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The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica

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Microbiota in the gastrointestinal tract (GIT) plays an essential role in the health and well-being of the host. With the exception of chickens, this area has been poorly studied within birds. The avian GIT harbours unique microbial communities. Birds require rapid energy bursts to enable energy-intensive flying. The passage time of feed through the avian GIT is only 2–3.5 h, and thus requires the presence of microbiota that is extremely efficient in energy extraction. This investigation has used high-throughput 16S rRNA gene sequencing to explore the GIT microbiota of the flighted bird, the Japanese quail (Coturnix japonica). We are reporting, for the first time, the diversity of bacterial phylotypes inhabiting all major sections of the quail GIT including mouth, esophagus, crop, proventriculus, gizzard, duodenum, ileum, cecum, large intestine and feces. Nine phyla of bacteria were found in the quail GIT; however, their distribution varied significantly between GIT sections. Cecal microbiota was the most highly differentiated from all the other communities and showed highest richness at an OTU level but lowest richness at all other taxonomic levels being comprised of only 15 of total 57 families in the quail GIT. Differences were observed in the presence and absence of specific phylotypes between sexes in most sections.

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We wish to thank Clive and Erika Wylie, the owners of Banyard Game Farms who provided the birds used in this study. We thank Honglei Chen for operating the Illumina MiSeq instrument. The data analysis was performed on Isaac Newton High Performance Computing System at Central Queensland University. We wish to acknowledge help from Jason Bell provided in all aspects of High Performance Computing as well as generous help we received from Tanka Prasai, Giselle Weegenaar, Ingrid Christiansen and Judy Couper.

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Correspondence to Dragana Stanley.

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Animal ethics approval for the present project was obtained from the Animal Ethics Committee of the Central Queensland University (A14/03-309).


This research was conducted within the Poultry CRC, established and supported under the Australian Government’s Cooperative Research Centres Program. Poultry CRC provides scholarship for Ngare Wilkinson.

Conflict of interest

The authors declare that they have no competing interests.

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Wilkinson, N., Hughes, R.J., Aspden, W.J. et al. The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica . Appl Microbiol Biotechnol 100, 4201–4209 (2016).

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