Reconstruction of bacterial regulatory networks in environmental terrestrial samples

• Grant number: 18/21133-2
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: January 28, 2019
• End date: December 01, 2019
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: Rafael Silva Rocha
• Grantee: Lummy Maria Oliveira Monteiro
• Supervisor: Peter F Stadler
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Institution abroad: Leipzig University, Germany
• Associated to the scholarship: 16/19179-9 - Deciphering the architecture/function relationship in complex bacterial promoters through synthetic biology approaches, BP.DR

Abstract

The sharing of genetic information among microbial communities can be represented by a complex network that interconnects the most diverse information, as for example: metabolites, specific genes, enzymes, substrates and also the transcription factors. For instance, the survival and coexistence of a microbial community could be explained or understood through genes expressed by that community, as well as the metabolic products that these organisms produce and share. Since transcription factors are responsible for regulating organisms lives and consequently a community, they can be used to explain and decipher the behavior of these communities. In this sense, these communities could be studied and understood at a regulatory level. Currently, several studies use metagenomics approaches as a potential to understand and explore the dynamics and diversity of microbial communities. However, the understanding of communities behave at regulation level (i.e., set of bacterial regulators present in this community) remains incomplete since many transcriptional regulators are not yet well characterized. In this context, the objective of this project is to develop a systemic approach to analyze the bacterial regulatory network in terrestrial metagenomes, integrating technologies to decode the distribution, abundance, association and statistical correlations of bacterial transcriptions factors in a global ecological scale using a community systems biology approach. Seeking to understand and decipher the behavior of the biological system through bioinformatics tools, our goal is to recover patterns of transcription factors prevalent in various terrestrial metagenomes. Deciphering the complex regulatory network (metaregulation) of a metagenomic community through transcription factor would be the main goal of this project. These data will contribute to the understanding of the complex inter-species and intra-populations relation of microbial communities in a global challenge by analyzing the transcription factors network in a metagenome.

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)

MONTEIRO, LUMMY MARIA OLIVEIRA; SARAIVA, JOAO PEDRO; TOSCAN, RODOLFO BRIZOLA; STADLER, PETER F.; SILVA-ROCHA, RAFAEL; DA ROCHA, ULISSES NUNES. redicTF: prediction of bacterial transcription factors in complex microbial communities using deep learnin. ENVIRONMENTAL MICROBIOME, v. 17, n. 1, FEB 8 2022. (19/15675-0, 18/21133-2, 16/19179-9)