Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance

Abt, 2012, Commensal bacteria calibrate the activation threshold of innate antiviral immunity, Immunity, 37, 158, 10.1016/j.immuni.2012.04.011 Ackerman, 2017, The mycobiome of the human urinary tract: potential roles for fungi in urology, Ann. Transl. Med., 5, 31, 10.21037/atm.2016.12.69 Beck, 2000, Genealogies of mouse inbred strains, Nat. Genet., 24, 23, 10.1038/71641 Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J.R. Stat. Soc. Series B, 57, 289 Benson, 2013, GenBank, Nucleic Acids Res., 41, D36, 10.1093/nar/gks1195 Beura, 2016, Normalizing the environment recapitulates adult human immune traits in laboratory mice, Nature, 532, 512, 10.1038/nature17655 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Buffington, 2016, Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring, Cell, 165, 1762, 10.1016/j.cell.2016.06.001 Callahan, 2016, DADA2: High-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581, 10.1038/nmeth.3869 Caporaso, 2011, Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc. Natl. Acad. Sci. USA, 108, 4516, 10.1073/pnas.1000080107 Caporaso, 2012, Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J., 6, 1621, 10.1038/ismej.2012.8 Chou, 1998, A population study of house mice (Mus musculus castaneus) inhabiting rice granaries in Taiwan, Zool. Stud., 37, 201 Chudnovskiy, 2016, Host-protozoan interactions protect from mucosal infections through activation of the inflammasome, Cell, 167, 444, 10.1016/j.cell.2016.08.076 De Cáceres, 2009, Associations between species and groups of sites: indices and statistical inference, Ecology, 90, 3566, 10.1890/08-1823.1 Dethlefsen, 2007, An ecological and evolutionary perspective on human-microbe mutualism and disease, Nature, 449, 811, 10.1038/nature06245 Didion, 2016, R2d2 Drives Selfish Sweeps in the House Mouse, Mol. Biol. Evol., 33, 1381, 10.1093/molbev/msw036 Dowle, M., and Srinivasan, A. (2016). Data.table: extension of ‘data.frame’. R package version 1.10.0 (https://cran.r-project.org/web/packages/data.table/index.html). Dufrene, 1997, Species assemblages and indicator species: the need for a flexible asymetrical approach, Ecol. Monogr., 67, 345 Dwass, 1957, Modified randomization tests for nonparametric hypotheses, Ann. Math. Stat., 28, 181, 10.1214/aoms/1177707045 Edgar, 2013, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods, 10, 996, 10.1038/nmeth.2604 Gensollen, 2016, How colonization by microbiota in early life shapes the immune system, Science, 352, 539, 10.1126/science.aad9378 Gomez, 2008, A population study of house mice (Mus musculus) inhabiting different habitats in an Argentine urban area, Int. Biodet. Biodeg., 62, 270, 10.1016/j.ibiod.2007.08.004 Gomez de Agüero, 2016, The maternal microbiota drives early postnatal innate immune development, Science, 351, 1296, 10.1126/science.aad2571 Howitt, 2016, Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut, Science, 351, 1329, 10.1126/science.aaf1648 2012, A framework for human microbiome research, Nature, 486, 215, 10.1038/nature11209 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234 Ichinohe, 2011, Microbiota regulates immune defense against respiratory tract influenza A virus infection, Proc. Natl. Acad. Sci. USA, 108, 5354, 10.1073/pnas.1019378108 Kash, 2006, Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus, Nature, 443, 578, 10.1038/nature05181 Klein, 2012, Mechanisms of sex disparities in influenza pathogenesis, J. Leukoc. Biol., 92, 67, 10.1189/jlb.0811427 Kobasa, 2007, Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus, Nature, 445, 319, 10.1038/nature05495 Kolde, R. (2015). pheatmap: Pretty Heatmaps. R package version 1.0.8. Kruskal, 1952, Use of ranks in one-criterion variance analysis, J Am Stat Assoc., 47, 583, 10.1080/01621459.1952.10483441 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Lasry, 2016, Inflammatory networks underlying colorectal cancer, Nat. Immunol., 17, 230, 10.1038/ni.3384 Ley, 2008, Worlds within worlds: evolution of the vertebrate gut microbiota, Nat. Rev. Microbiol., 6, 776, 10.1038/nrmicro1978 Li, 2015, MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, 31, 1674, 10.1093/bioinformatics/btv033 Lim, 2016, The bacterial microbiome and virome milestones of infant development, Trends Microbiol., 24, 801, 10.1016/j.tim.2016.06.001 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 Manichaikul, 2010, Robust relationship inference in genome-wide association studies, Bioinformatics, 26, 2867, 10.1093/bioinformatics/btq559 Mann, 1947, On a test of whether one of two random variables is stochastically larger than the other, Ann. Math. Stat., 18, 50, 10.1214/aoms/1177730491 Marshall, 1981, Taxonomy, 17 McFall-Ngai, 2007, Adaptive immunity: care for the community, Nature, 445, 153, 10.1038/445153a McMurdie, 2013, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS ONE, 8, e61217, 10.1371/journal.pone.0061217 Morgan, 2015, argyle: an R Package for analysis of illumina genotyping arrays, G3 (Bethesda), 6, 281, 10.1534/g3.115.023739 Morgan, 2016, The mouse universal genotyping array: from substrains to subspecies, G3 (Bethesda), 6, 263, 10.1534/g3.115.022087 Neuwirth, E. (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1-2 (http://colorbrewer2.org). Nishioka, 1995, The origin of common laboratory mice, Genome, 38, 1, 10.1139/g95-001 Norman, 2014, Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities, Gastroenterology, 146, 1459, 10.1053/j.gastro.2014.02.001 Oh, 2014, TLR5-mediated sensing of gut microbiota is necessary for antibody responses to seasonal influenza vaccination, Immunity, 41, 478, 10.1016/j.immuni.2014.08.009 Oksanen, J. (2017). vegan: Community Ecology Package. R package version 2.4-2. Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O’Hara, R.B., Simpson, G.L., Solymos, P., et al. (2016). vegan: community ecology package. R package version 2.4-1. (https://cran.r-project.org/web/packages/vegan/index.html). Paradis, 2004, APE: analyses of phylogenetics and evolution in R language, Bioinformatics, 20, 289, 10.1093/bioinformatics/btg412 Paulson, J.N., Talukder, H., Pop, M., and Bravo, H.C. (2017). MetagenomeSeq: Statistical analysis for sparse high-throughput sequencing. Bioconductor package version 1.18.0 (Bioconductor). Peter, 2016, Admixture, population structure, and F-statistics, Genetics, 202, 1485, 10.1534/genetics.115.183913 Pfeiffer, 2016, Viral immunity. Transkingdom control of viral infection and immunity in the mammalian intestine, Science, 351, aad5872, 10.1126/science.aad5872 Phifer-Rixey, 2015, Insights into mammalian biology from the wild house mouse Mus musculus, eLife, 4, 10.7554/eLife.05959 Pickrell, 2012, Inference of population splits and mixtures from genome-wide allele frequency data, PLoS Genet., 8, e1002967, 10.1371/journal.pgen.1002967 Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res., 41, D590, 10.1093/nar/gks1219 2014 Reese, 2016, Sequential infection with common pathogens promotes human-like immune gene expression and altered vaccine response, Cell Host Microbe, 19, 713, 10.1016/j.chom.2016.04.003 Seedorf, 2014, Bacteria from diverse habitats colonize and compete in the mouse gut, Cell, 159, 253, 10.1016/j.cell.2014.09.008 Smith, 1993, A serologic survey for viruses and Mycoplasma pulmonis among wild house mice (Mus domesticus) in southeastern Australia, J. Wildl. Dis., 29, 219, 10.7589/0090-3558-29.2.219 Sommer, 2013, The gut microbiota--masters of host development and physiology, Nat. Rev. Microbiol., 11, 227, 10.1038/nrmicro2974 Stappenbeck, 2016, Accounting for reciprocal host-microbiome interactions in experimental science, Nature, 534, 191, 10.1038/nature18285 Tanaka, 2003, A novel inflammation-related mouse colon carcinogenesis model induced by azoxymethane and dextran sodium sulfate, Cancer Sci., 94, 965, 10.1111/j.1349-7006.2003.tb01386.x Taubenberger, 2008, The pathology of influenza virus infections, Annu. Rev. Pathol., 3, 499, 10.1146/annurev.pathmechdis.3.121806.154316 Tisoncik, 2012, Into the eye of the cytokine storm, Microbiol. Mol. Biol. Rev., 76, 16, 10.1128/MMBR.05015-11 Torre, 2015, Global cancer statistics, 2012, CA Cancer J. Clin., 65, 87, 10.3322/caac.21262 Viladomiu, 2017, IgA-coated E. coli enriched in Crohn’s disease spondyloarthritis promote TH17-dependent inflammation, Sci. Transl. Med., 9, eaaf9655, 10.1126/scitranslmed.aaf9655 Wickham, 2007, Reshaping data with the reshape package, J. Stat. Softw., 21, 1 Wickham, 2009 Wilke, C.O. (2016). cowplot: streamlined plot theme and plot annotation for ‘ggplot2’. R package version 0.6.2. (https://cran.r-project.org/web/packages/cowplot/index.html). Wood, 2014, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biol., 15, R46, 10.1186/gb-2014-15-3-r46 Yang, 2011, Subspecific origin and haplotype diversity in the laboratory mouse, Nat. Genet., 43, 648, 10.1038/ng.847 Yewdell, 1981, Expression of influenza A virus internal antigens on the surface of infected P815 cells, J. Immunol., 126, 1814, 10.4049/jimmunol.126.5.1814 Zackular, 2013, The gut microbiome modulates colon tumorigenesis, MBio, 4, 10.1128/mBio.00692-13 Zackular, 2016, Manipulation of the gut microbiota reveals role in colon tumorigenesis, mSphere, 1, 10.1128/mSphere.00001-15 Zinkernagel, 1974, Immunological surveillance against altered self components by sensitised T lymphocytes in lymphocytic choriomeningitis, Nature, 251, 547, 10.1038/251547a0 Zinkernagel, 1974, Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system, Nature, 248, 701, 10.1038/248701a0