Search

SUMMARY From the results of metagenomic research studies, we are just beginning to understand the positive and negative effects of the microbiome on the host. Metagenomics is the study of genetic materials from environmental or host-associated microbiota to identify the microbial diversity and its functions. These new sequencing techniques aim at analysing not only the human microbiome, but also that of the most commercial animal species, including poultry. High-throughput sequencing technologies have facilitated studies of the microbiome complex by allowing more comprehensive identification of microbes than traditional culture methods. Poultry digestive tract has significant bacterial activity, which can be seen as a unique complex microbial ecosystem. Microbial com-munity in gastrointestinal tract (GIT) plays an important role in overall health and function of host, be it in human or animals. Newly developed sequencing platforms such as next-generation sequencing (NGS) have allowed the important researches into the diversity and functions of gut microbiota of various livestock animals. Beginning in the chicken crop, starch breakdown, and lactate fermentation are mediated by various Lactobacillus spp. at cell densities up to 109/g. Lactobacillialso dominate the proventriculus, and the gizzard. In the gizzard, where the majority of mechanical and chemical breakdown of feed is performed, the low pH of gastric juices containing hydrochloric acid and pepsin decrease the total number of cells below 108 /g. The small intestine harbours large (108–109 /g) bacterial populations dominated by Lactobacillus, Enterococcus, and various Clostridiaceae. The most abundant groups in the chicken caeca were found to be Clostridiaceae, Bacteroidaceae, Lactobacillus and Proteobacteria.In our article, the latest research results on the gastrointestinal microbiome of the domestic chicken are reviewed.