Abstract

MANTILLA MARTINEZ, Marcela Judith  and  TORRES SAEZ, Rodrigo Gonzalo. Metagenomic approaches for characterization of poultry microbiome. A review. Rev. colomb. biotecnol [online]. 2019, vol.21, n.2, pp.77-97.  Epub Jan 20, 2020. ISSN 0123-3475.  https://doi.org/10.15446/rev.colomb.biote.v21n2.78390.

Chicken and eggs are an important source of protein for humans worldwide. Production of these foods has been intensified in recent years and around 150 million tonnes of chicken meat is expected to be produced by 2020 (OECD / FAO, 2018). However, one of the biggest problems linked to poultry production processes are the infectious diseases caused by pathogenic microorganisms. Among the most relevant are found microorganisms such as Salmonella ssp, Campylobacter spp, and Escherichia coli. Therefore, it is important to understand the mechanisms involved in the colonization of pathogenic microorganisms that can affect poultry and their interactions with the gastrointestinal microbiota, which are key in improving nutrient absorption and strengthening the immune system, which it influences the growth, welfare and health of the chicken. However, there is little information related to the gastrointestinal microbiota of chicken. Until recently, the characterization was limited to microorganisms that could be recovered through culture traditional. Therefore, in the last time, it has been intensified use of molecular techniques, among those is remarked metagenomics, which offers an alternative for a better understanding of bacterial interactions, the identification of antibiotic resistance genes, identification of mobile genetic elements, and the design of strategies for more effective interventions with the aim of breaking the chain of transmission of pathogenic microorganisms during the poultry production cycle. In this review, the main metagenomics approaches are describe aimed to study microbiomes from poultry, sequencing techniques and bioinformatics tools used for its characterization.

Keywords : Metagenomics; 16s RNA; shotgun; poultry; gastrointestinal microbiome.

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