Highly variable microbiota development in the chicken gastrointestinal tract

• Published in: PloS one Vol. 8; no. 12; p. e84290
• Main Authors: Stanley, Dragana, Geier, Mark S, Hughes, Robert J, Denman, Stuart E, Moore, Robert J
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 31-12-2013; Public Library of Science (PLoS)
• Subjects: Agriculture; Animal Nutritional Physiological Phenomena - physiology; Animals; Bacteria; Base Sequence; Biodiversity; Bioinformatics; Biology; Birds; Cecum; Chickens; Chickens - microbiology; Chickens - physiology; Chicks; Clinical trials; Colonization; Controlled conditions; Deoxyribonucleic acid; DNA; DNA Primers - genetics; DNA sequencing; DNA, Ribosomal - genetics; Feed conversion; Feeds; Gastrointestinal system; Gastrointestinal tract; Gastrointestinal Tract - microbiology; Gene sequencing; Hatcheries; Health sciences; High-Throughput Nucleotide Sequencing; Hygiene; Industrial research; Infections; Juveniles; Microbiota; Microbiota (Symbiotic organisms); Microbiota - genetics; Molecular Sequence Data; Pictures; Poultry; R&D; Research & development; Species Specificity; Studies; Taxonomy; Variation; Veterinary Science; England; Queensland Australia; United Kingdom > UK; Australia; New South Wales Australia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0084290

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.