Understanding the Effects of Self-Induced Anaerobic Fermentation on Coffee Beans Quality: Microbiological, Metabolic, and Sensory Studies.

In this study, an investigation of the microbial community structure and chemical changes in different layers of a static coffee beans fermentation tank (named self-induced anaerobic fermentation-SIAF) was conducted at different times (24, 48, and 72 h). The microbial taxonomic composition comprised a high prevalence of Enterobacteriaceae and Nectriaceae and low prevalence of lactic acid bacteria and yeast, which greatly differs from the traditional process performed in open tanks. No major variation in bacterial and fungal diversity was observed between the bottom, middle, and top layers of the fermentation tank.

A review on enzyme-producing lactobacilli associated with the human digestive process: From metabolism to application.

Complex carbohydrates, proteins, and other food components require a longer digestion process to be absorbed by the lining of the alimentary canal. In addition to the enzymes of the gastrointestinal tract, gut microbiota, comprising a large range of bacteria and fungi, has complementary action on the production of digestive enzymes. Within this universe of "hidden soldiers", lactobacilli are extensively studied because of their ability to produce lactase, proteases, peptidases, fructanases, amylases, bile salt hydrolases, phytases, and esterases.

Global cocoa fermentation microbiome: revealing new taxa and microbial functions by next generation sequencing technologies.

This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions.

Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking.

This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium.

Co-culturing fructophilic lactic acid bacteria and yeast enhanced sugar metabolism and aroma formation during cocoa beans fermentation.

Glucose and fructose are the main fermentable sugars in cocoa pulp. During fermentation, glucose is consumed within 48-72 h and fructose only after 120 h, mainly associated with the preferential use of glucose by microorganisms. In the first stage of this study, the complete genome sequence of a lactic acid bacterium with high fructose consumption capacity (Lactobacillus plantarum LPBF35) was reported.

An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa.

Exploring the contribution of fructophilic lactic acid bacteria to cocoa beans fermentation: Isolation, selection and evaluation.

Fructophilic lactic acid bacteria (FLAB) are a recently discovered group whose main characteristic is to prefer D-fructose over D-glucose. In this study, laboratory cocoa beans fermentation was analyzed by Illumina-based amplicon sequencing, indicating the presence of potential FLAB of the genera Fructobacillus and Lactobacillus. Eighty efficient fructose-fermenting isolates, obtained from fermenting cocoa pulp beans mass, were identified by 16S rRNA gene sequencing as Pediococcus acidilactici (n = 52), Lactobacillus plantarum (n = 10), Pediococcus pentosaceus (n = 10), Bacillus subtilis (n = 4), and Leuconostoc pseudomesenteroides (n = 4).

Lignocellulosic biomass: Acid and alkaline pretreatments and their effects on biomass recalcitrance - Conventional processing and recent advances.

Lignocellulosic biomass is one of the most abundant organic resources worldwide and is a promising source of renewable energy and bioproducts. It basically consists of three fractions, cellulose, hemicelluloses and lignin, which confer a recalcitrant structure. As such, pretreatment steps are required to make each fraction available for further use, with acidic, alkaline and combined acidic-alkaline treatments being the most common techniques.

First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing.

In Colombia, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. This process has a great influence on sensory quality and prestige of Colombian coffee in international markets, but has never been studied. Here we use an Illumina-based amplicon sequencing to investigate bacterial and fungal communities associated with spontaneous coffee-bean fermentation in Colombia.

Biotechnological approaches for cocoa waste management: A review.

Cocoa beans provide raw materials for global food industries valued in excess of $47 billion in world exportations. Through on-farm processing, about 80% of cocoa fruit is discarded as residual biomass, including cocoa pod husks, cocoa bean shells and cocoa sweatings. Farmers routinely discard these residues/by-products during the initial cocoa bean processing steps, occupying vast areas and raising social and environmental concerns.

Exploring the impacts of postharvest processing on the aroma formation of coffee beans - A review.

The aim of this review is to describe the volatile aroma compounds of green coffee beans and evaluate sources of variation in the formation and development of coffee aroma through postharvest processing. The findings of this survey showed that the volatile constituents of green coffee beans (e.g.