Microbial Diversity and Contribution to the Formation of Volatile Compounds during Fine-Flavor Cacao Bean Fermentation

Foodomics as a Tool for Evaluating Food Authenticity and Safety from Field to Table: A Review

The globalization of the food industry chain and the increasing complexity of the food supply chain present significant challenges for food authenticity and raw material processing. Food authenticity identification now extends beyond mere adulteration recognition to include quality evaluation, label compliance, traceability determination, and other quality-related aspects. Consequently, the development of high-throughput, accurate, and rapid analytical techniques is essential to meet these diversified needs. Foodomics, an innovative technology emerging from advancements in food science, enables both a qualitative judgment and a quantitative analysis of food authenticity and safety. This review also addresses crucial aspects of fully processing food, such as verifying the origin, processing techniques, label authenticity, and detecting adulterants, by summarizing the omics technologies of proteomics, lipidomics, flavoromics, metabolomics, genomics, and their analytical methodologies, recent developments, and limitations. Additionally, we analyze the advantages and application prospects of multi-omics strategies. This review offers a comprehensive perspective on the food chain, food safety, and food processing from field to table through omics approaches, thereby promoting the stable and sustained development of the food industry.

Multiomics analysis reveals microbial diversity and activity through spontaneous fermentation of Theobroma cacao

To gain insight into the active microbiota during spontaneous fermentation of Theobroma cacao L., this study assessed protein diversity during 120 h using a combined metabarconding and metaproteomics approach. During the first days of fermentation, most of the peptides were associated with T. cacao and yeast (0-72 h). Peptides associated with bacteria became more abundant after 72 h of fermentation, coinciding with a decrease in peptides associated with cocoa (96-120 h). In addition to the known microorganisms involved in fermentation, such as Saccharomyces, Lactobacillus and Acetobacter, novel genera were also metabolically active, including Microvirga, Inquilinus, Candolleomyces and Lasiodiplodia.. The results showed a consistency in the main genera detected by both techniques, but the identification of unexplored genera such as Inquilinus, Microvirga, Cyphellophora and Ashbya gossypii, among others, suggests that this omics approach needs to be used together for more comprehensive results on spontaneous fermentation. In conclusion, studies combining techniques such as metabarcoding and metaproteomics should be considered in fermentation studies, as a single technique would result in omissions regarding the activity of certain microorganisms that may be important for the course of spontaneous fermentation.

Exploring volatile compounds and microbial dynamics: Kluyveromyces marxianus and Hanseniaspora opuntiae reduce Forastero cocoa fermentation time

Traditional cocoa bean fermentation is a spontaneous process and can result in heterogeneous sensory quality. For this reason, yeast-integrated starter cultures may be an option for creating consistent organoleptic profiles. This study proposes the mixture of Hanseniaspora opuntiae and Kluyveromyces marxianus (from non-cocoa fermentation) as starter culture candidates. The microorganisms and volatile compounds were analyzed during the cocoa fermentation process, and the most abundant were correlated with predominant microorganisms. Results showed that Kluyveromyces marxianus, isolated from mezcal fermentation, was identified as the dominant yeast by high-throughput DNA sequencing. A total of 63 volatile compounds identified by HS-SPME-GC-MS were correlated with the more abundant bacteria and yeast using Principal Component Analysis and Agglomerative Hierarchical Clustering. This study demonstrates that yeasts from other fermentative processes can be used as starter cultures in cocoa fermentation and lead to the formation of more aromatic esters, decrease the acetic acid content.

Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity

The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.

Evaluation of stress tolerance and design of alternative culture media for the production of fermentation starter cultures in cacao

Ecuador is one of the world's leading producers of cacao beans, and Nacional x Trinitario cacao represents one of the most distinctive varieties due to its flavor and aroma characteristics. This study aimed to evaluate the effect of the starter culture isolated from microbial diversity during the spontaneous fermentation of Nacional x Trinitario cacao. A total of 249 microbial isolates were obtained from spontaneous culture, with Lactiplantibacillus (45 %), Saccharomyces (17 %), and Acetobacter (2 %) being the most relevant genera for fermentation. Tolerance tests were conducted to select microorganisms for the starter culture. Lactiplantibacillus plantarum exhibited the highest tolerance at pH 5 and 6 % ethanol and tolerated concentrations up to 15 % for glucose and fructose. Acetobacter pasteurianus grew at pH 2 and 6 % ethanol, tolerating high sugar concentrations of up to 15 % for glucose and 30 % for fructose, with growth observed in concentrations up to 5 % for lactic and acetic acid. Subsequently, a laboratory-scale fermentation was conducted with the formulated starter culture (SC) comprising S. cerevisiae, L. plantarum, and A. pasteurianus, which exhibited high tolerance to various stress conditions. The fermentation increased alcoholic compounds, including citrusy, fruity aromas, and floral notes such as 2-heptanol and phenylethyl alcohol, respectively 1.6-fold and 5.6-fold compared to the control. Moreover, the abundance of ketones 2-heptanone and 2-nonanone increased significantly, providing sweet green herbs and fruity woody aromas. Cacao fermented with this SC significantly enhanced the favorable aroma-producing metabolites characteristic of Fine-aroma cacao. These findings underscore the potential of tailored fermentation strategies to improve cacao product quality and sensory attributes, emphasizing the importance of ongoing research in optimizing fermentation processes for the cacao industry.

Changes in GC-MS metabolite profile, antioxidant capacity and anthocyanins content during fermentation of fine-flavor cacao beans from Ecuador

The fermentation of fine-flavor cacao beans is a key process contributing to the enhancement of organoleptic attributes and monetary benefits for cacao farmers. This work aimed to describe the dynamics of the gas chromatography-mass spectrometry (GC-MS) metabolite profile as well as the antioxidant capacity and anthocyanin contents during fermentation of fine-flavor cacao beans. Samples of Nacional x Trinitario cacao beans were obtained after 0, 24, 48, 72, 96, and 120 hours of spontaneous fermentation. Total phenolic content (TPC), ferric reducing antioxidant power (FRAP), and total anthocyanin content were measured by ultraviolet-visible (UV-Vis) spectrophotometry. Volatiles were adsorbed by headspace solid phase microextraction (HS-SPME) while other metabolites were assessed by an extraction-derivatization method followed by gas chromatography-mass spectrometry (GC-MS) detection and identification. Thirty-two aroma-active compounds were identified in the samples, including 17 fruity, and 9 floral-like volatiles as well as metabolites with caramel, chocolate, ethereal, nutty, sweet, and woody notes. Principal components analysis and Heatmap-cluster analysis of volatile metabolites grouped samples according to the fermentation time. Additionally, the total anthocyanin content declined during fermentation, and FRAP-TPC values showed a partial correlation. These results highlight the importance of fermentation for the improvement of the fine-flavor characteristics of cacao beans.

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.

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.

Development of Candida autochthonous starter for cigar fermentation via dissecting the microbiome

Introduction

The main goal of tobacco fermentation technology is to minimize the alkaloid content while improving flavor substance content.

Methods

This study revealed the microbial community structure and their metabolic functions during cigar leaf fermentation by high-throughput sequencing and correlation analysis, and evaluated the fermentation performance of functional microbes based on in vitro isolation and bioaugmentation fermentation.

Results

The relative abundance of Staphylococcus and Aspergillus increased first but then decreased during the fermentation, and would occupy the dominant position of bacterial and fungal communities, respectively, on the 21st day. Correlation analysis predicted that Aspergillus, Staphylococcus and Filobasidium could contribute to the formation of saccharide compounds, Bacillus might have degradation effects on nitrogenous substances. In particular, Candida, as a co-occurring taxa and biomarker in the later stage of fermentation, could not only degrade nitrogenous substrates and synthesize flavor substances, but also contribute to maintaining the stability of microbial community. Moreover, based on in vitro isolation and bioaugmentation inoculation, it was found that Candida parapsilosis and Candida metapsilosis could significantly reduce the alkaloids content and increase the content of flavor components in tobacco leaves.

Discussion

This study found and validated the critical role of Candida in the fermentation of cigar tobacco leaves through high-throughput sequencing and bioaugmentation inoculation, which would help guide the development of microbial starters and directional regulation of cigar tobacco quality.

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.