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Diversity analysis of bacteriophages associated to microbial community during the composting process

Grant number: 14/16450-8
Support type:Scholarships in Brazil - Master
Effective date (Start): March 01, 2015
Effective date (End): September 30, 2016
Field of knowledge:Interdisciplinary Subjects
Cooperation agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
Principal researcher:João Carlos Setubal
Grantee:Deyvid Emanuel Amgarten
Home Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Associated research grant:11/50870-6 - Studies of microbial diversity in the Zoological Park of the State of São Paulo, AP.BTA.TEM
Associated scholarship(s):15/14334-3 - Phage Orthologous Clusters: A database of phage information, BE.EP.MS

Abstract

Metagenomic studies have defined the structure and diversity of microbial communities in environmental samples. The data bring light to the uncultured microbial majority and help us to understand what are the organisms acting in complex processes. The thematic project in which this proposal is inserted (process 2011/50870-6) aims to characterize the diversity in different environmental niches of the São Paulo Zoo Park, among them the composting community. Several analyses have been made in order to define the prokaryotic diversity in the composting metagenomic data, but viral diversity remains untouched. Taking into account the new perspectives in the viral metagenomic field, promising results produced by several groups around the world and our own preliminary results, this project aims to characterize the bacteriophage diversity associated to the microbial community during the composting process. In order to accomplish that, we will perform a thorough data mining of the metagenomic data generated. In addition, we will extend the analysis and characterization of phages from composting that were isolated using Pseudomonas aeruginosa and other bacteria as host. Preliminary sequencing results obtaining from these phages indicate high quantity of unknown sequences. Data generated by both approaches will be annotated and stored in a database and we expect to obtain partial and/or complete genomes from new phages associated with the thermophilic composting community. (AU)

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Scientific publications
(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)
AMGARTEN, DEYVID; BRAGA, LUCAS P. P.; DA SILVA, ALINE M.; SETUBAL, JOAO C. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. FRONTIERS IN GENETICS, v. 9, AUG 7 2018. Web of Science Citations: 13.
AMGARTEN, DEYVID; MARTINS, LAYLA FARAGE; LOMBARDI, KAREN CRISTINA; ANTUNES, LUCIANA PRINCIPAL; SILVA DE SOUZA, ANA PAULA; NICASTRO, GIANLUCCA GONCALVES; KITAJIMA, ELLIOTT WATANABE; QUAGGIO, RONALDO BENTO; UPTON, CHRIS; SETUBAL, JOAO CARLOS; DA SILVA, ALINE MARIA. Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, v. 18, MAY 4 2017. Web of Science Citations: 6.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.