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Enfoque metagenómico para la caracterización del microbioma de aves corral. Revisión
Metagenomic approaches for characterization of poultry microbiome. A review
DOI:
https://doi.org/10.15446/rev.colomb.biote.v21n2.78390Palabras clave:
Metagenómica, 16s RNA, shotgun, aves de corral, microbiota gastrointestinal (es)Metagenomics, 16s RNA, shotgun, poultry, gastrointestinal microbiome (en)
El pollo y el huevo son una fuente importante de proteína para el ser humano a nivel mundial. La producción de estos alimentos se ha intensificado durante los últimos años y se prevé que se produzca alrededor de 150 millones de toneladas de carne de pollo en 2020 (OCDE / FAO, 2018). Sin embargo, uno de los mayores problemas ligados a los procesos de producción avícola lo constituyen las enfermedades infecciosas ocasionadas por microorganismos patógenos. Entre los más relevantes se encuentran microorganismos como Salmonella ssp, Campylobacter spp, y Escherichia coli. Por lo tanto, es importante comprender los mecanismos implicados en la colonización de microorganismos patógenos que afectan a las aves de corral y sus interacciones con la microbiota gastrointestinal las cuales son clave en la mejora de la absorción de nutrientes y el fortalecimiento del sistema inmune, que influye en el crecimiento, el bienestar y la salud de las aves de corral. Sin embargo, hay poca información relacionada con la microbiota gastrointestinal de pollos parrilleros y gallinas productoras de huevo. Hasta hace poco, la caracterización se limitaba a los microorganismos que podían recuperarse a través de cultivos tradicionales. Por lo anterior, en el último tiempo se ha intensificado el uso de técnicas moleculares, entre las que se destaca la metagenómica, la cual ofrece una alternativa para una mejor comprensión de las interacciones bacterianas, la identificación de genes de resistencia a los antibióticos, identificación de elementos genéticos móviles, y el diseño de estrategias para intervenciones más efectivas con el objetivo de romper la cadena de transmisión de microorganismos patógenos durante el ciclo de producción avícola. En esta revisión, se describen los principales enfoques metagenómicos para el estudio de microbiomas de aves de corral, las técnicas de secuenciación y herramientas bioinformáticas usadas para su caracterización.
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.
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