Computational analyses of the viral diversity present in the composting microbial community at the Sao Paulo Zoo Park

• Grant number: 14/16450-8
• Support Opportunities: Scholarships in Brazil - Master
• Start date: March 01, 2015
• End date: September 30, 2016
• Field of knowledge: Interdisciplinary Subjects
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: João Carlos Setubal
• Grantee: Deyvid Emanuel Amgarten
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• 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.

Scientific publications

(The scientific publications listed on this page originate from the Web of Science or SciELO databases. Their authors have cited FAPESP grant or fellowship project numbers awarded to Principal Investigators or Fellowship Recipients, whether or not they are among the authors. This information is collected automatically and retrieved directly from those bibliometric databases.)

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. (14/16450-8, 11/50870-6)

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; et al. Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, v. 18, MAY 4 2017. (14/16450-8, 15/14334-3, 11/50870-6)

Academic Publications

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

AMGARTEN, Deyvid Emanuel. Computational analysis of the viral diversity in the Sao Paulo Zoo composting microbial community. 2016. Master's Dissertation - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.