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Research Article
María Velasco-Galilea
Institut de Recerca i Tecnologia Agroalimentaries
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9533-7412
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.
Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that the farm exerted the largest influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with the farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.
Conclusions: this study reveals different degrees of influence attributable to environment and animal management. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be causative of different animal performance.
Keywords
cecal microbiota, meat rabbit, housing conditions, feed restriction, antibiotics, 16S MiSeq Illumina sequencing, analysis of variance, multivariate approach
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View the published article at Animal Microbiome.
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On 13 Oct, 2020
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On 12 Oct, 2020
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On 11 Oct, 2020
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On 16 Sep, 2020
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On 07 Sep, 2020
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On 06 Sep, 2020
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On 05 Sep, 2020
Editor invited
On 05 Sep, 2020
Version 2
Posted 29 Aug, 2020
No comments provided
Editorial decision: Revise before peer review
On 28 Aug, 2020
Review #1 received
Received 27 Aug, 2020
Reviewer #3 agreed
On 26 Aug, 2020
Review #3 received
Received 26 Aug, 2020
Review #2 received
Received 26 Aug, 2020
Reviewer #1 agreed
On 25 Aug, 2020
Reviewer #2 agreed
On 25 Aug, 2020
Reviewers invited
Invitations sent on 25 Aug, 2020
Editor assigned
On 23 Aug, 2020
Submission checks complete
On 22 Aug, 2020
Editor invited
On 22 Aug, 2020
No comments provided
Editorial decision: Minor revision
On 03 Aug, 2020
Review #3 received
Received 30 Jul, 2020
Review #2 received
Received 28 Jul, 2020
Review #1 received
Received 28 Jul, 2020
Reviewer #3 agreed
On 21 Jul, 2020
Reviewer #1 agreed
On 20 Jul, 2020
Reviewer #2 agreed
On 20 Jul, 2020
Reviewers invited
Invitations sent on 08 Jul, 2020
First submitted
On 03 Jul, 2020
Editor assigned
On 03 Jul, 2020
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Editor invited
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See the published version of this preprint at Animal Microbiome.
This is a preprint, 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
María Velasco-Galilea
Institut de Recerca i Tecnologia Agroalimentaries
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9533-7412
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: Published
View the published article at Animal Microbiome.
No community comments so far
Editorial decision: Accept
On 13 Oct, 2020
Editor assigned
On 12 Oct, 2020
Submission checks complete
On 11 Oct, 2020
Editor invited
On 11 Oct, 2020
No comments provided
Editorial decision: Major revision
On 16 Sep, 2020
Review #1 received
Received 11 Sep, 2020
Reviewer #1 agreed
On 07 Sep, 2020
Reviewers invited
Invitations sent on 07 Sep, 2020
Editor assigned
On 06 Sep, 2020
Submission checks complete
On 05 Sep, 2020
Editor invited
On 05 Sep, 2020
Version 2
Posted 29 Aug, 2020
No comments provided
Editorial decision: Revise before peer review
On 28 Aug, 2020
Review #1 received
Received 27 Aug, 2020
Reviewer #3 agreed
On 26 Aug, 2020
Review #3 received
Received 26 Aug, 2020
Review #2 received
Received 26 Aug, 2020
Reviewer #1 agreed
On 25 Aug, 2020
Reviewer #2 agreed
On 25 Aug, 2020
Reviewers invited
Invitations sent on 25 Aug, 2020
Editor assigned
On 23 Aug, 2020
Submission checks complete
On 22 Aug, 2020
Editor invited
On 22 Aug, 2020
No comments provided
Editorial decision: Minor revision
On 03 Aug, 2020
Review #3 received
Received 30 Jul, 2020
Review #2 received
Received 28 Jul, 2020
Review #1 received
Received 28 Jul, 2020
Reviewer #3 agreed
On 21 Jul, 2020
Reviewer #1 agreed
On 20 Jul, 2020
Reviewer #2 agreed
On 20 Jul, 2020
Reviewers invited
Invitations sent on 08 Jul, 2020
First submitted
On 03 Jul, 2020
Editor assigned
On 03 Jul, 2020
Submission checks complete
On 02 Jul, 2020
Editor invited
On 02 Jul, 2020
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
View the published article at Animal Microbiome.
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.
Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that the farm exerted the largest influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with the farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.
Conclusions: this study reveals different degrees of influence attributable to environment and animal management. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be causative of different animal performance.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
The full text of this article is available to read as a PDF.
This is a list of supplementary files associated with this preprint. Click to download.
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