Chicken Gut Microbiota: Importance and Detection Technology

Abstract

Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.

Assembly of hundreds of novel bacterial genomes from the chicken caecum

“…The emergence of cheaper DNA sequencing technologies [17,18] has led to an explosion in studies which have sought to characterise the chicken gastrointestinal microbiota, particularly using 16S rRNA gene-based methods. Using this methodology, it has been found that the chicken caecal microbiota in the first few weeks of life is predominantly colonised by members of the Firmicutes, mostly of the order Clostridiales [8,19]. While valuable, marker-gene studies do not enable an in-depth functional and genomic characterisation of the microbiome.…”

Assembly of hundreds of novel bacterial genomes from the chicken caecum

“…The emergence of cheaper DNA sequencing technologies (17, 18) has led to an explosion in studies which have sought to characterise the chicken gastrointestinal microbiota, particularly using 16S rRNA gene based methods. Using this methodology, it has been found that the chicken caecal microbiota in the first few weeks of life is predominantly colonised by members of the Firmicutes , mostly of the order Clostridiales (8, 19). Whilst valuable, marker-gene studies do not enable an in-depth functional and genomic characterisation of the microbiome.…”

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

“…Improvements in sequencing technologies have led to a better understanding of the microbiota of many livestock species [1][2][3][4], leading some to suggest that we could optimise the composition of microbiota in these economically important animals to improve production and sustainability [5]. However, to do so would require a good understanding of the types of microbes which naturally occur in these animals and the role they play in nutrition and health.…”