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Rumen sampling methods bias bacterial communities observed

The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sam...

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Autores principales: Hagey, Jill V., Laabs, Maia, Maga, Elizabeth A., DePeters, Edward J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9070869/
https://www.ncbi.nlm.nih.gov/pubmed/35511785
http://dx.doi.org/10.1371/journal.pone.0258176
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author Hagey, Jill V.
Laabs, Maia
Maga, Elizabeth A.
DePeters, Edward J.
author_facet Hagey, Jill V.
Laabs, Maia
Maga, Elizabeth A.
DePeters, Edward J.
author_sort Hagey, Jill V.
collection PubMed
description The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method (oral stomach tubing vs cannulated grab sample), as well as rumen fraction type (liquid vs solid), bias the bacterial and archaeal communities observed. Liquid samples were further divided into liquid strained through cheesecloth and unstrained. Fecal samples were also collected to determine how these differed from the rumen sample types. The abundance of major archaeal communities was not different at the family level in samples acquired via rumen cannula or stomach tube. In contrast to the stable archaeal communities across sample type, the bacterial order WCHB1-41 (phylum Kiritimatiellaeota) was enriched in both liquid strained and unstrained samples as well as the family Prevotellaceae as compared to grab samples. However, these liquid samples had significantly lower abundance of Lachnospiraceae compared with grab samples. Solid samples strained of rumen liquid most closely resembled the grab samples containing both rumen liquid and solid particles obtained directly from the rumen cannula; therefore, inclusion of particulate matter is important for an accurate representation of the rumen bacteria. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with grab samples.
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spelling pubmed-90708692022-05-06 Rumen sampling methods bias bacterial communities observed Hagey, Jill V. Laabs, Maia Maga, Elizabeth A. DePeters, Edward J. PLoS One Research Article The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method (oral stomach tubing vs cannulated grab sample), as well as rumen fraction type (liquid vs solid), bias the bacterial and archaeal communities observed. Liquid samples were further divided into liquid strained through cheesecloth and unstrained. Fecal samples were also collected to determine how these differed from the rumen sample types. The abundance of major archaeal communities was not different at the family level in samples acquired via rumen cannula or stomach tube. In contrast to the stable archaeal communities across sample type, the bacterial order WCHB1-41 (phylum Kiritimatiellaeota) was enriched in both liquid strained and unstrained samples as well as the family Prevotellaceae as compared to grab samples. However, these liquid samples had significantly lower abundance of Lachnospiraceae compared with grab samples. Solid samples strained of rumen liquid most closely resembled the grab samples containing both rumen liquid and solid particles obtained directly from the rumen cannula; therefore, inclusion of particulate matter is important for an accurate representation of the rumen bacteria. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with grab samples. Public Library of Science 2022-05-05 /pmc/articles/PMC9070869/ /pubmed/35511785 http://dx.doi.org/10.1371/journal.pone.0258176 Text en https://creativecommons.org/publicdomain/zero/1.0/This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Hagey, Jill V.
Laabs, Maia
Maga, Elizabeth A.
DePeters, Edward J.
Rumen sampling methods bias bacterial communities observed
title Rumen sampling methods bias bacterial communities observed
title_full Rumen sampling methods bias bacterial communities observed
title_fullStr Rumen sampling methods bias bacterial communities observed
title_full_unstemmed Rumen sampling methods bias bacterial communities observed
title_short Rumen sampling methods bias bacterial communities observed
title_sort rumen sampling methods bias bacterial communities observed
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9070869/
https://www.ncbi.nlm.nih.gov/pubmed/35511785
http://dx.doi.org/10.1371/journal.pone.0258176
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