Many studies have used 16S rRNA gene data to characterise the microbial communities which colonise the gastrointestinal tracts of chickens and to characterise the development of these communities over time. The vast majority of these studies have focussed on the chicken caeca as this is where the largest concentration of microbes can be found. The caecal microbiota has been suggested to play an important role in nutrition via the production of short chain fatty acids, nitrogen recycling and amino acid production.
In early life it is generally observed that the caeca contain high abundances of Enterobacteriales and over the first few weeks of life these decline and members of the Clostridiales come to predominate, with some studies also showing a large increase in Bacteroidetes. However, the results from some studies do not entirely follow this pattern and variability in microbiota composition between flocks can be high. Several studies have also examined samples from the small intestine which are less rich and diverse than caecal samples and contain a high abundance of Lactobacilli. Several studies have directly compared samples taken from the small intestine with those from the caeca at specific timepoints, and at various life stages. Compared ileal and caecal samples from commercial Ross-hybrids, taking samples at day 1, 3, 7 14, 21, 28, and 49 days of age.
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