Abstract

Introduction: Advances in the development of nucleic acid-based methods have dramatically facilitated studies of host–microbial interactions. Fecal DNA analysis can provide information about the host’s microbiota and gastrointestinal pathogen burden. Numerous studies have been conducted in mammals, yet birds are less well studied. Avian fecal DNA extraction has proved challenging, partly due to the mixture of fecal and urinary excretions and the deficiency of optimized protocols. This study presents an evaluation of the performance in avian fecal DNA extraction of six commercial kits from different bird species, focusing on penguins.

Material and methods: Six DNA extraction kits were first tested according to the manufacturers’ instructions using mallard feces. The kit giving the highest DNA yield was selected for further optimization and evaluation using Antarctic bird feces.

Results: Penguin feces constitute a challenging sample type: most of the DNA extraction kits failed to yield acceptable amounts of DNA. The QIAamp cador Pathogen kit (Qiagen) performed the best in the initial investigation. Further optimization of the protocol resulted in good yields of high-quality DNA from seven bird species of different avian orders.

Conclusion: This study presents an optimized approach to DNA extraction from challenging avian fecal samples.

Details

Title
Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species
Author
Eriksson, Per 1   VIAFID ORCID Logo  ; Mourkas, Evangelos 2 ; González-Acuna, Daniel 3 ; Olsen, Björn 4 ; Ellström, Patrik 1 

1  Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden 
2  Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden; The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK 
3  Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile 
4  Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden 
Publication year
2017
Publication date
2017
Publisher
Taylor & Francis Ltd.
e-ISSN
20008686
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1080/20008686.2017.1386536
ProQuest document ID
2215253368
Copyright
© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This work is licensed under the Creative Commons  Attribution – Non-Commercial License http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.