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Research Article
Kasun H Bodawatta
Københavns Universitet
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6095-9059
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Background Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for two weeks or two months, respectively. Results We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. Conclusions Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. Secondly, the satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.
Keywords
non-invasive sampling, museum alcohol bird collections, microbiomes, Passeriformes, digestive tract microbiota
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CURRENT STATUS: Under Review
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Posted 30 Jan, 2020
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Review #1 received
Received 22 Feb, 2020
Reviewer #1 agreed
On 11 Feb, 2020
Reviewers invited
Invitations sent on 10 Feb, 2020
Editor assigned
On 29 Jan, 2020
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On 28 Jan, 2020
Editor invited
On 28 Jan, 2020
No comments provided
Editorial decision: Major revision
On 24 Jan, 2020
Review #1 received
Received 23 Jan, 2020
Reviewers invited
Invitations sent on 07 Jan, 2020
Reviewer #1 agreed
On 07 Jan, 2020
Editor assigned
On 26 Dec, 2019
Submission checks complete
On 25 Dec, 2019
Editor invited
On 25 Dec, 2019
First submitted
On 20 Dec, 2019
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Subject Areas
General Microbiology
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This preprint is under consideration at Animal Microbiome. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Kasun H Bodawatta
Københavns Universitet
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6095-9059
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 2
Posted 30 Jan, 2020
No community comments so far
Review #1 received
Received 22 Feb, 2020
Reviewer #1 agreed
On 11 Feb, 2020
Reviewers invited
Invitations sent on 10 Feb, 2020
Editor assigned
On 29 Jan, 2020
Submission checks complete
On 28 Jan, 2020
Editor invited
On 28 Jan, 2020
No comments provided
Editorial decision: Major revision
On 24 Jan, 2020
Review #1 received
Received 23 Jan, 2020
Reviewers invited
Invitations sent on 07 Jan, 2020
Reviewer #1 agreed
On 07 Jan, 2020
Editor assigned
On 26 Dec, 2019
Submission checks complete
On 25 Dec, 2019
Editor invited
On 25 Dec, 2019
First submitted
On 20 Dec, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for two weeks or two months, respectively. Results We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. Conclusions Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. Secondly, the satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
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