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Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing

  • Host Microbe Interactions
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Abstract

Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9–98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1–85.3 %) and Actinobacteria (median 1.7 %; 0–18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4–97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.

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Acknowledgments

Part of this study was presented at ISME15 in Seoul, South Korea. JFGM acknowledges financial support by PRODEP (Secretaria de Educacion Publica, Mexico, grant number DSA/103.5/14/11021). The authors also wish to thank the QIIME and PICRUSt developers and users for their valuable help through the QIIME and PICRUSt Forums.

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Authors and Affiliations

  1. Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León (UANL), General Escobedo, NL, 66050, Mexico

    Jose F. Garcia-Mazcorro & Jose P. Gomez-Vazquez

  2. Research Group Medical Eco-Biology, Faculty of Veterinary Medicine, UANL, General Escobedo, NL, 66050, Mexico

    Jose F. Garcia-Mazcorro

  3. Department of Genetics, Faculty of Veterinary Medicine, UANL, General Escobedo, NL, 66050, Mexico

    Stephany A. Castillo-Carranza

  4. Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843-4474, USA

    Blake Guard

  5. Molecular Research LP, Shallowater, TX, 79363, USA

    Scot E. Dowd

  6. Schubot Exotic Bird Health Center, Texas A&M University, College Station, TX, 77843-4467, USA

    Donald J. Brigthsmith

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  1. Jose F. Garcia-Mazcorro
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Correspondence to Jose F. Garcia-Mazcorro.

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Garcia-Mazcorro, J.F., Castillo-Carranza, S.A., Guard, B. et al. Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing. Microb Ecol 73, 224–235 (2017). https://doi.org/10.1007/s00248-016-0840-7

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