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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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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. |
format | Online Article Text |
id | pubmed-4053703 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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