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. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.

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. The administration of living lactobacilli cells has been shown to increase nutrient digestibility. However, it is still little known how these microbial-derived enzymes act in the human body. Enzyme secretion may be affected by variations in temperature, pH, and other extreme conditions faced by the bacterial cells in the human body. Besides, lactobacilli administration cannot itself be considered the only factor interfering with enzyme secretion, human diet (microbial substrate) being determinant in their metabolism. This review highlights the potential of lactobacilli to release functional enzymes associated with the digestive process and how this complex metabolism can be explored to contribute to the human diet. Enzymatic activity of lactobacilli is exerted in a strain-dependent manner, i.e., within the same lactobacilli species, there are different enzyme contents, leading to a large variety of enzymatic activities. Thus, we report current methods to select the most promising lactobacilli strains as sources of bioactive enzymes. Finally, a patent landscape and commercial products are described to provide the state of art of the transfer of knowledge from the scientific sphere to the industrial application.

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. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.

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. The notable genomic features of L. plantarum LPBF35 were the presence of alcohol/acetaldehyde dehydrogenase gene and improved PTS system, confirming its classification as a "facultatively" fructophilic bacterium. Subsequently, this bacterium was introduced into cocoa fermentation process in single and mixed cultures with Pediococcus acidilactici LPBF66 or Pichia fermentans YC5.2. Community composition by Illumina-based amplicon sequencing and viable counts indicated suppression of wild microflora in all treatments. At the beginning of the fermentation processes, cocoa pulp consisted of approximately 73.09 mg/g glucose and 73.64 mg/g fructose. The L. plantarum LPBF35 + P. fermentans YC5.2 process showed the lowest levels of residual sugars after 72 h of fermentation (7.89 and 4.23 mg/g, for fructose and glucose, respectively), followed by L. plantarum LPBF35 + Ped. acidilactici LPBF66 (8.85 and 6.42 mg/g, for fructose and glucose, respectively), single L. plantarum LPBF35 treatment (4.15 and 10.15 mg/g, for fructose and glucose, respectively), and spontaneous process (22.25 and 14.60 mg/g, for fructose and glucose, respectively). The positive interaction between L. plantarum LPBF35 and P. fermentans YC5.2 resulted in an improved formation of primary (ethanol, lactic acid, and acetic acid) and secondary (2-methyl-1-butanol, isoamyl acetate, and ethyl acetate) metabolites during fermentation. The primary metabolites accumulated significantly in cocoa beans fermented by P. fermentans YC5.2 + L. plantarum LPBF35, causing important reactions of color development and key flavor molecules formation. The results of this study suggest that fructophilic lactic acid bacteria and yeast is a microbial consortium that could improve sugar metabolism and aroma formation during cocoa beans fermentation.

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). The growth characteristics of all the 10 L. plantarum strains classified them as "facultatively" fructophilic bacteria, i.e., they grew on glucose without an external electron acceptor but the growth on fructose was faster. Among them, L. plantarum LPBF 35 was characterized by producing a range of aroma-impacting compounds (acetaldehyde, ethyl acetate, nonanal, and octanoic acid), being introduced into a cocoa fermentation process. Although the process started with approximately equal amounts of glucose and fructose, a concomitant, but faster utilization of fructose, was observed in cocoa fermentation conducted with L. plantarum LPBF 35 (with no residual fructose observed) when compared to control fermentation using a glucophilic strain (8.77 mg/g residual fructose) and a spontaneous process (8.38 mg/g residual fructose). L. plantarum LPBF 35 also showed an ideal profile of organic acid metabolism (citric acid consumption and lactic acid production) associated with cocoa fermentation. These results proved new insights on cocoa microbial activity and brings new perspectives on the use of lactic acid bacteria as starter culture.

Chemical composition and health properties of coffee and coffee by-products.

Coffee can be an ally in the fight against diseases such as type 2 diabetes, cancer, hepatic injury, cirrhosis, depression, suicidal behavior, and neurological and cardiovascular disorders. The properties of coffee also favor gastrointestinal tract and gut microbiota establishment. Coffee bioactive components include phenolic compounds (chlorogenic acids, cafestol and kahweol), alkaloids (caffeine and trigonelin), diterpenes (cafestol and kahweol) and other secondary metabolites. The image of coffee as a super functional food has helped to increase coffee consumption across the globe. This chapter addresses the main health promotion mechanisms associated with coffee consumption. Related topics on coffee production chain, world consumption and reuse of coffee by-products in the production of high-value-adding molecules with potential applications in the food industry are addressed and discussed.

In Vitro Probiotic Properties and DNA Protection Activity of Yeast and Lactic Acid Bacteria Isolated from A Honey-Based Kefir Beverage.

The probiotic characteristics of three acid-tolerant microbial strains, viz., Lactobacillus satsumensis LPBF1, Leuconostoc mesenteroides LPBF2 and Saccharomyes cerevisiae LPBF3, isolated from a honey-based kefir functional beverage, were studied following the requirements established by the Food and Agriculture Organization of the United Nation/World Health Organization (FAO/WHO), including host-associated stress resistance, epithelium adhesion ability, and antimicrobial activity. The three microbial strains tolerated different pH values (2.0, 3.0, 4.0 and 7.0) and bile salt concentrations (0.3% and 0.6%), and survive in the presence of simulated gastric juice, which are conditions imposed by the gastrointestinal tract. In addition, they showed high percentages of hydrophobicity, auto aggregation and anti-pathogenic against Escherichia coli and Staphylococcus aureus, with no hemolytic activity. The protective capacity of human DNA through microbial treatment was investigated by single-cell gel electrophoresis (SCGE) comet assay. The three selected strains showed DNA protection effect against damage caused by hydroxyl radical (H2O2). However, when the S. cerevisiae treatment was applied, the most effective DNA protection index was observed, which can be associated to its high production of extracellular antioxidants as reveled by the 2,2-diphenyl-1-picryl-hydrazylhydrate (DPPH) method. These results indicated that the three selected microbial strains could be useful for preventing oxidative DNA damage and cellular oxidation in food products. As well-adapted microbial cells, the selected strains can be used for production of non-dairy functional beverages, especially for vegans and/or vegetarians and lactose intolerants.

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. Microbial-derived metabolites were further analysed by high-performance liquid chromatography and gas chromatography-mass spectrometry. Highly diverse bacterial groups, comprising 160 genera belonging to 10 phyla, were found. Lactic acid bacteria (LAB), mainly represented by the genera Leuconostoc and Lactobacillus, showed relative prevalence over 60% at all sampling times. The structure of the fungal community was more homogeneous, with Pichia nakasei dominating throughout the fermentation process. Lactic acid and acetaldehyde were the major end-metabolites produced by LAB and Pichia, respectively. In addition, 20 volatile compounds were produced, comprising alcohols, organic acids, aldehydes, esters, terpenes, phenols, and hydrocarbons. Interestingly, 56 microbial genera, associated with native soil, seawater, plants, insects, and human contact, were detected for the first time in coffee fermentation. These microbial groups harbour a remarkable phenotypic diversity and may impart flavours that yield clues to the terroir of Colombian coffees.

Draft Genome Sequence of Pediococcus acidilactici Strain LPBC161, Isolated from Mature Coffee Cherries during Natural Fermentation.

Here, we report the draft genome sequence of Pediococcus acidilactici strain LPBC161, a lactic acid bacterium isolated from mature coffee cherries in Brazil. The genome sequence of P. acidilactici LPBC161 provides valuable information on the mechanisms of adaptation and metabolism of lactic acid bacteria (LAB) in the environment and stressor factors of coffee processing.

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., alcohols, aldehydes, and alkanes) have no significant influence on the final coffee aroma composition, as only a few such compounds remain in the beans after roasting. On the other hand, microbial-derived, odor-active compounds produced during removal of the fruit mucilage layer, including esters, higher alcohols, aldehydes, and ketones, can be detected in the final coffee product. Many postharvest processing including drying and storage processes could influence the levels of coffee aroma compositions, which remain to be elucidated. Better understanding of the effect of these processes on coffee aroma composition would assist coffee producers in the optimal selection of postharvest parameters that favor the consistent production of flavorful coffee beans.

Evaluation of a potentially probiotic non-dairy beverage developed with honey and kefir grains: Fermentation kinetics and storage study.

The aim of this work was to study the fermentation process of honey with kefir grains through a comprehensive understanding of its rheological properties, probiotic cell viability, instrumental color parameters and kinetic aspects in a batch bioreactor and during storage. The results showed that kefir grains were well adapted to bioreactor conditions, reaching high levels of cell viability (over 106 CFU mL-1 for total yeast and bacteria), phenolic compounds content (190 GAE/100 g) and acidification after 24 h of fermentation at 30 ℃. Colorimetric analysis showed that lightness (L*) and redness (a*) remained constant, while yellowness intensities (b*) decreased during fermentation time. After 35 days of storage, honey kefir beverage maintained its chemical characteristics and microbial viability as required to be classified as a probiotic product. The Ostwald-de-Waele (R2 ≥ 0.98) and Herschel-Bulkley (R2 ≥ 0.99) models can be used to predict the behavior of honey kefir beverage. The parameters analyzed in this study should be taken into account for industrial production of this novel non-dairy beverage.