Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.

Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed...

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Autores principales:	Hannah Lees, Jonathan Swann, Simon M Poucher, Jeremy K Nicholson, Elaine Holmes, Ian D Wilson, Julian R Marchesi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/644d55be95c84a4dafd6463d20a3a45e
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spelling	oai:doaj.org-article:644d55be95c84a4dafd6463d20a3a45e2021-11-25T06:00:14ZAge and microenvironment outweigh genetic influence on the Zucker rat microbiome.1932-620310.1371/journal.pone.0100916https://doaj.org/article/644d55be95c84a4dafd6463d20a3a45e2014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0100916https://doaj.org/toc/1932-6203Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?Hannah LeesJonathan SwannSimon M PoucherJeremy K NicholsonElaine HolmesIan D WilsonJulian R MarchesiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 9, p e100916 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hannah Lees Jonathan Swann Simon M Poucher Jeremy K Nicholson Elaine Holmes Ian D Wilson Julian R Marchesi Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.
description	Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?
format	article
author	Hannah Lees Jonathan Swann Simon M Poucher Jeremy K Nicholson Elaine Holmes Ian D Wilson Julian R Marchesi
author_facet	Hannah Lees Jonathan Swann Simon M Poucher Jeremy K Nicholson Elaine Holmes Ian D Wilson Julian R Marchesi
author_sort	Hannah Lees
title	Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.
title_short	Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.
title_full	Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.
title_fullStr	Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.
title_full_unstemmed	Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.
title_sort	age and microenvironment outweigh genetic influence on the zucker rat microbiome.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/644d55be95c84a4dafd6463d20a3a45e
work_keys_str_mv	AT hannahlees ageandmicroenvironmentoutweighgeneticinfluenceonthezuckerratmicrobiome AT jonathanswann ageandmicroenvironmentoutweighgeneticinfluenceonthezuckerratmicrobiome AT simonmpoucher ageandmicroenvironmentoutweighgeneticinfluenceonthezuckerratmicrobiome AT jeremyknicholson ageandmicroenvironmentoutweighgeneticinfluenceonthezuckerratmicrobiome AT elaineholmes ageandmicroenvironmentoutweighgeneticinfluenceonthezuckerratmicrobiome AT iandwilson ageandmicroenvironmentoutweighgeneticinfluenceonthezuckerratmicrobiome AT julianrmarchesi ageandmicroenvironmentoutweighgeneticinfluenceonthezuckerratmicrobiome
_version_	1718414286279147520

Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.

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