Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacteria and Fungi

ABSTRACT: Metagenomic sequencing of microbial diversity in spontaneous fermentation of cocoa beans from Brazil

PROVIDER: PRJNA407677 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6159231_1.fastq.gz	Fastqsanger.gz
	SRR6159231_2.fastq.gz	Fastqsanger.gz
	SRR6159232_1.fastq.gz	Fastqsanger.gz
	SRR6159232_2.fastq.gz	Fastqsanger.gz
	SRR6162951_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Proteomic and peptidomic UHPLC-ESIProteomic and peptidomic UHPLC-ESI MS/MS analysis of cocoa beans fermented using the Styrofoam box method MS/MS analysis of cocoa beans fermented using the Styrofoam box method

Project description:Fermentation is essential for cocoa flavour development, as during this process key flavour precursors are formed from the degradation of the major cocoa bean storage proteins. This work characterises the peptide and protein profiles of Theobroma cacao beans of the genotype IMC 67 at different fermentation stages, using the Styrofoam box fermentation method and employing UHPLC-ESI MS/MS for the analysis of peptides and proteins extracted from the beans. A total of 1058 endogenous peptides were identified and quantified over four fermentation time points. The majority of these peptides were formed during the early stage of fermentation and originated predominantly from the proteolysis of two storage proteins - vicilin and a 21 kDa albumin. The changes in the peptide profile over fermentation were subsequently evaluated, and potential markers for assessing the degree of fermentation were identified. In particular, changes of the relative abundance of the major cocoa proteins detected can be proposed as potential markers for the fermentation stage. Furthermore, PCA analysis of both the peptidomic and proteomic data has allowed differentiation of beans at different fermentation stages.

2020-02-05 | PXD014434 | Pride

UHPLC-MS/MS analysis of the proteomic profiles of cocoa beans from different genotypes

Project description:Amongst other compounds, cocoa flavour is dependent on peptides that are formed during fermentation of cocoa beans from proteins such as albumin and vicilin. In this study the proteomic profiles of cocoa beans from four genotypes (ICS 1, ICS 39, IMC 67 and SCA 6) with different genetic background and flavour profiles have been analysed by employing a bottom-up label free LC-MS/MS approach. From a total of 430 identified proteins, 250 proteins were found significantly differentially expressed among the four cocoa genotypes analysed. Of these, 61 proteins with a fold change of 2 or more were further investigated, showing that the majority is involved in stress response. Furthermore, several of these 61 proteins could also be linked to oxidation-reduction processes. PCA analysis allowed a clear separation of the genotypes based on their proteomic profile, with an aminohydrolase and a sulphite oxidase greatly contributing to the separation. Aspartyl protease was more abundant in the genotypes ICS 1 and ICS compared to IMC 67, while a serine carboxypeptidase was significantly more expressed in the genotype ICS 39 in comparison with the other genotypes. Both these enzymes catalyse the degradation of storage proteins during fermentation. A Beta-amylase, an enzyme which catalyses the release of maltose was detected at a significantly higher level in the genotype SCA 6 compared to ICS 1 and IMC 67. Two Amine oxidases were significantly more abundant in the genotype SCA 6 compared to ICS 39, and in the genotype ICS 1 versus ICS 39, while two alcohol dehydrogenase were higher expressed in the genotype SCA 6 compared to IMC 67. These enzyme catalyse oxidation of amines and alcohols with release of aldehydes and ketones. The data shows that UHPLC-MS/MS can be employed to differentiate cocoa beans from various varieties, and thus in theory be linked to differences in their flavour profile.

2019-08-15 | PXD011984 | Pride

Characterization of the proteome of Theobroma cacao beans by nanoUHPLC-ESI MS/MS

Project description:Cocoa seed storage proteins play an important role in flavour development as aroma precursors are formed from their degradation during fermentation. Major proteins in the beans of Theobroma cacao are the storage proteins belonging to the vicilin and albumin fraction. Although both these classes of proteins have been fully characterized, there is still limited information on the expression and abundance of other proteins present in cocoa beans. This work is the first attempt to characterize the whole cocoa bean proteome by nanoUHPLC-ESI MS/MS analysis using tryptic digests of cocoa bean protein extracts. The results of this analysis show that a total of 906 proteins could be identified using a species-specific Theobroma cacao database. The majority of the identified proteins were involved with metabolism and energy. However, a significant number of the identified proteins were linked to protein synthesis and processing. Several proteins were also involved with plant response to stress conditions and defence. Albumin and vicilin storage proteins showed the highest intensity values among all detected proteins, although only seven entries were identified as storage proteins. A comparison of MS/MS data searches carried out against larger non-specific databases confirmed that using a species-specific database can increase the number of identified proteins, and at the same time reduce the number of false positives. The results of this work will be useful in developing tools which can allow the comparison of the proteomic profile of cocoa beans from different genotypes and geographic origins.

2018-01-04 | PXD005586 | Pride

food fermentation metagenome

Project description:Metagenome-Assembled Genomes from cocoa beans fermentation

| PRJNA659258 | ENA

Cocoa metagenome

Project description:Functional metagenomic analysis of cocoa bean fermentation

| PRJEB5194 | ENA

food fermentation metagenome

Project description:Shotgun metagenomic study of cocoa bean fermentation

| PRJDB13568 | ENA

metaproteomic analysis of microbiota and metabolic pathways involved in taste formation during Chinese traditional fish sauce

Project description:Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervising and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previous metagenomic database. Most of the identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. The proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation showed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis.

2022-05-20 | PXD031089 | Pride

Bacteria and fungi

Project description:Studies of microbial and fungi diversity in contaminated sediment

| PRJNA799043 | ENA

Escherichia coli

Project description:Escherichia coli isolates from cocoa beans

| PRJNA487888 | ENA

Cocoa Fermentation

Project description:Cocoa Fermentation Metagenome

| PRJNA483234 | ENA