Metagenomic prospection of quorum sensing related bacteria during spontaneous cocoa beans fermentation

• Grant number: 17/13759-6
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: October 01, 2017
• End date: August 31, 2022
• Field of knowledge: Biological Sciences - Microbiology
• Principal Investigator: Elaine Cristina Pereira de Martinis
• Grantee: Otávio Guilherme Gonçalves de Almeida
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated scholarship(s): 18/26719-5 - Molecular taxonomy and genomic characterization of genes regulated by Quorum Sensing pathways in isolates of Lactic Acid Bacteria from different food matrices, BE.EP.DD

Abstract

The process of fermentation of cocoa beans is not well standardized, since the it is carried out by microorganisms that are autochthonous from cocoa beans. It is a highly complex process because there is a microbial succession that starts with yeasts and it is mantained and finished by lactic acid and acetic acid bacteria. In this way, many authors tried to achieve a bacterial well defined starter culture to guarantee the standardization in the characteristic chocolate flavor, that is dependent of microbial metabolites released during this process. Nevertheless, it is not described yet in literature a starter culture that may be applied successfully in the fermentative process. Moreover, some authors mentioned the quality of chocolate might be related to the presence of genes related to Quorum Sensing (QS) or Quorum Quenching (QQ) classic pathways. In that context, it is important to understand the dynamic of the fermentation process under bacterial communication view, isolating strains that dominate in process to develop, after phenotypic characterization, a starter well defined culture. In conclusion, our goals are: (I) study the microbiota of cocoa beans fermentation during specific times; (II) to sequence genomic DNA extracted from fermentation samples and to analyze with Illumina HiSeq 2500 platforms; (III) do bioinformatic analysis to identify bacterial strains that express genes related to QS and QQ; (IV) enumerate, isolate and perform phenotypic analysis in QS bioassays to measure QS expression genes in vitro; (V) use HPLC-MS/MS to quantify the autoinducer molecules present in isolated bacterial cultures; (VI) propose a starter culture with well-defined bacterial populations for cocoa fermentation. The results of this project should contribute for improvement and selection of flavors during cocoa beans fermentation. (AU)

Scientific publications

(10)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DE ALMEIDA, OTAVIO GUILHERME GONCALVES; CAPIZZANI, CAROLINA PAULINO DA COSTA; TONANI, LUDMILLA; GRIZANTE BARIAO, PATRICIA HELENA; DA CUNHA, ANDERSON FERREIRA; DE MARTINIS, ELAINE CRISTINA PEREIRA; TORRES, LIDIA ALICE GOMES MONTEIRO MARIN; VON ZESKA KRESS, MARCIA REGINA. The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, v. 10, NOV 11 2020. (17/13759-6, 17/25300-8)

GONCALVES DE ALMEIDA, OTAVIO GUILHERME; VITULO, NICOLA; DE MARTINIS, ELAINE CRISTINA PEREIRA; FELIS, GIOVANNA E.. Pangenome analyses of LuxS-coding genes and enzymatic repertoires in cocoa-related lactic acid bacteria. Genomics, v. 113, n. 4, p. 1659-1670, JUL 2021. (17/13759-6, 18/13564-3)

FRAZILIO, DIEGO ARAUJO; DE ALMEIDA, OTAVIO GUILHERME GONCALVES; NINO-ARIAS, FABIAN CAMILO; DE MARTINIS, ELAINE CRISTINA PEREIRA. Finding a common core microbiota in two Brazilian dairies through culture and DNA metabarcoding studies. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE, v. 56, n. 12, p. 5326-5335, DEC 2019. (17/13759-6)

RUEDA FURLAN, JOAO PEDRO; GONCALVES DE ALMEIDA, OTAVIO GUILHERME; PEREIRA DE MARTINIS, ELAINE CRISTINA; STEHLING, ELIANA GUEDES. Characterization of an Environmental Multidrug-Resistant Acinetobacter seifertii and Comparative Genomic Analysis Reveals Co-occurrence of Antimicrobial Resistance and Metal Tolerance Determinants. FRONTIERS IN MICROBIOLOGY, v. 10, SEP 18 2019. (18/01890-3, 18/19539-0, 17/13759-6)

DE ALMEIDA, OTAVIO GUILHERME GONCALVES; PEREIRA, MARITA GIMENEZ; OXARAN, VIRGINIE; DE MARTINIS, ELAINE CRISTINA PEREIRA; ALVES, VIRGINIA FARIAS. In silico metatranscriptomic approach for tracking biofilm-related effectors in dairies and its importance for improving food safety. FRONTIERS IN MICROBIOLOGY, v. 13, p. 8-pg., 2022-08-25. (18/13564-3, 17/13759-6)

GONCALVES DE ALMEIDA, OTAVIO GUILHERME; PEREIRA DE MARTINIS, ELAINE CRISTINA. Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing. ELECTRONIC JOURNAL OF GENERAL MEDICINE, v. 16, n. 3, 2019. (17/13759-6)

ALMEIDA, O. G. G.; PINTO, U. M.; MATOS, C. B.; FRAZILIO, D. A.; BRAGA, V. F.; VON ZESKA-KRESS, M. R.; DE MARTINIS, E. C. P.. Does Quorum Sensing play a role in microbial shifts along spontaneous fermentation of cocoa beans? An in silico perspective. Food Research International, v. 131, MAY 2020. (17/13759-6)

FRAZILIO, DIEGO ARAUJO; ALMEIDA, OTAVIO GUILHERME GONCALVES DE; OLIVEIRA, CARLOS AUGUSTO FERNANDES DE; LEE, SARAH HWA IN; CORASSIN, CARLOS HUMBERTO; ALVES, VIRGINIA FARIAS; DE MARTINIS, ELAINE CRISTINA PEREIRA. Metataxonomics contributes to unravel the microbiota of a Brazilian dairy. JOURNAL OF DAIRY RESEARCH, v. 87, n. 3, p. 360-363, AUG 2020. (17/13759-6, 12/50507-1)

PEREIRA, MARITA GIMENEZ; DE ALMEIDA, OTAVIO GUILHERME GONCALVES; DA SILVA, HEVELIN REGIANE AUGUSTO; ISHIZAWA, MARILIA HARUMI; DE MARTINIS, ELAINE CRISTINA PEREIRA. Studies on host-foodborne bacteria in intestinal three-dimensional cell culture model indicate possible mechanisms of interaction. WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, v. 37, n. 2, FEB 2021. (17/18928-0, 17/13759-6, 16/16293-5)

ALMEIDA, OTAVIO G.; FREITAS, CAIO F.; CARVALHO, LARA M. V. F.; DE MARTINIS, ELAINE C. P.; NERO, LUIS A.. Analysis of two sampling treatments of beef for microbiome studies based on metataxonomic. Letters in Applied Microbiology, v. 76, n. 4, p. 7-pg., 2023-04-03. (17/13759-6)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

ALMEIDA, Otávio Guilherme Gonçalves de. Metagenomic prospection of quorum sensing related bacteria during spontaneous cocoa beans fermentation. 2022. Doctoral Thesis - Universidade de São Paulo (USP). Faculdade de Ciências Farmacêuticas de Ribeirão Preto (PCARP/BC) Ribeirão Preto.