Understanding the microbiota of laboratory animals

The laboratory mouse is the primary animal model used to study mammalian biology.  There remains, however, a shocking paucity of knowledge about the microbes that are associated with lab mice. 

What we do know is that differences in lab mouse microbiota can have profound effects on phenotypes associated with behaviour, immunity, tumour development, and metabolism.  A poor understanding of mouse-associated microbes limits our abilty to understand how microbes affect animal physiology and is a major but often hidden source of variation between animal studies conducted in different labs.

We have worked to amass a large assembly of novel microbial species isolated from the intestines of laboratory mice.  We now collaborate extensively with Dana Philpott (UofT Immunology) and Emma Allen-Vercoe (U Guelph) and together we have isolated over 100 bacterial species, a large fraction of which have never before been studied.

We have extended our collaborative network to include the labs of KC Huang and Justin Sonnenburg at Stanford and their former post-doc, Carolina Tropini, who started her own lab at UBC. We also share strains openly with the miBC-2, a collection of mouse-derived microbes assembled by a team led by Dr. Thomas Clavel at U. Aachen in Germany.

PUBLICATIONS ON LAB ANIMAL MICROBIOTA

  • Afrizal A, Jennings SAV, Hitch TCA, Riedel T, Basic M, Panyot A, Treichel N, Hager FT, Wong EO, Wolter B, Viehof A, von Strempel A, Eberl C, Buhl EM, Abt B,Bleich A, Tolba R, Blank LM, Navarre WW, Kiessling F, Horz HP, Torow N, Cerovic V, Stecher B, Strowig T, Overmann J, and T. Clavel (2022) Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities. Cell Host Microbe. 30(11):1630-1645.e25. doi: 10.1016/j.chom.2022.09.011.
  • Wong EO, Brownlie EJE, Ng KM, Kathirgamanathan S, Yu FB, Merrill BD, Huang KC, Martin A, Tropini C, Navarre WW. (2022) The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut. mBio. 13(2):e0294921. doi: 10.1128/mbio.02949-21.
  • Brownlie EJE, Chaharlangi D, Wong EO, Kim D, Navarre WW. (2022) Acids produced by lactobacilli inhibit the growth of commensal Lachnospiraceae and S24-7 bacteria. Gut Microbes. 14(1):2046452. doi:10.1080/19490976.2022.2046452.
  • Hezaveh K, Shinde RS, Klötgen A, Halaby MJ, Lamorte S, Ciudad MT, Quevedo R, Neufeld L, Liu ZQ, Jin R, Grünwald BT, Foerster EG, Chaharlangi D, Guo M, Makhijani P, Zhang X, Pugh TJ, Pinto DM, Co IL, McGuigan AP, Jang GH, Khokha R, Ohashi PS, O’Kane GM, Gallinger S, Navarre WW, Maughan H, Philpott DJ, Brooks DG, McGaha TL. (2022) Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity. Immunity. 55(2):324-340.e8. doi:10.1016/j.immuni.2022.01.006.
  • Hersch SJ, Radan B, Ilyas B, Lavoie P, and WW Navarre. (2021) A stress-induced block in dicarboxylate uptake and utilization in Salmonella. J Bacteriol. 203(9):e00487-20. doi: 10.1128/JB.00487-20.
  • Fields FR, Li X, Navarre WW, Naito M. (2020) Complete Genome Sequence of Streptococcus salivarius DB-B5, a Novel Probiotic Candidate Isolated from the Supragingival Plaque of a Healthy Female Subject. Microbiol Resour Announc. 9(40):e00916-20. doi: 10.1128/MRA.00916-20.
  • Hersch SJ and W.W. Navarre. (2020) The Salmonella LysR Family Regulator RipR Activates the SPI-13-Encoded Itaconate Degradation Cluster. Infect Immun. 88(10):e00303-20. doi: 10.1128/IAI.00303-20.
  • Irrazabal T, Thakur BK, Kang M, Malaise Y, Streutker C, Wong EOY, Copeland J,Gryfe R, Guttman DS, Navarre WW, Martin A. (2020) Limiting oxidative DNA damage reducesmicrobe-induced colitis-associated colorectal cancer. Nat Commun. 11(1):1802. doi: 10.1038/s41467-020-15549-6. 
  • Saha, S., Martin, A., and W.W. Navarre. (2019) Meta-analysis Identifies Microbial Signatures of Disease in Murine Models of Inflammatory Bowel Disease.  BioRxiv (doi: https://doi.org/10.1101/515205) (submitted)
  • Belcheva, A., Irrazabal, T., Robertson, S.J., Streutker, C., Maughan, H., Rubino, S., Moriyama, E.H., Copeland, J.K., Kumar, S., Green, B., Geddes, K., Pezo, R.C., Navarre, W.W., Milosevic, M., Wilson, B.C., Girardin, S.E., Wolever, T.M., Edelmann, W., Guttman, D.S., Philpott, D.J. and A. Martin. (2014)  Gut microbial metabolism drives transformation of Msh2-deficient colon epithelial cells.Cell 158(2):288-99

Silencing of foreign genes by bacterial H-NS like proteins

How do new pathogens arise, seemingly from nowhere?  How do they adapt to the human host after evolving for millenia in non-host environments?

The genes necessary for pathogens to cause disease are often recently acquired from a foreign source via a process known as horizontal (or lateral) transfer.  Virulence and antibiotic resistance genes are often carried on phages, plasmids, and transposable elements.  These include genes found in pathogenic E. coli, Salmonella, Vibrio, Yersinia, Bacillus anthracis, and Staphylococcus. 

Often these foreign genes look different than the other genes in the genome and are more AT-rich than the other genes in the genome in a surprising majority of cases. We discovered the H-NS protein of Salmonella and E. coli, selectively silences the expression of AT-rich genes.  This includes about 15-20% of the genome including almost every gene involved in virulence.  Because of this H-NS is the master virulence regulator of the cell that also protects the cell from the detrimental consequences that could occur when newly acquired genes integrate into the resident genome.  H-NS silenced genes need to be expressed (counter-silenced) at specific times during infection and projects are underway to explore the different mechanisms by which counter-silencing can occur.  In collaboration with Dr. Jun Liu we have also explored the function of Lsr2, an H-NS like molecule from Mycobacteria, the causative agent of tuberculosis.

PUBLICATIONS ON BACTERIAL GENE SILENCING

  • Duan B, Ding P, Navarre WW, Liu J, Xia B. (2021) Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol. 38(10):4135-4148. doi:10.1093/molbev/msab136.
  • Rafiei N, Cordova M, Navarre WW, Milstein JN. (2019) Growth Phase-Dependent Chromosome Condensation and Heat-Stable Nucleoid-Structuring Protein Redistribution in Escherichia coli under Osmotic Stress. J Bacteriol. 201(23):e00469-19. doi: 10.1128/JB.00469-19.
  • Ali, S.S., Soo, J., Rao, C., Leung, A.S., Ngai, D.H-M., Ensminger, A.W., and W.W. Navarre. (2014) Silencing by H-NS potentiated the evolution of Salmonella.  PLoS Pathogens (in press)
  • Wang, H., Epstein, S., Ali, S.S., Navarre, W.W. and J. Milstein (2014) A biomechanical mechanism for initiating DNA packaging.  Nucleic Acids Research doi: 10.1093/nar/gku896
  • Ali, S.S., Whitney, J.C., Stevenson, J., Robinson, H., Howell, P.L., and W.W. Navarre (2013) Structural Insights into the Regulation of Foreign Genes in Salmonella by the Hha/H-NS Complex. Journal of Biological Chemistry 288(19):13356-13369.
  • Ali, S.S., Xia, B., Liu, J., and W. W. Navarre (2012) Silencing of foreign DNA in bacteria. Current Opinion in Microbiology 15(2):175-181
  • Ali, S.S., Beckett, E., Bae, S.J., and W.W. Navarre (2011) The 5.5 protein of phage T7 inhibits H-NS through interactions with the central oligomerization domain. Journal of Bacteriology, 193(18):4881-4892
  • Gordon, B.R., Li, Y., Cote, A., Weirauch, M., Ding, P., Hughes, T., Navarre, W.W., Xia, B. and J. Liu (2011) Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.  Proc. Natl. Acad. Sci. USA. 108(26):10690-10695

Protein Translation in Control of Virulence Gene Expression

Navarre NIH lambda
art by Herve Roy

During a screen for Salmonella mutants that are unable to cause disease in mice we discovered that deletion of two closely linked genes, poxA and yjeK, led to a severe defect in Salmonella virulence. The protein encoded by the poxA gene is related to the lysyl-tRNA synthetase family of enzymes (i.e. the enzymes that charge tRNAs with the amino acid lysine).  YjeK encodes an enzyme that converts lysine to an unusual molecule called beta-lysine.  We have determined that PoxA and YjeK act in a common pathway to modify another protein called EF-P (elongation factor P).  The addition of beta-lysine to EF-P by PoxA and YjeK represents an entirely new mechanism of post-translational modification.

In the absence of the PoxA, YjeK, or EF-P, Salmonella cells are susceptible to a number of different forms of cellular stress.  Notably these mutant cells display increased sensitivity to several classes of antibiotics.  They also display unusual metabolic hyperactivity.  This pathway could be a novel target for new antimicrobial compounds.

PUBLICATIONS ON EF-P

  • Hersch, S.J., Elgamal, S., Katz, A., Ibba, M., and W.W. Navarre (2014) Translation Initiation Rate Determines the Impact of Ribosome Stalling on Bacterial Protein Synthesis. Journal of Biological Chemistry 289(41):28160-28171
  • Elgamal, S., Katz, A., Hersch, S.J., Newsom, D., White, P., Navarre, W.W. and M. Ibba (2014) EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genetics 10(8):e1004553. doi:10.1371/journal.pgen.1004553
  • Katz, A., Solden, L., Zou, S.B., Navarre W.W., and M. Ibba (2014) Molecular evolution of protein-RNA mimicry as a mechanism for translational control. Nucleic Acids Research 42(5):3261-3271.
  • Hersch, S.J., Wang, M., Zou, S.B., Moon, K-M., Foster, L.J., Ibba, M., and W.W. Navarre (2013) Divergent protein motifs direct EF-P mediated translational regulation in Salmonella and E. coli.  mBio 4(2) e00180-13.  doi: 10.1128/mBio.00180-13.
  • Zou, S.B., Hersch, S.J., Roy, H., Wiggers, J.B., Leung, A.L., Buranyi, S.G., Xie, J.L., Dare, K., Ibba, M., and W.W. Navarre (2012) Loss of elongation factor P disrupts bacterial outer membrane integrity. Journal of Bacteriology 194(2):413-425    * Note: Authors correction in Journal of Bacteriology (2012), 194(16):4484.
  • Roy, H., Zou S.B., Bullwinkle, T.B., Wolfe, B.S., Gilreath, M.S., Forsyth, C.J., Navarre, W.W., and M. Ibba  (2011) The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine. Nature Chemical Biology, 7(10):667-669