Highly variable microbiota development in the chicken gastrointestinal tract

PLoS One. 2013 Dec 31;8(12):e84290. doi: 10.1371/journal.pone.0084290. eCollection 2013.


Studies investigating the role that complex microbiotas associated with animals and humans play in health and wellbeing have been greatly facilitated by advances in DNA sequencing technology. Due to the still relatively high sequencing costs and the expense of establishing and running animal trials and collecting clinical samples, most of the studies reported in the literature are limited to a single trial and relatively small numbers of samples. Results from different laboratories, investigating similar trials and samples, have often produced quite different pictures of microbiota composition. This study investigated batch to batch variations in chicken cecal microbiota across three similar trials, represented by individually analysed samples from 207 birds. Very different microbiota profiles were found across the three flocks. The flocks also differed in the efficiency of nutrient use as indicated by feed conversion ratios. In addition, large variations in the microbiota of birds within a single trial were noted. It is postulated that the large variability in microbiota composition is due, at least in part, to the lack of colonisation of the chicks by maternally derived bacteria. The high hygiene levels maintained in modern commercial hatcheries, although effective in reducing the burden of specific diseases, may have the undesirable effect of causing highly variable bacterial colonization of the gut. Studies in humans and other animals have previously demonstrated large variations in microbiota composition when comparing individuals from different populations and from different environments but this study shows that even under carefully controlled conditions large variations in microbiota composition still occur.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animal Nutritional Physiological Phenomena / physiology*
  • Animals
  • Base Sequence
  • Biodiversity*
  • Chickens / microbiology*
  • Chickens / physiology
  • DNA Primers / genetics
  • DNA, Ribosomal / genetics
  • Gastrointestinal Tract / microbiology*
  • High-Throughput Nucleotide Sequencing
  • Microbiota / genetics*
  • Molecular Sequence Data
  • Species Specificity


  • DNA Primers
  • DNA, Ribosomal

Grant support

This project was conducted within the Poultry Cooperative Research Centre, established and supported under the Australian Government’s Cooperative Research Centres Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.