42. Suzuki K, et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc Natl Acad Sci USA.2004;101:1981-1986.[ PubMed:14766966 43. Barroso-Batista J, Demengeot J, Gordo I. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nat Commun. 2015: 6: 8945. [ PubMed 26615893] 44. Mirpuri J, et al. Proteobacteria-specific Ig A regulates maturation of the intestinal microbiota. Gut Microbes.2014;5:28-39.[ PubMed:24637807] 45. Singh K, Chang C, Gershwin ME. Iga deficiency and autoimmunity. Autoimmun Rev 2014 13:163-177.[ PubMed:24157629 46. Palm NW, et al. Immunoglobulin a coating identifies colitogenic bacteria in inflammatory bowel disease.cel2014;158:1000-1010.[ PubMed:2517l403] 47. Kau AL, et al. Functional characterization of lg A targeted bacterial taxa from undernourished malawian children that produce diet-dependent enteropathy. Science Translational Medicine 2015:7:276ra24-276ra24 48. McLoughlin K, Schluter 3, Rakoff-Nahoum S, Smith AL, Foster KR Host Selection of Microbiota ia Differential Adhesion Cell Host Microbe 2016: 19: 550-559.[PubMed: 27053168 49. Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol. 2005; 152: 36-51. [PubMed: 16182563] 50 Kremer JR, Mastronarde dN, Mclntosh JR Computer visualization of three-dimensional imag data using IMOD, J Struct Biol. 1996, 116: 71-76. [ PubMed: 8742726] 51. Mastronarde DN. Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOd package. J Microsc. 2008, 230: 212-217. [PubMed: 184451491 52. McClure R, et al. Computational analysis of bacterial rNA-Seq data. Nucleic Acids Res 2013 4l:e140.[ PubMed:23716638] 53 Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013: 29: 15-21 [ PubMed:23104886] 54. Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015: 31: 166-169.[PubMed: 25260700 55. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010: 26: 139-140. [PubMed 19910308] 56. Caporaso JG, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms ISME J 2012: 6: 1621-1624 [PubMed: 22402401] 57. Thompson LR, et al. A communal catalogue reveals Earths multiscale microbial diversity. Nature 017;551:457-463.[ PubMed:29088705 58. Amir A, et al. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns mSystems. 2017; 2doi: 10. 1 128/mSystems.00191-16 59. De Santis TZ, et al. Greengenes, a chimera-checked 16S rRNa gene database and workbench compatible with ARB. Applied and Environmental Microbiology. 2006; 72: 5069-5072[PubMed 16820507] 60. Mirarab S, Nguyen N, Warnow T. SEPP: SATe-enabled phylogenetic placement. Pac Symp Biocomput2012:247-258.[ PubMed:22174280 61. Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker gene surveys. Nat Methods. 2013: 10: 1200-1202 [PubMed: 24076764] 62. Love Ml, Huber w, Anders s. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biol. 2014: 15:550. [PubMed 25516281 64. Lozupone C, Knight R UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology. 2005, 71: 8228-8235 [PubMed 16332807 65. Anderson M. A new method for non-parametric multivariate analysis of variance. Austral Ecology.2001;26:32-46 cience. Author manuscript; available in PMC 2018 November 1842. Suzuki K, et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc Natl Acad Sci USA. 2004; 101:1981–1986. [PubMed: 14766966] 43. Barroso-Batista J, Demengeot J, Gordo I. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nat Commun. 2015; 6:8945. [PubMed: 26615893] 44. Mirpuri J, et al. Proteobacteria-specific IgA regulates maturation of the intestinal microbiota. Gut Microbes. 2014; 5:28–39. [PubMed: 24637807] 45. Singh K, Chang C, Gershwin ME. IgA deficiency and autoimmunity. Autoimmun Rev. 2014; 13:163–177. [PubMed: 24157629] 46. Palm NW, et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell. 2014; 158:1000–1010. [PubMed: 25171403] 47. Kau AL, et al. Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Science Translational Medicine. 2015; 7:276ra24–276ra24. 48. McLoughlin K, Schluter J, Rakoff-Nahoum S, Smith AL, Foster KR. Host Selection of Microbiota via Differential Adhesion. Cell Host Microbe. 2016; 19:550–559. [PubMed: 27053168] 49. Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol. 2005; 152:36–51. [PubMed: 16182563] 50. Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J Struct Biol. 1996; 116:71–76. [PubMed: 8742726] 51. Mastronarde DN. Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package. J Microsc. 2008; 230:212–217. [PubMed: 18445149] 52. McClure R, et al. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res. 2013; 41:e140. [PubMed: 23716638] 53. Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29:15–21. [PubMed: 23104886] 54. Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31:166–169. [PubMed: 25260700] 55. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26:139–140. [PubMed: 19910308] 56. Caporaso JG, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012; 6:1621–1624. [PubMed: 22402401] 57. Thompson LR, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017; 551:457–463. [PubMed: 29088705] 58. Amir A, et al. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems. 2017; 2doi: 10.1128/mSystems.00191-16 59. DeSantis TZ, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology. 2006; 72:5069–5072. [PubMed: 16820507] 60. Mirarab S, Nguyen N, Warnow T. SEPP: SATé-enabled phylogenetic placement. Pac Symp Biocomput. 2012:247–258. [PubMed: 22174280] 61. Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker￾gene surveys. Nat Methods. 2013; 10:1200–1202. [PubMed: 24076764] 62. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15:550. [PubMed: 25516281] 63. R. C. Team. R: A language and environment for statistical computing. 2013 64. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology. 2005; 71:8228–8235. [PubMed: 16332807] 65. Anderson MJ. A new method for non−parametric multivariate analysis of variance. Austral Ecology. 2001; 26:32–46. Donaldson et al. Page 8 Science. Author manuscript; available in PMC 2018 November 18. Author Manuscript Author Manuscript Author Manuscript Author Manuscript