scholarly journals Metagenome-assembled genomes contributes to unravel the microbiome of cocoa fermentation

2021 ◽  
Author(s):  
O.G.G. Almeida ◽  
E.C.P De Martinis
Keyword(s):  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Acetic Acid Bacteria ◽  
Raw Material ◽  
Microbial Succession ◽  
Metabolic Potential ◽  
Short Reads ◽  
Leuconostoc Pseudomesenteroides ◽  
Cocoa Fermentation

Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of Operational Taxonomic Units. However, it is also important to determine MAGs, which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five datasets: one from Ghana and four from Brazil. Besides, in silico approaches were used to describe putative phenotypes and metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) fungi - Yamadazyma tenuis (n=1); (ii) lactic acid bacteria - Limosilactobacillus fermentum (n=5), Liquorilactobacillus cacaonum (n=1) , Liquorilactobacillus nagelli (n=1), Leuconostoc pseudomesenteroides (n=1) and Lactiplantibacillus plantarum subsp. plantarum (n=1); (iii) acetic acid bacteria - Acetobacter senegalensis (n=2) and Kozakia baliensis (n=1) and (iv) Bacillus subtilis (n=1) Brevundimonas sp. (n=2) and Pseudomonas sp. (n=1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some detected for the first time in this environment ( Liquorilactobacillus vini , Komagataeibacter saccharivorans and Komagataeibacter maltaceti ) and other previously described ( Fructobacillus pseudoficulneus and Acetobacter pasteurianus ). Taken all together, the MAGs were useful to provide an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. Importance The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds, in a microbial succession that depends on yeasts, lactic acid bacteria and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely know, and yet it advanced from culture-based studies to the advent of Next Generation DNA sequencing, with the generation of a myriad of data, that need bioinformatic approaches to be properly analysed. Although the majority metagenomic of studies have been based on short reads (OTUs), it is also important to analyse entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose, and in this paper, MAGs from cocoa fermentation microbiomes were described, as well the possible implications of their phenotypic and metabolic potentials are discussed.

scholarly journals Dynamics and Biodiversity of Populations of Lactic Acid Bacteria and Acetic Acid Bacteria Involved in Spontaneous Heap Fermentation of Cocoa Beans in Ghana

2007 ◽  
Vol 73 (6) ◽  
pp. 1809-1824 ◽  
Author(s):  
Nicholas Camu ◽  
Tom De Winter ◽  
Kristof Verbrugghe ◽  
Ilse Cleenwerck ◽  
Peter Vandamme ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Fermentation Process ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Acetic Acid Bacteria ◽  
Cocoa Bean ◽  
Rrna Gene ◽  
Cocoa Bean Fermentation ◽  
Leuconostoc Pseudomesenteroides

ABSTRACT The Ghanaian cocoa bean heap fermentation process was studied through a multiphasic approach, encompassing both microbiological and metabolite target analyses. A culture-dependent (plating and incubation, followed by repetitive-sequence-based PCR analyses of picked-up colonies) and culture-independent (denaturing gradient gel electrophoresis [DGGE] of 16S rRNA gene amplicons, PCR-DGGE) approach revealed a limited biodiversity and targeted population dynamics of both lactic acid bacteria (LAB) and acetic acid bacteria (AAB) during fermentation. Four main clusters were identified among the LAB isolated: Lactobacillus plantarum, Lactobacillus fermentum, Leuconostoc pseudomesenteroides, and Enterococcus casseliflavus. Other taxa encompassed, for instance, Weissella. Only four clusters were found among the AAB identified: Acetobacter pasteurianus, Acetobacter syzygii-like bacteria, and two small clusters of Acetobacter tropicalis-like bacteria. Particular strains of L. plantarum, L. fermentum, and A. pasteurianus, originating from the environment, were well adapted to the environmental conditions prevailing during Ghanaian cocoa bean heap fermentation and apparently played a significant role in the cocoa bean fermentation process. Yeasts produced ethanol from sugars, and LAB produced lactic acid, acetic acid, ethanol, and mannitol from sugars and/or citrate. Whereas L. plantarum strains were abundant in the beginning of the fermentation, L. fermentum strains converted fructose into mannitol upon prolonged fermentation. A. pasteurianus grew on ethanol, mannitol, and lactate and converted ethanol into acetic acid. A newly proposed Weissella sp., referred to as “Weissella ghanaensis,” was detected through PCR-DGGE analysis in some of the fermentations and was only occasionally picked up through culture-based isolation. Two new species of Acetobacter were found as well, namely, the species tentatively named“ Acetobacter senegalensis” (A. tropicalis-like) and “Acetobacter ghanaensis” (A. syzygii-like).

scholarly journals The Key to Acetate: Metabolic Fluxes of Acetic Acid Bacteria under Cocoa Pulp Fermentation-Simulating Conditions

2014 ◽  
Vol 80 (15) ◽  
pp. 4702-4716 ◽  
Author(s):  
Philipp Adler ◽  
Lasse Jannis Frey ◽  
Antje Berger ◽  
Christoph Josef Bolten ◽  
Carl Erik Hansen ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Isotope Labeling ◽  
Acetic Acid Bacteria ◽  
Building Blocks ◽  
Conversion Rates ◽  
Cellular Energetics ◽  
Cocoa Fermentation

ABSTRACTAcetic acid bacteria (AAB) play an important role during cocoa fermentation, as their main product, acetate, is a major driver for the development of the desired cocoa flavors. Here, we investigated the specialized metabolism of these bacteria under cocoa pulp fermentation-simulating conditions. A carefully designed combination of parallel13C isotope labeling experiments allowed the elucidation of intracellular fluxes in the complex environment of cocoa pulp, when lactate and ethanol were included as primary substrates among undefined ingredients. We demonstrate that AAB exhibit a functionally separated metabolism during coconsumption of two-carbon and three-carbon substrates. Acetate is almost exclusively derived from ethanol, while lactate serves for the formation of acetoin and biomass building blocks. Although this is suboptimal for cellular energetics, this allows maximized growth and conversion rates. The functional separation results from a lack of phosphoenolpyruvate carboxykinase and malic enzymes, typically present in bacteria to interconnect metabolism. In fact, gluconeogenesis is driven by pyruvate phosphate dikinase. Consequently, a balanced ratio of lactate and ethanol is important for the optimum performance of AAB. As lactate and ethanol are individually supplied by lactic acid bacteria and yeasts during the initial phase of cocoa fermentation, respectively, this underlines the importance of a well-balanced microbial consortium for a successful fermentation process. Indeed, AAB performed the best and produced the largest amounts of acetate in mixed culture experiments when lactic acid bacteria and yeasts were both present.

scholarly journals Brewers’ spent grain as substrate for dextran biosynthesis by Leuconostoc pseudomesenteroides DSM20193 and Weissella confusa A16

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Prabin Koirala ◽  
Ndegwa Henry Maina ◽  
Hanna Nihtilä ◽  
Kati Katina ◽  
Rossana Coda
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Raw Materials ◽  
Degree Of Polymerization ◽  
Raw Material ◽  
Fermentation Time ◽  
Viscosity Increase ◽  
Spent Grain ◽  
Leuconostoc Pseudomesenteroides ◽  
Weissella Confusa

Abstract Background Lactic acid bacteria can synthesize dextran and oligosaccharides with different functionality, depending on the strain and fermentation conditions. As natural structure-forming agent, dextran has proven useful as food additive, improving the properties of several raw materials with poor technological quality, such as cereal by-products, fiber-and protein-rich matrices, enabling their use in food applications. In this study, we assessed dextran biosynthesis in situ during fermentation of brewers´ spent grain (BSG), the main by-product of beer brewing industry, with Leuconostoc pseudomesenteroides DSM20193 and Weissella confusa A16. The starters performance and the primary metabolites formed during 24 h of fermentation with and without 4% sucrose (w/w) were followed. Results The starters showed similar growth and acidification kinetics, but different sugar utilization, especially in presence of sucrose. Viscosity increase in fermented BSG containing sucrose occurred first after 10 h, and it kept increasing until 24 h concomitantly with dextran formation. Dextran content after 24 h was approximately 1% on the total weight of the BSG. Oligosaccharides with different degree of polymerization were formed together with dextran from 10 to 24 h. Three dextransucrase genes were identified in L. pseudomesenteroides DSM20193, one of which was significantly upregulated and remained active throughout the fermentation time. One dextransucrase gene was identified in W. confusa A16 also showing a typical induction profile, with highest upregulation at 10 h. Conclusions Selected lactic acid bacteria starters produced significant amount of dextran in brewers’ spent grain while forming oligosaccharides with different degree of polymerization. Putative dextransucrase genes identified in the starters showed a typical induction profile. Formation of dextran and oligosaccharides in BSG during lactic acid bacteria fermentation can be tailored to achieve specific technological properties of this raw material, contributing to its reintegration into the food chain.

scholarly journals Effect of starter culture and inulin addition on microbial viability, texture, and chemical characteristics of whole or skim milk Kefir

2012 ◽  
Vol 32 (4) ◽  
pp. 580-865 ◽  
Author(s):  
Flávia Daiana Montanuci ◽  
Tatiana Colombo Pimentel ◽  
Sandra Garcia ◽  
Sandra Helena Prudencio
Keyword(s):  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Starter Culture ◽  
Skim Milk ◽  
Acetic Acid Bacteria ◽  
Chemical Characteristics ◽  
Microbial Viability ◽  
Lactose Concentration ◽  
Textural Changes

The effect of inulin addition and starters (Kefir grains or commercial starter culture) on the microbial viability, texture, and chemical characteristics of Kefir beverages prepared with whole or skim milk was evaluated during refrigerated storage. The type of starter did not influence microbial viability during the storage of the beverages, but the chemical and textural changes (decreases in pH, lactose concentration, and inulin and increased acidity, firmness, and syneresis) were more pronounced in the formulations fermented with grains than those fermented with the starter culture. The addition of inulin did not influence acidity or viability of lactic acid bacteria, but in general, its effect on the survival of acetic acid bacteria, Lactococcus and yeasts, firmness, and syneresis depended on the type of milk and starter culture used. Generally, the yeast, acetic acid bacteria, and Leuconostoc counts increased or remained unchanged, while the total population of lactic acid bacteria and Lactococcus were either reduced by 1 to 2 logs or remained unchanged during storage.

Detection and Enumeration of Lactic Acid Bacteria, Acetic Acid Bacteria and Yeast in Kefir Grain and Milk Using Quantitative Real-Time PCR

2014 ◽  
Vol 35 (1) ◽  
pp. 102-107 ◽  
Author(s):  
Dong-Hyeon Kim ◽  
Jung-Whan Chon ◽  
Hyunsook Kim ◽  
Hong-Seok Kim ◽  
Dasom Choi ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Real Time ◽  
Real Time Pcr ◽  
Acetic Acid Bacteria ◽  
Quantitative Real Time Pcr ◽  
Kefir Grain

Novel biocompatible silver nanoparticles for controlling the growth of lactic acid bacteria and acetic acid bacteria in wines

Food Control ◽  
2015 ◽  
Vol 50 ◽  
pp. 613-619 ◽  
Author(s):  
A. García-Ruiz ◽  
J. Crespo ◽  
J.M. López-de-Luzuriaga ◽  
M.E. Olmos ◽  
M. Monge ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Acetic Acid Bacteria

scholarly journals Fermentation of Cocoa Beans

2021 ◽  
Author(s):  
Romel E. Guzmán-Alvarez ◽  
José G. Márquez-Ramos
Keyword(s):  
Acetic Acid ◽  
Scientific Information ◽  
Acetic Acid Bacteria ◽  
Cocoa Bean ◽  
Microbial Succession ◽  
Cocoa Bean Fermentation ◽  
Wide Range ◽  
The World ◽  
Flavor Precursors ◽  
Cocoa Fermentation

Cocoa bean fermentation is a spontaneous process driven by an ordered microbial succession of a wide range of yeasts, lactic acid and acetic acid bacteria, some aerobic sporeforming bacteria and various species of filamentous fungi. The process of cocoa fermentation is a very important step for developing chocolate flavor precursors which are attributable to the metabolism of succession microbial. The microbial ecology of cocoa has been studied in much of the world. In Venezuela, studies have been carried out with Criollo, Forastero, and Trinitario cocoa, fermented under various conditions, the results obtained coinciding with the reported scientific information. Fermentation must be associated with the type of cocoa available, carried out knowing the final processing and derivative (paste, butter, powder). The results shown in this chapter correspond to investigations carried out with cocoa from three locations in Venezuela. The quantification, identification, isolation, functionality of the most representative microbiota involved in the fermentation of these grains was sought. This to give possible answers to the fermentation times and improvement of the commercial quality. Likewise, generate greater interest on the part of the producers in carrying out the fermentation.

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