Microbial Ecology

, Volume 76, Issue 4, pp 851–855 | Cite as

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

  • Sarah A. KnutieEmail author
  • Kiyoko M. Gotanda


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.


Avian Feces Fecal collection Method Microbiome 



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

Funding Information

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.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Ethical Approval

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


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsUSA
  2. 2.Department of ZoologyUniversity of CambridgeCambridgeUK

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