Metagenomic analysis of poultry's gut microbiota: Exploring probiotic potential, multi-drug resistance genes, and horizontal gene transfer.

• Grant number: 23/10686-9
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: December 01, 2023
• End date: July 31, 2026
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Alessandro de Mello Varani
• Grantee: Julia Memrava Cabrera
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated research grant: 18/25511-1 - Bioprospecting of bacteriocin-producing bacteria: from culture optimization to the application in animal production systems, AP.TEM

Abstract

The gut microbiota of poultry is a complex community, encompassing bacteria, phages, archaea, fungi, and protozoa. Changes in the composition and diversity of this microbiota can have significant impacts on poultry health, affecting their production, performance, and welfare. Genomics-based studies, particularly metagenomic sequencing techniques, have revolutionized this field of science, offering new opportunities to investigate poultry microbiota more deeply. Such approaches have generated a vast amount of highly complex data and information, which warrant in-depth exploration. Therefore, the objective of this project is to investigate the intestinal microbiota of poultry (Gallus gallus domesticus) by analyzing sequencing data available in public databases. Specifically, we will explore 908 entries in the Sequence Read Archive (SRA) derived from sequencing the gut microbiome of poultry, and 1,511 metagenome-assembled genomes (MAGs). To do this, we will employ a range of bioinformatics tools and apply metagenomic analysis methods. Furthermore, we aim to explore the probiotic potential of the present microorganisms, investigate genes associated with multi-drug resistance, understand the role played by horizontal gene transfer in poultry microbiota, and identify the CRISPR-Cas loci, to generate an evolutionary understanding of the bacteria that constitute this microbiome. We hope that the results obtained in this project will contribute to a better understanding of the importance of intestinal microbiota in poultry. This understanding could provide valuable insights for promoting animal health and welfare, in addition to contributing to the improvement of sustainable and efficient poultry production.