Abstract

The development and succession of the microbiota in ileal mucus and lumen samples from three breeds of broiler chicken (Cobb 500, n = 36; Hubbard JA87, n = 38; and Ross 308, n = 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 Enterococcus or Escherichia with relatively low numbers of Lactobacillus. Escherichia became the most abundant genus in samples where Enterococcus was previously the dominant taxa. The next phase of development was marked by an increase in the abundance of Candidatus Arthromitus in the mucus and Lactobacillus in the lumen. The high abundance of Candidatus Arthromitus persisted between 7 and 14 d.p.h after which Lactobacillus became the most abundant genus in both the mucus and lumen. Dominance of the ileal microbiota by Lactobacillus was a transient feature. By 42 d.p.h, the relative abundance of Lactobacillus had fallen while a range of other taxa including Escherichia, Turicibacter, 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.

Highlights

  • The intestinal microbiota of an individual chicken may be composed of between 200 and 350 different bacterial species [1] while around 640 bacterial species have so far been identified in the chicken gastrointestinal tract [2]

  • Lactobacillus mucosae was present at 3 d.p.h but other species of Lactobacillus such as Lactobacillus vaginalis did not colonize the ileum until later time points

  • A pattern of succession followed with Candidatus Arthromitus and Clostridioides appearing in the ileal microbiome at 7 d.p.h

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Summary

Introduction

The intestinal microbiota of an individual chicken may be composed of between 200 and 350 different bacterial species [1] while around 640 bacterial species have so far been identified in the chicken gastrointestinal tract [2]. In recent years it has become apparent that this diverse range of bacteria are not innocuous bystanders but play a range of roles in the host, from metabolism to immune maturation [3]. In the face of antibiotic resistance and a need to find new approaches to infectious disease control, the question of how certain bacteria modulate host immunity is of particular interest to the broiler industry which produces chickens for meat. Recent observational studies of the ileal microbiota are limited. More recent studies which have used NGS focus on differences in microbiota composition between a treatment group and an untreated control. This study aims to revisit the topic of normal ileal microbiota development using the increased resolution of NGS to shed light on microbial succession

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