Studies of microbial diversity in the Zoological Park of the State of São Paulo

• Grant number: 11/50870-6
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants
• Start date: August 01, 2012
• End date: July 31, 2018
• Field of knowledge: Biological Sciences - Microbiology
• Principal Investigator: João Carlos Setubal
• Grantee: João Carlos Setubal
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Pesquisadores principais: Aline Maria da Silva
• Associated scholarship(s): 17/12645-7 - Characterization of three new Pseudomonas aeruginosa bacteriophages, BP.IC; 16/23639-5 - Use of phenotypic and molecular tests for the identification of bacteria with the ability to biodegrade hydrocarbons, BP.IC; 14/16450-8 - Diversity analysis of bacteriophages associated to microbial community during the composting process, BP.MS; + associated scholarships 14/15413-1 - Prospection and characterization of industrial interest thermostable enzymes in metagenomic and metatranscriptomic data at São Paulo Zoo Park composting facilities, BP.PD; 13/05325-5 - Computational Analysis of glycoside hydrolase genes in metagenomic data from composting, BP.MS; 13/08148-7 - Metagenomic and metatranscriptomic studies of the microbial community from the São Paulo Zoo composting operation, BP.DD - associated scholarships

Abstract

This project has as general objectives the collection, analysis, and investigation of molecular data from three microbiomes found in the Zoological Park of São Paulo state. These microbiomes are: Atlantic Rain Forest vegetation compost, water from a lake, and stool sample from Alouatta monkeys. The choice of microbiomes seeks to cover to some extent the environmental diversity found in the park and the Zoo mission of animal species protection. We will use an array of methodologies, with the main ones being metagenomic DNA sequencing, microbial isolate identification by mass spectrometry, and bioinformatics. We will generate several databases, two websites, an isolate collection, international scientific publications, and educational materials for park visitors and K-12 students. The project team includes researchers from USP (Butantan and Zona Leste campuses), from UNIFESP (Vila Clementino and Diadema campuses), and Fundação Parque Zoológico de São Paulo. The project is responsive to the call for applications from FAPESP’s BIOTA-microorganismos program, emphasizing the biodiversity characterization of microbes and specific biomes; the establishment of microbial strain collections; development of strategies to identify strains with industrial and biotechnological potential; and mining of microbial gene products for enzymes of technological interest. (AU)

Scientific publications

(9)

(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)

BRAGA, STEFANIA PEGORIN; DOS SANTOS, ALEXANDRE PAES; PAGANINI, THAIS; BARBOSA, DEIBS; CONDOMITTI EPAMINO, GEORGE WILLIAN; MORAIS, CARLOS; MARTINS, LAYLA FARAGE; SILVA, ALINE MARIA; SETUBAL, JOAO CARLOS; VALLIM, MARCELO AFONSO; et al. First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans. Brazilian Journal of Microbiology, v. 50, n. 4, p. 1051-1062, OCT 2019. (16/07360-0, 11/50870-6, 16/14542-8)

BRAGA, LUCAS P. P.; SOUCY, SHANNON M.; AMGARTEN, DEYVID E.; DA SILVA, ALINE M.; SETUBAL, JOAO C.. Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation. FRONTIERS IN ECOLOGY AND EVOLUTION, v. 6, JAN 26 2018. (11/50870-6)

LIMA-JUNIOR, JAMES DALTRO; VIANA-NIERO, CRISTINA; CONDE OLIVEIRA, DANIEL V.; MACHADO, GABRIEL ESQUITINI; DA SILVA RABELLO, MICHELLE CRISTIANE; MARTINS-JUNIOR, JOAQUIM; MARTINS, LAYLA FARAGE; DIGIAMPIETRI, LUCIANO ANTONIO; DA SILVA, ALINE MARIA; SETUBAL, JOAO CARLOS; et al. Characterization of mycobacteria and mycobacteriophages isolated from compost at the Sao Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U. BMC Microbiology, v. 16, JUN 17 2016. (11/50870-6, 11/18326-4, 12/04911-5, 14/01825-6)

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)

PEREZ BRAGA, LUCAS PALMA; PEREIRA, ROBERTA VERCIANO; MARTINS, LAYLA FARAGE; SILVA MOURA, LIVIA MARIA; SANCHEZ, FABIO BELTRAME; LEISTER PATANE, JOSE SALVATORE; DA SILVA, ALINE MARIA; SETUBAL, JOAO CARLOS. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics, v. 22, n. 1, SEP 10 2021. (11/50870-6, 18/19247-0)

AMGARTEN, DEYVID; IHA, BRUNO KOSHIN VAZQUEZ; PIROUPO, CARLOS MORAIS; DA SILVA, ALINE MARIA; SETUBAL, JOAO CARLOS. vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks. PHAGE-THERAPY APPLICATIONS AND RESEARCH, v. 3, n. 4, p. 9-pg., 2022-12-01. (11/50870-6)

SILVA, NATALIA MARIA; SILVA ARAUJO DE OLIVEIRA, ALINE MARCIA; PEGORIN, STEFANIA; GIUSTI, CAMILA ESCANDURA; FERRARI, VITOR BATISTA; BARBOSA, DEIBS; MARTINS, LAYLA FARAGE; MORAIS, CARLOS; SETUBAL, JOAO CARLOS; VASCONCELLOS, SUZAN PANTAROTO; et al. Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting. PLoS One, v. 14, n. 4, APR 18 2019. (11/50870-6, 16/23639-5)

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)

ANTUNES, LUCIANA PRINCIPAL; MARTINS, LAYLA FARAGE; PEREIRA, ROBERTA VERCIANO; THOMAS, ANDREW MALTEZ; BARBOSA, DEIBS; LEMOS, LEANDRO NASCIMENTO; MACHADO SILVA, GIANLUCA MAJOR; SILVA MOURA, LIVIA MARIA; CONDOMITTI EPAMINO, GEORGE WILLIAN; DIGIAMPIETRI, LUCIANO ANTONIO; et al. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. SCIENTIFIC REPORTS, v. 6, DEC 12 2016. (11/50870-6)