Abstract
The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system.Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different sections of chickens' gut. The most common methodologies are targeted amplicon sequencing followed by metagenome shotgun sequencing as well as metaproteomics aiming at a broad range of topics such as dietary effects, animal diseases, bird performance and host genetics. However, the respective analyses are still at the beginning and currently there is a lack of information in regard to the activity and functional characterization of the gut microbial communities. In the future, the use of multi-omics approaches may enhance research related to chicken production, animal and also public health. Furthermore, combinations with other disciplines such as genomics, immunology and physiology may have the potential to elucidate the definition of a “healthy” gut microbiota.
Highlights
The global population is increasing continuously and is estimated to comprise about 9.6 billion individuals by 2050
While the genera Anaeroplasma, Oscillibacter, Papillibacter, Peptococcus and Subdoligranulum were more abundant in the lumen, Lactobacillus, Ruminococcus, Turicibacter, Clostridium XlVa and Clostridium XlVb were detected in higher abundances in the mucosa. These observations emphasized the importance of studying the variations between the bacterial communities of the lumen and mucosa throughout the different sections of the gastrointestinal tract (GIT) to improve our understanding of host-microbe interactions
Other studies characterized the different sections of the GIT of broilers under varying conditions analyzing bird performance [36,37,38], antimicrobial feed additives [11,39,40], gender [41], disease [42], host genetics [18,41], spatial microbial diversity [30,43] and meat flavor [33]
Summary
The global population is increasing continuously and is estimated to comprise about 9.6 billion individuals by 2050. Poultry production has intensified during the last years and is predicted to produce about 130 million tons of chicken meat in 2020 (OECD/FAO) to match the demands of a growing world population. Such extreme growth is only feasible with proper strategies for disease control and prevention to minimize the impact of bacterial, parasitic or viral infections of the animals and simultaneously reduce associated ecological damage and waste of resources. The animals' fodder accounts for 70% of the total costs in chicken production [3] and poultry diets are expensive since egg and meat production require high amounts of energy and protein sources. New perspectives will elucidate yet unknown aspects of the chickens' gut microbiome
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