Cargando…

16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations

16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling p...

Descripción completa

Detalles Bibliográficos
Autores principales: Weinroth, Margaret D., Oakley, Brian, Ramírez, Gustavo A., Reyes, Arquimides, Harris, Caitlin E., Buhr, R. Jeff
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9627029/
https://www.ncbi.nlm.nih.gov/pubmed/36338471
http://dx.doi.org/10.3389/fphys.2022.996654
_version_ 1784822872517115904
author Weinroth, Margaret D.
Oakley, Brian
Ramírez, Gustavo A.
Reyes, Arquimides
Harris, Caitlin E.
Buhr, R. Jeff
author_facet Weinroth, Margaret D.
Oakley, Brian
Ramírez, Gustavo A.
Reyes, Arquimides
Harris, Caitlin E.
Buhr, R. Jeff
author_sort Weinroth, Margaret D.
collection PubMed
description 16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling practices in broiler chicken studies such as: the required number of birds selected from a flock to adequately capture microbiome diversity, the differences between cecal pairs within the same bird, and whether cloacal swabs are representative of other alimentary tract (AT) locations. To do this, nine market age broilers were euthanized and immediately sampled in ten AT locations: crop, gizzard, proventriculus, duodenum, jejunum, ileum, cecal samples from each pouch, colon, and cloacal swab. DNA was extracted and subjected to 16S rRNA gene amplification and sequencing. Each location within the broiler AT hosts distinct microbial communities. When each sampling location was considered, it was found that sampling after 2.8 birds (range 2–4) resulted in less than 10% new amplicon sequencing variants (ASV) being added while sampling after 7.6 birds (range 6–10) increases new observed ASVs by less than 1%. Additionally, when cecal pairs from the same bird were evaluated, it was found that cecal pair mates are an adequate replication if interested in the total cecal microbiome but may be less useful if a rare lineage is of interest. Furthermore, when compared to other AT locations, the cecal microbiome was enriched in Firmicutes and Bacteroides while several lineages, most notably Lactobacillus, were under-represented. Finally, when cloacal swabs were compared to other AT locations, community similarity exhibited a direct distance relationship, i.e., the more aborad samples were the more similar they were to the swab. These findings indicate that while cloacal swabs can approximate overall changes in microbiome composition, they are not adequate for inferring changes to specific taxa in other parts of the AT tract—even those that are highly abundant within the microbial community. These data provide new insights guiding appropriate sample size selection within flocks and add to the consensus data regarding cecal pair similarity and destructive versus non-destructive sampling methods.
format Online
Article
Text
id pubmed-9627029
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-96270292022-11-03 16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations Weinroth, Margaret D. Oakley, Brian Ramírez, Gustavo A. Reyes, Arquimides Harris, Caitlin E. Buhr, R. Jeff Front Physiol Physiology 16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling practices in broiler chicken studies such as: the required number of birds selected from a flock to adequately capture microbiome diversity, the differences between cecal pairs within the same bird, and whether cloacal swabs are representative of other alimentary tract (AT) locations. To do this, nine market age broilers were euthanized and immediately sampled in ten AT locations: crop, gizzard, proventriculus, duodenum, jejunum, ileum, cecal samples from each pouch, colon, and cloacal swab. DNA was extracted and subjected to 16S rRNA gene amplification and sequencing. Each location within the broiler AT hosts distinct microbial communities. When each sampling location was considered, it was found that sampling after 2.8 birds (range 2–4) resulted in less than 10% new amplicon sequencing variants (ASV) being added while sampling after 7.6 birds (range 6–10) increases new observed ASVs by less than 1%. Additionally, when cecal pairs from the same bird were evaluated, it was found that cecal pair mates are an adequate replication if interested in the total cecal microbiome but may be less useful if a rare lineage is of interest. Furthermore, when compared to other AT locations, the cecal microbiome was enriched in Firmicutes and Bacteroides while several lineages, most notably Lactobacillus, were under-represented. Finally, when cloacal swabs were compared to other AT locations, community similarity exhibited a direct distance relationship, i.e., the more aborad samples were the more similar they were to the swab. These findings indicate that while cloacal swabs can approximate overall changes in microbiome composition, they are not adequate for inferring changes to specific taxa in other parts of the AT tract—even those that are highly abundant within the microbial community. These data provide new insights guiding appropriate sample size selection within flocks and add to the consensus data regarding cecal pair similarity and destructive versus non-destructive sampling methods. Frontiers Media S.A. 2022-10-19 /pmc/articles/PMC9627029/ /pubmed/36338471 http://dx.doi.org/10.3389/fphys.2022.996654 Text en Copyright © 2022 Weinroth, Oakley, Ramírez, Reyes, Harris and Buhr. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Physiology
Weinroth, Margaret D.
Oakley, Brian
Ramírez, Gustavo A.
Reyes, Arquimides
Harris, Caitlin E.
Buhr, R. Jeff
16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations
title 16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations
title_full 16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations
title_fullStr 16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations
title_full_unstemmed 16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations
title_short 16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations
title_sort 16s rrna gene-based assessment of common broiler chicken sampling methods: evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations
topic Physiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9627029/
https://www.ncbi.nlm.nih.gov/pubmed/36338471
http://dx.doi.org/10.3389/fphys.2022.996654
work_keys_str_mv AT weinrothmargaretd 16srrnagenebasedassessmentofcommonbroilerchickensamplingmethodsevaluatingintraflocksamplesizececalpairsimilarityandcloacalswabsimilaritytootheralimentarytractlocations
AT oakleybrian 16srrnagenebasedassessmentofcommonbroilerchickensamplingmethodsevaluatingintraflocksamplesizececalpairsimilarityandcloacalswabsimilaritytootheralimentarytractlocations
AT ramirezgustavoa 16srrnagenebasedassessmentofcommonbroilerchickensamplingmethodsevaluatingintraflocksamplesizececalpairsimilarityandcloacalswabsimilaritytootheralimentarytractlocations
AT reyesarquimides 16srrnagenebasedassessmentofcommonbroilerchickensamplingmethodsevaluatingintraflocksamplesizececalpairsimilarityandcloacalswabsimilaritytootheralimentarytractlocations
AT harriscaitline 16srrnagenebasedassessmentofcommonbroilerchickensamplingmethodsevaluatingintraflocksamplesizececalpairsimilarityandcloacalswabsimilaritytootheralimentarytractlocations
AT buhrrjeff 16srrnagenebasedassessmentofcommonbroilerchickensamplingmethodsevaluatingintraflocksamplesizececalpairsimilarityandcloacalswabsimilaritytootheralimentarytractlocations