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Effects of water decontamination methods and bedding material on the gut microbiota

Author

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  • Willie A Bidot
  • Aaron C Ericsson
  • Craig L Franklin

Abstract

Rodent models are invaluable to understanding health and disease in many areas of biomedical research. Unfortunately, many models suffer from lack of phenotype reproducibility. Our laboratory has shown that differences in gut microbiota (GM) can modulate phenotypes of models of colon cancer and inflammatory bowel disease. We and others have also shown that a number of factors associated with rodent research, including vendor, cage system, and bedding can alter GM. The objective of this study was to expand these studies to examine the effect of additional bedding materials and methods of water decontamination on GM diversity and composition. To this end, Crl:CD1 (ICR) mice were housed on corn cob or compressed paper chip bedding and provided water that was decontaminated by four different methods: autoclaving with reverse osmosis, autoclaving with hydrochloric acid, autoclaving with sulfuric acid, and autoclaving alone. Feces was collected at day 0, and at day 28 (endpoint), fecal and cecal samples were collected. DNA was extracted from samples, amplified by PCR using conserved bacterial primer sets and subjected to next generation sequencing. Sequence data were analyzed using Qiime and groups were compared using principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA). Two factor PERMANOVA of cecal GM data revealed significant changes when comparing bedding and water decontamination methods, while no significant effects were noted in the fecal GM data. Subsequent PERMANOVA and PCoA of cecal data revealed that several combinations of bedding and water decontamination methods resulted in differing GM, highlighting the complexity by which environmental factors interact to modulate GM.

Suggested Citation

  • Willie A Bidot & Aaron C Ericsson & Craig L Franklin, 2018. "Effects of water decontamination methods and bedding material on the gut microbiota," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-16, October.
  • Handle: RePEc:plo:pone00:0198305
    DOI: 10.1371/journal.pone.0198305
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    References listed on IDEAS

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    1. Aaron C Ericsson & J Wade Davis & William Spollen & Nathan Bivens & Scott Givan & Catherine E Hagan & Mark McIntosh & Craig L Franklin, 2015. "Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-19, February.
    2. Melissa K Friswell & Helen Gika & Ian J Stratford & Georgios Theodoridis & Brian Telfer & Ian D Wilson & Andrew J McBain, 2010. "Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice," PLOS ONE, Public Library of Science, vol. 5(1), pages 1-9, January.
    3. Carol Kilkenny & William J Browne & Innes C Cuthill & Michael Emerson & Douglas G Altman, 2010. "Improving Bioscience Research Reporting: The ARRIVE Guidelines for Reporting Animal Research," PLOS Biology, Public Library of Science, vol. 8(6), pages 1-5, June.
    4. Francis S. Collins & Lawrence A. Tabak, 2014. "Policy: NIH plans to enhance reproducibility," Nature, Nature, vol. 505(7485), pages 612-613, January.
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