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Computational Analysis of glycoside hydrolase genes in metagenomic data from composting

Grant number: 13/05325-5
Support Opportunities:Scholarships in Brazil - Master
Effective date (Start): July 01, 2013
Effective date (End): June 30, 2015
Field of knowledge:Biological Sciences - Microbiology - Applied Microbiology
Principal Investigator:João Carlos Setubal
Grantee:Leandro Nascimento Lemos
Host 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


There is growing interest from industry sectors in substituting enzymes for chemical catalyzers in processes that occur under high temperature, pressure, salt concentration or metal concentration. One of the critical sectors is biofuel production from renewable biomass. Composting is a process that is particularly amenable to bioprospection of microbial products related to biomass degradation. The main objective of this work is to characterize the diversity and abundance of glycoside hydrolases (GHs) in different stages of the composting process used in the São Paulo Zoo, using as basic data the metagenome sequences generated under the FAPESP project number 11/50870-6. Specifically we plan to identifiy GH-coding genes in several samples; anlyze diversity and abundance of the main GH families; anlyze diversity and abundance of the microbes whose genome code for these GHs; verify which of the identified GHs are new with respect to known ones; and compare GH profiles of the various samples to each other and to other biomass degrading metagenomes. In order to achieve these objectives we will use 3rd party servers and software as well as build our own computational analysis pipeline and relational database.

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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)
LEMOS, LEANDRO N.; PEREIRA, ROBERTA V.; QUAGGIO, RONALDO B.; MARTINS, LAYLA F.; MOURA, LIVIA M. S.; DA SILVA, AMANDA R.; ANTUNES, LUCIANA P.; DA SILVA, ALINE M.; SETUBAL, JOAO C.. Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting. FRONTIERS IN MICROBIOLOGY, v. 8, . (13/05325-5)
PYLRO, VICTOR S.; MORAIS, DANIEL K.; DE OLIVEIRA, FRANCISLON S.; DOS SANTOS, FAUSTO G.; LEMOS, LEANDRO N.; OLIVEIRA, GUILHERME; ROESCH, LUIZ F. W.. BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies. MICROBIAL ECOLOGY, v. 72, n. 2, p. 443-447, . (13/05325-5)
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
LEMOS, Leandro Nascimento. Reconstruction and analysis of microbial genomes from composting metagenomic data. 2015. Master's Dissertation - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.

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