title: Quantitative Imaging of Gut Microbiota Spatial Organization.
abstract: Genomic technologies have significantly advanced our understanding of the composition and diversity of host-associated microbial populations. However, their spatial organization and functional interactions relative to the host have been more challenging to study. Here we present a pipeline for the assessment of intestinal microbiota localization within immunofluorescence images of fixed gut cross-sections that includes a flexible software package, BacSpace, for high-throughput quantification of microbial organization. Applying this pipeline to gnotobiotic and human microbiota-colonized mice, we demonstrate that elimination of microbiota-accessible carbohydrates (MACs) from the diet results in thinner mucus in the distal colon, increased proximity of microbes to the epithelium, and heightened expression of the inflammatory marker REG3β. Measurements of microbe-microbe proximity reveal that a MAC-deficient diet alters monophyletic spatial clustering. Furthermore, we quantify the invasion of Helicobacter pylori into the glands of the mouse stomach relative to host mitotic progenitor cells, illustrating the generalizability of this approach.
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Kristen A
authors.initials: KA
authors.lastname: Earle
authors.affiliation: Department of Physics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Billings
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Sigal
authors.affiliation: Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Lichtman
authors.affiliation: Department of Medical Biochemistry, University of Gothenburg, 40530 Gothenburg, Sweden.
authors.forename: Gunnar C
authors.initials: GC
authors.lastname: Hansson
authors.affiliation: Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Joshua E
authors.initials: JE
authors.lastname: Elias
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Manuel R
authors.initials: MR
authors.lastname: Amieva
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: kchuang@stanford.edu.
authors.forename: Kerwyn Casey
authors.initials: KC
authors.lastname: Huang
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: jsonnenburg@stanford.edu.
authors.forename: Justin L
authors.initials: JL
authors.lastname: Sonnenburg
mesh_terms: D000818:Animals; D001431:Bacteriological Techniques / Q000379:methods*; D050260:Carbohydrate Metabolism; D004032:Diet / Q000379:methods; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D016480:Helicobacter pylori / Q000254:growth & development; D054884:Host-Pathogen Interactions; D051379:Mice; D008856:Microscopy, Fluorescence / Q000379:methods*; D061848:Optical Imaging / Q000379:methods*