Abstract

Considering the widespread use of antibiotics in the poultry industry, impact of antibiotics on gut microbiota and immune system of the bird is of major concern. A better understanding of how antibiotics use change gut microbiota in relation to poultry production is thus definitively required. Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural information obtained by metagenomic analyses, metaproteomic approaches provide, in addition, functional data about the investigated microbiota. This review focuses on the effect of antibiotic administration on the status gut microbiota of broiler chicken post hatch. The advent ofomics technologies for analyzing total DNAs, RNAs, proteins, metabolites, and bacteria will provide a better glimpse of microbiota activities at localized intestinal sites. Combining classical with modern techniques is a powerful strategy to fill gaps in our knowledge of animal intestinal microbiomes. In addition, further interdisciplinary approaches will be essential as we proceed to a new era of antibiotic use in food animals.

Keywords: Antibiotics; Microbiome; Next-generation sequencing; Broiler chicken

Abbreviations: T-RFLP: Terminal Restriction Fragment Length Polymorphism; PCR: Polymerase Chain Reaction; OTUs: Operational Taxonomic Units; DGGE: Denaturing Gradient Gel Electrophoresis; FCR: Feed Conversion Ratio; BMD: Bacitracin Methylene Disalicylate