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Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens

The gastrointestinal microbiota of chickens plays a central role in health and performance. Cloacal swabs, due to their proximity to the ceca (a vital site of functional activity), are an alternative, non-invasive method used for assaying microbial communities and might be a viable option for longit...

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Autores principales: Williams, Travis, Athrey, Giridhar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285018/
https://www.ncbi.nlm.nih.gov/pubmed/32408567
http://dx.doi.org/10.3390/microorganisms8050718
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author Williams, Travis
Athrey, Giridhar
author_facet Williams, Travis
Athrey, Giridhar
author_sort Williams, Travis
collection PubMed
description The gastrointestinal microbiota of chickens plays a central role in health and performance. Cloacal swabs, due to their proximity to the ceca (a vital site of functional activity), are an alternative, non-invasive method used for assaying microbial communities and might be a viable option for longitudinal studies. In this study, the microbiota of twenty paired cecal content and cloacal swab samples representing two dietary treatments was assessed using 16S rRNA V4 hypervariable region sequencing and was analyzed using the MOTHUR pipeline, Phyloseq, and Vegan packages. Paired t-test and Wilcoxon signed-rank tests showed significant differences in the Chao1 index (p-value <0.0001 and p-value <0.0001, respectively) but not in the Inverse Simpson species diversity estimator (p-value = 0.06763 and p-value = 0.06021, respectively) between the cecal content and cloacal swabs. β-diversity between the cloacal swabs and cecal microbiota also showed significant differences using PERMANOVA, HOMOVA, and weighted UniFrac testing (p-values < 0.001). Based on a paired sample analysis, this study provided evidence of the high inter-individual variation and randomness of cloacal microbiota, in contrast to cecal microbiota. Our findings indicated that cloacal swabs do not approximate the α or β diversity of cecal samples and are not suitable for longitudinal studies of gut microbiota.
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spelling pubmed-72850182020-06-17 Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens Williams, Travis Athrey, Giridhar Microorganisms Article The gastrointestinal microbiota of chickens plays a central role in health and performance. Cloacal swabs, due to their proximity to the ceca (a vital site of functional activity), are an alternative, non-invasive method used for assaying microbial communities and might be a viable option for longitudinal studies. In this study, the microbiota of twenty paired cecal content and cloacal swab samples representing two dietary treatments was assessed using 16S rRNA V4 hypervariable region sequencing and was analyzed using the MOTHUR pipeline, Phyloseq, and Vegan packages. Paired t-test and Wilcoxon signed-rank tests showed significant differences in the Chao1 index (p-value <0.0001 and p-value <0.0001, respectively) but not in the Inverse Simpson species diversity estimator (p-value = 0.06763 and p-value = 0.06021, respectively) between the cecal content and cloacal swabs. β-diversity between the cloacal swabs and cecal microbiota also showed significant differences using PERMANOVA, HOMOVA, and weighted UniFrac testing (p-values < 0.001). Based on a paired sample analysis, this study provided evidence of the high inter-individual variation and randomness of cloacal microbiota, in contrast to cecal microbiota. Our findings indicated that cloacal swabs do not approximate the α or β diversity of cecal samples and are not suitable for longitudinal studies of gut microbiota. MDPI 2020-05-12 /pmc/articles/PMC7285018/ /pubmed/32408567 http://dx.doi.org/10.3390/microorganisms8050718 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Williams, Travis
Athrey, Giridhar
Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens
title Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens
title_full Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens
title_fullStr Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens
title_full_unstemmed Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens
title_short Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens
title_sort cloacal swabs are unreliable sources for estimating lower gastro-intestinal tract microbiota membership and structure in broiler chickens
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285018/
https://www.ncbi.nlm.nih.gov/pubmed/32408567
http://dx.doi.org/10.3390/microorganisms8050718
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