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Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

BACKGROUND: Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, w...

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Autores principales: Hildebrand, Falk, Nguyen, Thi Loan Anh, Brinkman, Brigitta, Yunta, Roberto Garcia, Cauwe, Benedicte, Vandenabeele, Peter, Liston, Adrian, Raes, Jeroen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053703/
https://www.ncbi.nlm.nih.gov/pubmed/23347395
http://dx.doi.org/10.1186/gb-2013-14-1-r4
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author Hildebrand, Falk
Nguyen, Thi Loan Anh
Brinkman, Brigitta
Yunta, Roberto Garcia
Cauwe, Benedicte
Vandenabeele, Peter
Liston, Adrian
Raes, Jeroen
author_facet Hildebrand, Falk
Nguyen, Thi Loan Anh
Brinkman, Brigitta
Yunta, Roberto Garcia
Cauwe, Benedicte
Vandenabeele, Peter
Liston, Adrian
Raes, Jeroen
author_sort Hildebrand, Falk
collection PubMed
description BACKGROUND: Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, we investigate the variability of the healthy mouse microbiota of five common lab mouse strains using 16S rDNA pyrosequencing. RESULTS: We find initial evidence for richness-driven, strain-independent murine enterotypes that show a striking resemblance to those in human, and which associate with calprotectin levels, a marker for intestinal inflammation. After enterotype stratification, we find that genetic, caging and inter-individual variation contribute on average 19%, 31.7% and 45.5%, respectively, to the variance in the murine gut microbiota composition. Genetic distance correlates positively to microbiota distance, so that genetically similar strains have more similar microbiota than genetically distant ones. Specific mouse strains are enriched for specific operational taxonomic units and taxonomic groups, while the 'cage effect' can occur across mouse strain boundaries and is mainly driven by Helicobacter infections. CONCLUSIONS: The detection of enterotypes suggests a common ecological cause, possibly low-grade inflammation that might drive differences among gut microbiota composition in mammals. Furthermore, the observed environmental and genetic effects have important consequences for experimental design in mouse microbiome research.
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spelling pubmed-40537032014-06-12 Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice Hildebrand, Falk Nguyen, Thi Loan Anh Brinkman, Brigitta Yunta, Roberto Garcia Cauwe, Benedicte Vandenabeele, Peter Liston, Adrian Raes, Jeroen Genome Biol Research BACKGROUND: Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, we investigate the variability of the healthy mouse microbiota of five common lab mouse strains using 16S rDNA pyrosequencing. RESULTS: We find initial evidence for richness-driven, strain-independent murine enterotypes that show a striking resemblance to those in human, and which associate with calprotectin levels, a marker for intestinal inflammation. After enterotype stratification, we find that genetic, caging and inter-individual variation contribute on average 19%, 31.7% and 45.5%, respectively, to the variance in the murine gut microbiota composition. Genetic distance correlates positively to microbiota distance, so that genetically similar strains have more similar microbiota than genetically distant ones. Specific mouse strains are enriched for specific operational taxonomic units and taxonomic groups, while the 'cage effect' can occur across mouse strain boundaries and is mainly driven by Helicobacter infections. CONCLUSIONS: The detection of enterotypes suggests a common ecological cause, possibly low-grade inflammation that might drive differences among gut microbiota composition in mammals. Furthermore, the observed environmental and genetic effects have important consequences for experimental design in mouse microbiome research. BioMed Central 2013 2013-01-24 /pmc/articles/PMC4053703/ /pubmed/23347395 http://dx.doi.org/10.1186/gb-2013-14-1-r4 Text en Copyright © 2013 Hildebrand et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Hildebrand, Falk
Nguyen, Thi Loan Anh
Brinkman, Brigitta
Yunta, Roberto Garcia
Cauwe, Benedicte
Vandenabeele, Peter
Liston, Adrian
Raes, Jeroen
Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
title Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
title_full Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
title_fullStr Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
title_full_unstemmed Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
title_short Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
title_sort inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053703/
https://www.ncbi.nlm.nih.gov/pubmed/23347395
http://dx.doi.org/10.1186/gb-2013-14-1-r4
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