Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design.
Targeted manipulation of the gut flora is increasingly being recognized as a means to improve human health. Yet, the temporal dynamics and intra- and interindividual heterogeneity of the microbiome represent experimental limitations, especially in human cross-sectional studies. Therefore, rodent models represent an invaluable tool to study the host-microbiota interface. Progress in technical and computational tools to investigate the composition and function of the microbiome has opened a new era of research and we gradually begin to understand the parameters that influence variation of host-associated microbial communities. To isolate true effects from confounding factors, it is essential to include such parameters in model intervention studies. Also, explicit journal instructions to include essential information on animal experiments are mandatory. The purpose of this review is to summarize the factors that influence microbiota composition in mice and to provide guidelines to improve the reproducibility of animal experiments.
Department of Gastroenterology, Ghent University, B-9000 Ghent, Belgium.
Debby
D
Laukens
Inflammation Research Center, VIB, B-9052 Ghent, Belgium Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium.
Brigitta M
BM
Brinkman
Center for the Biology of Disease, VIB, B-3000 Leuven, Belgium Department Microbiology and Immunology, KU Leuven, B-3000 Leuven, Belgium.
Jeroen
J
Raes
Department of Gastroenterology, Ghent University, B-9000 Ghent, Belgium.
Martine
M
De Vos
Inflammation Research Center, VIB, B-9052 Ghent, Belgium Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium Methusalem Program, Ghent University, B-9000 Ghent, Belgium Peter.Vandenabeele@irc.vib-ugent.be.
Peter
P
Vandenabeele
D000818:Animals; D000069196:Gastrointestinal Microbiome / Q000502:physiology*; D006801:Humans; D023421:Models, Animal; D012107:Research Design / Q000592:standards*
animal facility; animal models; confounding factors; microbiome; microbiota