A Non-invasive Method to Collect Fecal Samples from Wild Birds for Microbiome Studies


Over the past few decades, studies have demonstrated that the gut microbiota strongly influences the physiology, behavior, and fitness of its host. Such studies have been conducted primarily in humans and model organisms under controlled laboratory conditions. More recently, researchers have realized the importance of placing host-associated microbiota studies into a more ecological context; however, few non-destructive methods have been established to collect fecal samples from wild birds. Here, we present an inexpensive and easy-to-use kit for the non-invasive collection of feces from small birds. The portability of the collection kit makes this method amenable to field studies, especially those in remote areas. The main components of the collection kit include a flat-bottomed paper bag, a large modified weigh boat (tray), vinyl-coated hardware cloth fencing (grate), a clothespin, and a 10% bleach solution (to sterilize the tray and grate). In the paper bag, a sterile tray is placed under a small grate, which prevents the birds from contacting the feces and reduces the risk of contamination. After capture, the bird is placed in the bag for 3–5 min until it defecates. After the bird is removed from the bag, the tray is extracted and the fecal sample is moved to a collection tube and frozen or preserved. We believe that our method is an affordable and easy option for researchers studying the gut microbiota of wild birds.

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We thank Johanna Harvey for field assistance and Brian Trevelline and three anonymous reviewers for comments on this manuscript.


The work was supported by funding through Instrumentl Crowdfunding to KMG and SAK; a Le Fonds Québécois de la Recherche sur la Nature et les Technologies Postdoctoral Fellowship, Natural Sciences and Engineering Council of Canada Banting Postdocotoral Fellowship, and British Ornithologists’ Union Research Grant to KMG; and a British Ecological Society Large Research Grant (5599-6643) and the University of Connecticut to SAK.

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Correspondence to Sarah A. Knutie.

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All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

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Knutie, S.A., Gotanda, K.M. A Non-invasive Method to Collect Fecal Samples from Wild Birds for Microbiome Studies. Microb Ecol 76, 851–855 (2018). https://doi.org/10.1007/s00248-018-1182-4

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  • Avian
  • Feces
  • Fecal collection
  • Method
  • Microbiome