d-fructose) and free amino acids (17 proteinogenic amino acids) were determined. The fermentation index was also evaluated. The aerobically incubated and fermented cocoa showed low levels of phenolic compounds in comparison to the unfermented cocoa and the anaerobically incubated cocoa. The level of methylxanthines was unaffected by all treatments. The contents of reducing sugars were more than 2-fold higher after both incubation treatments compared to fermentation. The level of free amino acids liberated was highest after anaerobic incubation followed by fermentation and aerobic incubation. The aerobically incubated cocoa showed the highest FI, while the anaerobically incubated cocoa may be considered under-fermented (FI <1.0). Statistical analysis (ANOVA) showed significant differences between all treatments, which was verified by principal component analysis.

Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.

Box fermentation and solar drying improve the nutrient composition and organoleptic quality of chocolate from cocoa beans

Chocolate is a well-liked and popular food product made from the cocoa bean. The objective of this research was to evaluate the effects of box fermentation and solar drying of cocoa bean on chocolate quality. Fermentation was carried out in a perforated wooden box for 168 h with periodic turning after every 48 h. The succession of microorganisms during fermentation and total microbial count were monitored. Both the fermented and unfermented samples were solar dried. During drying the change in weight of the beans, amount of solar radiation, and ambient wind speed of the atmosphere were measured. The approximate nutrient (crude protein, crude fat, total ash, crude fiber, and carbohydrate) and phytochemical (phenol) contents of the dried cocoa beans were evaluated. Sensory properties of chocolate, produced from the two samples (box fermented and dried as well as unfermented and dried) were compared. The initial temperature of the fermenting cocoa mash was 30°C. It rose to 46°C by the 96th h of fermentation and sharply declined to 38°C by the 120th h. Candida, Pseudomonas and Staphylococcus spp were probable organisms identified with the fermenting mass at the initial stage of the fermentation. Lactic acid bacteria dominated after 72 h. Bacillus spp was also observed until the 168th h. Solar drying of unfermented bean lasted for 4 days, while that of fermented bean lasted for 3 days. Fermentation increased the crude protein, total ash and carbohydrate contents of the cocoa beans. It also improved the appearance, and aroma of chocolate from the cocoa beans.

Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics

Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24-144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24-48 h (T1), 72-96 h (T2), and 120-144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products.

Effect of spontaneous fermentation location on the fingerprint of volatile compound precursors of cocoa and the sensory perceptions of the end-chocolate

Cocoa pod-opening delay and bean fermentation promote the organoleptic quality of chocolate. The present research investigated the changes in the volatile fingerprint of cocoa harvested at a traditional plantation. Cocoa beans extracted from 2-days pod-opening delay were simultaneously fermented for 5 days using container and then sun-dried to 7-8% moisture content at five different locations: Akoupé, San Pedro, Soubré, Djekanou and Daloa. The aromatic analysis were done on cocoa using the HS-SPME-GC/MS technique. Professional panelists evaluated the sensory perceptions of the chocolate. The results shows that cocoa fermented in both Daloa and Soubré regions were differentiated by 2,3-butanediol while those processed in other regions presented highest acetoin content. However, fermented cocoa from Soubré region exhibited most amount of 2,3-butanediol, diacetate A whereas 2,3,5,6-tetramethylpyrazine differentiated those from Daloa region. Sensory properties of chocolate were not linked to the aromatic compound precursors profile of beans. The fermentation performed in San Pédro region promote both the generation of more desirable aromatic compounds of cocoa and sensory attributes of the finished chocolate. The fermentation location generates a greater differentiation of the volatile fingerprint of cocoa and the sensory perceptions of the finished chocolate.

Phylogenomics of a Saccharomyces cerevisiae cocoa strain reveals adaptation to a West African fermented food population

Various yeast strains have been proposed as candidate starter cultures for cocoa fermentation, especially strains of Saccharomyces cerevisiae. In the current study, the genome of the cocoa strain S. cerevisiae IMDO 050523 was unraveled based on a combination of long- and short-read sequencing. It consisted of 16 nuclear chromosomes and a mitochondrial chromosome, which were organized in 20 contigs, with only two small gaps. A phylogenomic analysis of this genome together with another 105 S cerevisiae genomes, among which 20 from cocoa strains showed a geographical distribution of the latter, including S. cerevisiae IMDO 050523. Its genome clustered together with that of a West African fermented food population, indicating a wider adaptation to West African food niches than cocoa. Furthermore, S. cerevisiae IMDO 050523 contained genetic signatures involved in sucrose hydrolysis, pectin degradation, osmotolerance, and conserved amino acid changes in key ester-producing enzymes that could point toward specific niche adaptations.

Microbial Characterization of Retail Cocoa Powders and Chocolate Bars of Five Brands Sold in Italian Supermarkets

A microbial characterization of cocoa powder and chocolate bars of three batches of five different brands sold in Italian markets was performed. The results showed a variable microbial population consisting of mesophilic and thermophilic spore formation in both types of products. The chocolate bars were also contaminated with molds of environmental origin. Bacillus spp. and Geobacillus spp. were found in both products. The chocolate bars were also contaminated by molds belonging to the genera Penicillium and Cladosporium. The sporogenous strains mainly originate from the raw materials, i.e., cocoa beans, as the heat treatments involved (roasting of the beans and conching of the chocolate) are not sufficient to reach commercial sterility. Furthermore, the identified spore-forming species have often been isolated from cocoa beans. The molds isolated from chocolate seem to have an origin strictly linked to the final phases of production (environment and packaging). However, the level of contaminants is limited (<2 log CFU/g); the molds do not develop in both products due to their low Aw (<0.6) and do not affect the safety of the products. However, a case of mold development in chocolate bars was observed. Among the isolated molds, only Penicillium lanosocoeruleum demonstrated a high xero-tolerance and grew under some conditions on chocolate bars. Its growth could be explained by a cocoa butter bloom accompanied by the presence of humidity originating from the bloom or acquired during packaging.

Antagonistic activity of Lactiplantibacillus plantarum 6.2 extracted from cocoa fermentation and its supernatant on Gardnerella vaginalis

Search for alternative methods for the treatment of bacterial vaginosis has been growing, and probiotics being among them. The most well-known probiotic microorganisms are lactobacilli, which are naturally present in the vaginal microenvironment. Cocoa fermentation is a source of lactic acid bacteria, with lactobacilli being the most prominent. The aim of this study was to evaluate the antagonistic activity of Lactiplantibacillus plantarum 6.2 a strain of lactobacilli isolated from cocoa fermentation, and its cell-free supernatant on Gardnerella vaginalis. It was shown that Lpb. plantarum 6.2 and its supernatant, used at three concentrations, i.e., 40, 20 and 10 mg/mL, have a strong antagonistic activity against G. vaginalis, with a probable action of proteinaceous bacteriocins; the activity was lost after heat treatment. The ability to exclude and displace G. vaginalis from the adhesion site to vaginal HMVII epithelial cells was also demonstrated by the lactobacilli and the supernatant, with the latter showing a bactericidal effect. Thus, the Lpb. plantarum 6.2 strain presents itself as a good probiotic with potential to be used not only as a therapeutic alternative for vaginosis but also as a complement to existing therapies.

Adaptive Laboratory Evolution of Yeasts for Aroma Compound Production

Aroma compounds are important in the food and beverage industry, as they contribute to the quality of fermented products. Yeasts produce several aroma compounds during fermentation. In recent decades, production of many aroma compounds by yeasts obtained through adaptive laboratory evolution has become prevalent, due to consumer demand for yeast strains in the industry. This review presents general aspects of yeast, aroma production and adaptive laboratory evolution and focuses on the recent advances of yeast strains obtained by adaptive laboratory evolution to enhance the production of aroma compounds.

Yeasts as Producers of Flavor Precursors during Cocoa Bean Fermentation and Their Relevance as Starter Cultures: A Review

During the fermentation of cocoa beans, the yeasts produce volatile organic compounds (VOCs). Through reactions associated with amino acid metabolism, yeasts generate important aroma precursors as acetate esters and fatty acid ethyl esters are essential in developing fruity flavors and aromas in the final product (usually chocolate). In addition, some yeasts may have pectinolytic and antifungal activity, which is desirable in the post-harvest process of cocoa. The main yeast species in cocoa fermentation are Saccharomyces cerevisiae, Pichia kudriavzevii, and Hanseniaspora opuntiae. These produce higher alcohols and acetyl-CoA to make acetate–esters, compounds that produce floral and fruity notes. However, there are still controversies in scientific reports because some mention that there are no significant differences in the sensory characteristics of the final product. Others mention that the fermentation of cocoa by yeast has a significant influence on improving the sensory attributes of the final product. However, using yeasts as starter cultures for cocoa bean fermentation is recommended to homogenize sensory attributes such as notes and flavors in chocolate.

Traditional Fermented Foods from Ecuador: A Review with a Focus on Microbial Diversity

The development of early civilizations was greatly associated with populations’ ability to exploit natural resources. The development of methods for food preservation was one of the pillars for the economy of early societies. In Ecuador, food fermentation significantly contributed to social advances and fermented foods were considered exclusive to the elite or for religious ceremonies. With the advancement of the scientific research on bioprocesses, together with the implementation of novel sequencing tools for the accurate identification of microorganisms, potential health benefits and the formation of flavor and aroma compounds in fermented foods are progressively being described. This review focuses on describing traditional fermented foods from Ecuador, including cacao and coffee as well as less popular fermented foods. It is important to provide new knowledge associated with nutritional and health benefits of the traditional fermented foods.

Monitoring of cocoa post-harvest process practices on a small-farm level at five locations in Ecuador

Cocoa post-harvest practices were monitored on a small-farm scale (ca. 50 kg fresh beans) at five intermediaries from four provinces in Ecuador: (A) in Manabí, (B) and (E) in Los Ríos, (C) in Cotopaxi, (D) in Guayas. Temperature, pH (pulp, cotyledon), cell counts (yeasts, lactic acid bacteria, acetic acid bacteria) were recorded daily, and cut-tests and sensory descriptive analysis evaluated end quality. An overall inconsistency and variability in processing were observed with different fermentation devices (jute/plastic bags, wooden boxes), pre-drying, turning during fermentation, fermentation duration, and different drying processes (temperatures, direct/indirect). Key parameters (maximum temperature, pH cotyledon development) revealed a significant impact of the fermentation device on the post-harvest process and, therefore, on the fermentation development. 67–74 h in jute bags without turning was sufficient to reach well-fermented cocoa beans without moldy off-flavors, whereas 133 h in plastic bags without turning resulted in 3 ± 1% moldy beans and cocoa liquor with moldy off-flavor. Drying at high temperatures (80 ± 10 °C) with direct heat contact resulted in beans roasted to burnt off-flavor. Conclusively, the whole post-harvest process was crucial for well-fermented beans without off-flavor. Plastic bags seemed unsuitable, while jute bags could be an alternative to wooden boxes.

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Common fermentation devices in Ecuador: Jute bags, plastic bags, wooden boxes.

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High variability in overall post-harvest processing in Ecuador.

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Fermentation in jute bags could be an alternative to wooden boxes.

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Fermentation in plastic bags without turning seemed not suitable.

Unique metabolite profiles of Indonesian cocoa beans from different origins and their correlation with temperature

Chocolate flavors vary depending on the origin of the cocoa beans used. Differences in soil, microorganisms, and environmental factors contribute to the formation of flavor precursors in cocoa beans. During cocoa bean fermentation, environmental temperature has been shown to alter metabolite concentrations. However, the correlation between the metabolite profile of cocoa beans and the temperature of their region of origin has not been fully defined. In this study, the metabolite profiles of Indonesian cocoa beans of various origins were evaluated using gas chromatography/mass spectrometry-based analysis, and were found to differ depending on the origin of the bean. Subsequently, the correlation between metabolite profile and environmental temperature of the origin was assessed using orthogonal projection to latent structure regression (OPLS-R) analysis. The analysis revealed that seven metabolites were associated with temperature: γ-aminobutyric acid (GABA), ethanolamine, glycerol, isocitric acid + citric acid, succinic acid, malic acid, and saccharic acid. The findings of this study will be valuable to chocolate industries for the production of single-origin chocolates.