Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design

FEMS Microbiology Reviews
Debby LaukensPeter Vandenabeele

Abstract

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.

References

May 1, 1993·Immunology Today·P PozzilliP E Beales
Jul 31, 1999·Applied and Environmental Microbiology·F E DewhirstJ G Fox
Sep 29, 1999·Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology·J C MeslinC Andrieux
Nov 4, 2000·Nature Genetics·H Würbel
Aug 31, 2001·ILAR Journal·Robert O. Jacoby, J. Russell Lindsey
Oct 19, 2001·Proceedings of the National Academy of Sciences of the United States of America·B SiegmundC A Dinarello
Jan 5, 2002·Experimental Animals·S KitajimaY Ikeda
Oct 9, 2002·The Journal of Nutrition·Russell L CowlesTimothy P Carr
Nov 15, 2002·Proceedings of the National Academy of Sciences of the United States of America·Thaddeus S StappenbeckJeffrey I Gordon
Jun 1, 1962·The Journal of Experimental Medicine·R W SCHAEDLER, R J DUBOS
Oct 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fredrik BäckhedJeffrey I Gordon
Mar 26, 2005·Science·Fredrik BäckhedJeffrey I Gordon
Jul 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ruth E LeyJeffrey I Gordon
Nov 9, 2006·Mammalian Genome : Official Journal of the International Mammalian Genome Society·A Deloris AlexanderDavid W Threadgill
Jan 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Fredrik BäckhedJeffrey I Gordon
Mar 3, 2007·Pediatrics·Pablo F PerezAnne Donnet-Hughes
Jul 20, 2007·The Proceedings of the Nutrition Society·Lars A Hanson
Aug 11, 2007·Arteriosclerosis, Thrombosis, and Vascular Biology·Aldons J LusisSusanna S Wang
Oct 24, 2007·Annual Review of Immunology·S M VidalP Gros
Feb 19, 2008·Research in Microbiology·Esther JiménezJuan M Rodríguez
Apr 1, 2008·International Immunology·Yasuyo ShimomuraAtul K Bhan
Jul 1, 2008·Nature Reviews. Microbiology·Jeroen Raes, Peer Bork
Aug 22, 2008·The Journal of Nutrition·Lorenzo Morelli
Nov 19, 2008·Laboratory Animals·Kathleen R Pritchett-CorningCharles B Clifford
Apr 4, 2009·Nature Reviews. Immunology·June L Round, Sarkis K Mazmanian
Oct 20, 2009·Cell·Ivaylo I IvanovDan R Littman
Oct 21, 2009·The Journal of Immunology : Official Journal of the American Association of Immunologists·Javier Ochoa-RepárazLloyd H Kasper
Oct 30, 2009·Nucleic Acids Research·Victor M MarkowitzNikos C Kyrpides
Jan 31, 1963·The Journal of Experimental Medicine·R DubosR L Costello
Nov 6, 2009·Neonatology·Randal K BuddingtonMartin J Kullen
Mar 3, 2010·Annual Review of Immunology·David A Hill, David Artis
Mar 6, 2010·Science·Matam Vijay-KumarAndrew T Gewirtz

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Citations

Apr 8, 2016·International Journal of Medical Microbiology : IJMM·Philipp RauschJohn F Baines
Apr 12, 2016·Gastroenterology·M Bishr OmaryJerrold R Turner
May 21, 2016·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·M Bishr OmaryJerrold R Turner
May 28, 2016·Nature Reviews. Immunology·Michelle G Rooks, Wendy S Garrett
Jul 16, 2016·The Journal of Physiology·Aafke W F Janssen, Sander Kersten
Sep 30, 2016·Frontiers in Microbiology·Kim L HoangNicole M Gerardo
Oct 9, 2016·International Journal of Antimicrobial Agents·Kirsty BrownG Douglas Inglis
Mar 1, 2017·Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research·Jason D GussChristopher J Hernandez
Jun 2, 2017·Nature Protocols·Stefan WirtzMarkus F Neurath
Mar 6, 2016·Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism·Katarzyna WinekUlrich Dirnagl
Jun 18, 2017·Current Osteoporosis Reports·Jing Yan, Julia F Charles
Dec 15, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Kazuhiko MatsuoOsamu Yoshie
Feb 8, 2018·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Debby Bogaert, Alex van Belkum
Sep 7, 2017·American Journal of Physiology. Endocrinology and Metabolism·Matthias Van HulPatrice D Cani
Aug 30, 2017·Cold Spring Harbor Perspectives in Medicine·Roberto Pacifici
Oct 12, 2017·Calcified Tissue International·Emory Hsu, Roberto Pacifici
Jan 20, 2018·American Journal of Physiology. Endocrinology and Metabolism·Micah L BattsonChristopher L Gentile
Feb 13, 2018·Frontiers in Systems Neuroscience·Isabella M Fuentes, Julie A Christianson
Dec 12, 2017·FEMS Microbiology Reviews·Philippe J Sansonetti
Jun 8, 2018·Cardiovascular Research·Jessica M JohnstonEndre Kiss-Toth
Aug 3, 2016·Disease Models & Mechanisms·Paul N SchofieldJohn P Sundberg
Jun 30, 2018·Laboratory Animals·Romain-Daniel Gosselin
Aug 14, 2018·Beneficial Microbes·P Perez-PardoA D Kraneveld
Oct 27, 2018·Journal of Applied Microbiology·G Larivière-GauthierP Fravalo
Jan 18, 2018·Neurotherapeutics : the Journal of the American Society for Experimental NeuroTherapeutics·Laura M Cox, Howard L Weiner
Oct 20, 2018·Radiation Research·Joy GarrettJoseph R Dynlacht
Mar 2, 2018·Scientific Reports·Alexander Rodriguez-PalaciosFabio Cominelli
Sep 13, 2017·Nature Biotechnology·Christopher QuinceNicola Segata
Jan 24, 2018·Inflammatory Bowel Diseases·Cynthia Reinoso WebbMatthew B Grisham
Apr 4, 2017·Current Protocols in Immunology·Kathy D McCoyFrancesca Ronchi
Aug 3, 2019·The Journal of Pathology·Raquel Toribio-FernándezJose M Gonzalez-Granado

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Methods Mentioned

BETA
PCR
transgenic
cesarian section

Software Mentioned

ARRIVE
- It
PaMuFind
Me

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