Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice.
Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice.
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DOI：
10.1186/gb-2013-14-1-r4
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发表时间：
2013-01-24
期刊：
影响因子：
12.3
通讯作者：
Raes J
中科院分区：
文献类型：
--
作者：
Hildebrand F;Nguyen TL;Brinkman B;Yunta RG;Cauwe B;Vandenabeele P;Liston A;Raes J
小鼠模型是肠道微生物组研究的重要组成部分。不幸的是，大量的遗传背景和实验设置，以及个体间的变异，使交叉研究比较和对小鼠微生物群景观的全球理解变得复杂。在这里，我们使用16S rDNA焦磷酸测序研究了五种常见实验室小鼠品系的健康小鼠微生物群的变异性。我们发现了初步证据，丰富的驱动，应变独立的小鼠肠型，显示出惊人的相似之处，在人类，并与钙卫蛋白水平，肠道炎症的标志物。在肠型分层后，我们发现遗传、笼养和个体间变异分别对小鼠肠道微生物群组成的方差平均贡献19%、31.7%和45.5%。遗传距离与微生物群距离呈正相关，因此遗传相似的菌株比遗传遥远的菌株具有更多相似的微生物群。特定的小鼠品系富集了特定的操作分类单位和分类组，而“笼效应”可以跨越小鼠品系边界发生，并且主要由螺杆菌感染驱动。肠型的检测表明了一种常见的生态原因，可能是低度炎症，这可能导致哺乳动物肠道微生物群组成的差异。此外，观察到的环境和遗传效应对小鼠微生物组研究的实验设计具有重要影响。
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. 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. 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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影响因子：
11
作者：
de Carcer, Daniel Aguirre;Cuiv, Paraic O.;Morrison, Mark
通讯作者：
Morrison, Mark
影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
4.8
作者：
BORCARD, D;LEGENDRE, P;DRAPEAU, P
通讯作者：
DRAPEAU, P
DOI：
10.1073/pnas.1002601107
发表时间：
2010-06-29
影响因子：
11.1
作者：
Dominguez-Bello, Maria G.;Costello, Elizabeth K.;Knight, Rob
通讯作者：
Knight, Rob
影响因子：
3.3
作者：
Albert, Eric J.;Sommerfeld, Katrin;Gophna, Uri
通讯作者：
Gophna, Uri