Factors Affecting the Composition of the Laboratory Mouse Microbiome. Aaron C. Ericsson, DVM, PhD HESI Microbiome Workshop June 26, 2018

Transcription

1 Factors Affecting the Composition of the Laboratory Mouse Microbiome Aaron C. Ericsson, DVM, PhD HESI Microbiome Workshop June 26, 2018

2 The Microbiome Resident microbial communities Bacteria/archaea Viruses/phages Fungi Eukaryotes? Changes in composition associated with myriad conditions Animal models allow: Defined time course Controlled genetics and environment

3 The Rodent Microbiome Number of GM taxa shared between humans and mice at the level of phylum (A) and genus (B) Krych et al. (2013) PLoS One 8(5): e62578 See also Ley et al. (2005) PNAS 102 (31): 11070

4 Factors affecting the Gut Microbiota Ericsson and Franklin (2017) Lab Animal, 46(4):

5 Before you even start the study Barrier or conventional? Facility? Isolator? Temperature control? Food source? Rederivation? Quarantine? Husbandry? Animal Supplier Shipping Your Institution

6 Supplier specific Microbiota PC2 15.9% variation CD1 GMJAX CD1 GMTAC CD1 GMCRL CD1 GMHSD Observed OTUs Shannon Index a,b,c a,b,c a,d a,d b,e b,d c,d,e c 2.5 PC1 30.9% variation Hart et al. (2018) Scientific Reports (in press)

7 Supplier specific Microbiota GMJAX GMTAC GMCRL GMHSD Hart et al. (2018) Scientific Reports (in press)

8 Segmented Filamentous Bacteria See also Fahey et al. (2017) Comp Med 67: Ericsson et al. (2014) Comp Med 64:

9 What about the mycobiome and virome? Ordination based on fecal mycobiome, Colors represent mouse suppliers

10 Differences during development Cecal contents Feces Family Pasteurellaceae Aggregatibacter segnis Family Enterobacteriaceae Streptococcus spp. Lactobacillus spp.

11 Equilibration post shipping d7 (blue) and d30 (green) C57BL/6J BALB/cJ PC % variation d5 d2 Arrival Pre ship PC % variation d7 (blue) and d30 (green) d5 d2 Pre ship and arrival PC % variation PC % variation GM equilibrates at 1 to 2 weeks post shipping Montonye et al. (2018) Frontiers Microbiol 9:1085.

12 Quarantine has minimal effect C57BL/6J C57BL/6NHsd Korte et al. (2018) J Am Assn Lab Anim Sci 57(3):229.

13 Quarantine has minimal effect Mean (± SEM) Jaccard and Bray Curtis similarity indices from pre to post treatment (FBZ = fenbendazole, CY = cydectin) No significant differences associated with quarantine procedures Korte et al. (2018) J Am Assn Lab Anim Sci 57(3):229.

14 Bedding and caging affect cecal microbiota Ericsson et al. (2018) Scientific Reports 8:4065

15 IVC/aspen IVC/paper Static/aspen Static/paper Rodent Husbandry and the Cecal Microbiota Ericsson et al. (2018) Scientific Reports 8:4065

16 Bedding and H 2 O treatment matter Environmental factors (e.g., caging, bedding, water treatment) can significantly affect GM Factors can have synergistic effects Factors can have upstream effects that are muted in fecal communities Bidot et al. (manuscript under review)

17 Common antibiotic treatments Topical triple antibiotic (TAB) and oral enrofloxacin have long lasting effects on GM

18 The Inconvenient Truth about Rederivation Embryo transfer Normal delivery Mutant Mouse Surrogate Dam Rederived Mutant Every time a strain is rederived, a new GM is likely introduced

19 Influence of Genotype on GM Composition B6 IL 10 / C3H/HeJ IL 10 / OTU relative abundance GMCRL GMJAX GMTAC GMCRL GMJAX GMTAC Hart et al. (2017) Frontiers in Microbiol 8: 792.

20 Complex Microbiota Targeted Rederivation Embryo transfer Surrogate Dam 1 Rederived Mutant Mutant Mouse Surrogate Dam 2 Rederived Mutant

21 Controlling for Maternal Factors CD1 CD1 CD1 GMCRL CD1 GMJAX CD1 GMTAC Outbred CD1 colonies with four stable profiles now in 20 th generation

22 IL 10 / on C57BL/6J Background OTU relative abundance GMCRL GMJAX GMTAC Colonic lesion score Cecal lesion score GMCRL GMJAX GMTAC GMCRL GMJAX GMTAC Hart et al. (2017) Frontiers in Microbiol 8: 792.

23 IL 10 / on C3H/HeJ Background OTU relative abundance GMCRL GMJAX GMTAC Colonic lesion score Cecal lesion score GMCRL GMJAX GMTAC GMCRL GMJAX GMTAC Hart et al. (2017) Frontiers in Microbiol 8: 792.

24 Cross fostering/co housing

25 Fecal Microbiota Transfer (FMT) B6J pre FMT B6Hsd pre FMT B6Hsd donors B6J donors B6J 1w post FMT B6Hsd 1w post FMT B6J 2w post FMT B6Hsd 2w post FMT PC % variation B6J 4w post FMT PC % variation B6Hsd 4w post FMT PC % variation PC % variation Ericsson et al. (2017) Frontiers in Microbiol 8: 196. See also Lundberg et al. (2016) Gut Microbes 7:

26 Manipulating the GM Ericsson and Franklin (2015) ILAR Journal 56(2):

27 How normal is normal? Domestication Pathogens common Gnotobiotic rederivation Reduction in bacterial pathogens Improved diagnostics Reduction in viral pathogens Overall pathogen exposure Microbial diversity? Adapted from Weisbroth et al. (1996) Lab Anim 25:

28 Recommendations Bank fecal samples annually or before anticipated changes Collect baseline study samples to build subject into analysis Consider the experimental unit animal or cage? Use littermate controls when possible Use both sexes when possible Repeat studies in 2 nd generation Follow the ARRIVE guidelines

29 Acknowledgements NIH 2U42 OD NIH P40 OD Christine Wylie (WashU) MU DNA Core MU Informatics Research Core MU Comparative Medicine Program

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