title: Highly variable microbiota development in the chicken gastrointestinal tract.
abstract: 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.
authors.affiliation: Animal, Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia ; Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia ; School of Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland, Australia.
authors.forename: Dragana
authors.initials: D
authors.lastname: Stanley
authors.affiliation: Pig and Poultry Production Institute, South Australian Research and Development Institute, Roseworthy, South Australia, Australia ; Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia ; School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia.
authors.forename: Mark S
authors.initials: MS
authors.lastname: Geier
authors.affiliation: Pig and Poultry Production Institute, South Australian Research and Development Institute, Roseworthy, South Australia, Australia ; Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia ; School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Hughes
authors.affiliation: Animal, Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation, St Lucia, Queensland, Australia.
authors.forename: Stuart E
authors.initials: SE
authors.lastname: Denman
authors.affiliation: Animal, Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia ; Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia ; Department of Microbiology, Monash University, Clayton, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Moore
mesh_terms: D000824:Animal Nutritional Physiological Phenomena / Q000502:physiology*; D000818:Animals; D001483:Base Sequence; D044822:Biodiversity; D002645:Chickens / Q000382:microbiology* / Q000502:physiology; D017931:DNA Primers / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D041981:Gastrointestinal Tract / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D064307:Microbiota / Q000235:genetics*; D008969:Molecular Sequence Data; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D004275:DNA, Ribosomal