Skip to main content
Log in

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

  • Note
  • Published:
Microbial Ecology Aims and scope Submit manuscript


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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2


  1. Colston TJ, Jackson CR (2016) Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol. Ecol. 25:3776–3800.

    Article  PubMed  Google Scholar 

  2. Hird SM (2017) Evolutionary biology needs wild microbiomes. Front. Microbiol. 8:725.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Waite DW, Taylor MW (2015) Exploring the avian gut microbiota: current trends and future directions. Front. Microbiol. 6:673.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Kohl KD (2017) An introductory “How-to” Guide for incorporating microbiome research into integrative and comparative biology. Integr. Comp. Biol. 57:674–681.

    Article  PubMed  Google Scholar 

  5. Craven SE, Stern NJ, Line E, Bailey JS, Cox NA, Fedorka-Cray P (2000) Determination of the incidence of Salmonella spp., Campylobacter jejuni and Clostridium perfringens in wild birds near broiler chicken houses by sampling intestinal droppings. Avian Dis. 44:715–720.

    Article  CAS  PubMed  Google Scholar 

  6. Hird SM, Carstens BC, Cardiff SW, Dittmann DL, Brumfield RT (2014) Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater). PeerJ 2:e321.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Roggenbuck M, Bærholm Schnell I, Blom N, Bælum J, Bertelsen MF, Pontén TS, Sørensen SJ, Gilbert MTP, Graves GR, Hansen LH (2014) The microbiome of New World vultures. Nat. Commun. 5:1–8.

    Article  CAS  Google Scholar 

  8. Hird SM, Sanchez C, Carstens BC, Brumfield RT (2015) Comparative gut microbiota of 59 neotropical bird species. Front. Microbiol. 6:1403.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Kohl KD, Connelly JW, Dearing MD, Forbey JS (2016) Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse. FEMS Microbiol. Lett. 363:1–6.

    Article  CAS  Google Scholar 

  10. Scupham AJ, Patton TG, Bent E, Bayles DO (2008) Comparison of the cecal microbiota of domestic and wild turkeys. Microb. Ecol. 56:322–331.

    Article  PubMed  Google Scholar 

  11. Grond K, Lanctot RB, Jumpponen A, Sandercock BK (2017) Recruitment and establishment of the gut microbiome in arctic shorebirds. FEMS Microbiol. Ecol. 93:1–9.

    Article  CAS  Google Scholar 

  12. Stanley D, Geier MS, Chen H, Hughes RJ, Moore RJ (2015) Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences. BMC Microbiol. 15:51.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Wilkinson N, Hughes RJ, Aspden WJ, Chapman J, Moore RJ, Stanley D (2016) The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica. Appl. Microbiol. Biotechnol. 100:4201–4209.

    Article  CAS  PubMed  Google Scholar 

  14. Videvall E, Strandh M, Engelbrecht A, Cloete S, Cornwallis CK (2017) Measuring the gut microbiome in birds: comparison of faecal and cloacal sampling. Mol. Ecol. Resour.

    Article  Google Scholar 

  15. Zhao G, Zhou L, Dong Y, Cheng Y, Song Y (2017) The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China. MicrobiologyOpen 6:1–9.

    Article  CAS  Google Scholar 

  16. Pannwitz G, Wolf C, Harder T (2009) Active surveillance for avian influenza virus infection in wild birds by analysis of avian fecal samples from the environment. J. Wildl. Dis. 45:512–518.

    Article  CAS  PubMed  Google Scholar 

  17. Wright ME, Solo-Gabriele HM, Elmir S, Fleming LE (2009) Microbial load from animal feces at a recreational beach. Mar. Pollut. Bull. 58:1649–1656.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Graczyk TK, Fayer R, Trout JM, Lewis EJ, Farley CA, Sulaiman I, Lal AA (1998) Giardia sp. cysts and infectious Cryptosporidium parvum oocysts in the feces of migratory Canada geese (Branta canadensis). Appl. Environ. Microbiol. 64:2736–2738

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Bangert ARL, Ward ACS, Stauber EH et al (1988) A survey of the aerobic bacteria in the feces of captive raptors a survey of the aerobic bacteria in the feces of captive raptors. Avian Dis. 32:53–62.

    Article  CAS  PubMed  Google Scholar 

  20. Hancock DD, Besser TE, Rice DH, Ebel ED, Herriott DE, Carpenter LV (1998) Multiple sources of Escherichia coli O157 in feedlots and dairy farms in the Northwestern USA. Prev Vet Med 35:11–19.

    Article  CAS  PubMed  Google Scholar 

  21. Kohl KD, Luong K, Dearing MD (2015) Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida). J. Mammal. 96:90–93.

    Article  Google Scholar 

  22. van Dongen WFD, White J, Brandl HB, Moodley Y, Merkling T, Leclaire S, Blanchard P, Danchin É, Hatch SA, Wagner RH (2013) Age-related differences in the cloacal microbiota of a wild bird species. BMC Ecol. 13:11.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Dewar ML, Arnould JPY, Krause L, Trathan P, Dann P, Smith SC (2014) Influence of fasting during moult on the faecal microbiota of penguins. PLoS One 9:e99996.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Rutala WA, Weber DJ (2008) Guideline for disinfection and sterilization in healthcare facilities. Center for Disease Control and Prevention.

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Sarah A. Knutie.

Ethics declarations

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.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: