Development of the Ileal Microbiota in Three Broiler Breeds.

The development and succession of the microbiota in ileal mucus and lumen samples from three breeds of broiler chicken (Cobb 500, = 36; Hubbard JA87, = 38; and Ross 308, = 36) was observed between 3 and 42 days post hatch (d.p.h). Chicks were housed in the same room of a climate-controlled, biosecure chicken housing unit. Between 0 and 14 d.p.h, chicks were kept in three circular brooder pens ensuring a mixture of breeds in each brooder. From 22 d.p.h, chicks were removed from the brooders and kept in the same room. DNA was extracted from a pooled sample of ileal mucus and luminal contents taken from five birds of each breed at 3, 7, 14, 21, 28, and 42 d.p.h. High-throughput Illumina sequencing was performed for the V4 hypervariable region of the 16S rRNA gene. The initial microbiota in the ileum varied between breeds. The common features were a low diversity and general dominance by one or two taxa such as or with relatively low numbers of . became the most abundant genus in samples where was previously the dominant taxa. The next phase of development was marked by an increase in the abundance of Candidatus in the mucus and in the lumen. The high abundance of Candidatus persisted between 7 and 14 d.p.h after which became the most abundant genus in both the mucus and lumen. Dominance of the ileal microbiota by was a transient feature. By 42 d.p.h, the relative abundance of had fallen while a range of other taxa including , and members of Clostridiales increased. This general pattern was followed by all breeds, however, the rate at which succession occurred differed as Ross matured quicker than Cobb with Hubbard as an intermediate.