Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species
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 mamm...
Published in: | Infection Ecology & Epidemiology |
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Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi
2017
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-409017 https://doi.org/10.1080/20008686.2017.1386536 |
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ftuppsalauniv:oai:DiVA.org:uu-409017 2023-05-15T14:00:26+02:00 Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species Eriksson, Per Mourkas, Evangelos González-Acuna, Daniel Olsen, Björn Ellström, Patrik 2017 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-409017 https://doi.org/10.1080/20008686.2017.1386536 eng eng Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi Uppsala universitet, Infektionsmedicin Uppsala universitet, Institutionen för medicinska vetenskaper The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Infection Ecology & Epidemiology, 2000-8686, 2017, 7:1, http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-409017 doi:10.1080/20008686.2017.1386536 PMID 29152162 info:eu-repo/semantics/openAccess Antarctica Aves DNA extraction feces method evaluation and scatology Microbiology Mikrobiologi Article in journal info:eu-repo/semantics/article text 2017 ftuppsalauniv https://doi.org/10.1080/20008686.2017.1386536 2023-02-23T21:52:00Z 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. Article in Journal/Newspaper Antarc* Antarctic Antarctica Uppsala University: Publications (DiVA) Antarctic Infection Ecology & Epidemiology 7 1 1386536 |
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collection |
Uppsala University: Publications (DiVA) |
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ftuppsalauniv |
language |
English |
topic |
Antarctica Aves DNA extraction feces method evaluation and scatology Microbiology Mikrobiologi |
spellingShingle |
Antarctica Aves DNA extraction feces method evaluation and scatology Microbiology Mikrobiologi Eriksson, Per Mourkas, Evangelos González-Acuna, Daniel Olsen, Björn Ellström, Patrik Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species |
topic_facet |
Antarctica Aves DNA extraction feces method evaluation and scatology Microbiology Mikrobiologi |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Eriksson, Per Mourkas, Evangelos González-Acuna, Daniel Olsen, Björn Ellström, Patrik |
author_facet |
Eriksson, Per Mourkas, Evangelos González-Acuna, Daniel Olsen, Björn Ellström, Patrik |
author_sort |
Eriksson, Per |
title |
Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species |
title_short |
Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species |
title_full |
Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species |
title_fullStr |
Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species |
title_full_unstemmed |
Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species |
title_sort |
evaluation and optimization of microbial dna extraction from fecal samples of wild antarctic bird species |
publisher |
Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi |
publishDate |
2017 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-409017 https://doi.org/10.1080/20008686.2017.1386536 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_relation |
Infection Ecology & Epidemiology, 2000-8686, 2017, 7:1, http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-409017 doi:10.1080/20008686.2017.1386536 PMID 29152162 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1080/20008686.2017.1386536 |
container_title |
Infection Ecology & Epidemiology |
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7 |
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1 |
container_start_page |
1386536 |
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1766269526525083648 |