Earle Kristen A, Billings Gabriel, Sigal Michael, Lichtman Joshua S, Hansson Gunnar C, Elias Joshua E, Amieva Manuel R, Huang Kerwyn Casey, Sonnenburg Justin L
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Physics, Stanford University, Stanford, CA 94305, USA.
Cell Host Microbe. 2015 Oct 14;18(4):478-88. doi: 10.1016/j.chom.2015.09.002. Epub 2015 Oct 1.
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.
基因组技术极大地推进了我们对宿主相关微生物群落组成和多样性的理解。然而，它们相对于宿主的空间组织和功能相互作用一直更具研究挑战性。在这里，我们展示了一种用于评估固定肠道横断面免疫荧光图像中肠道微生物群定位的流程，其中包括一个灵活的软件包BacSpace，用于微生物组织的高通量定量分析。将该流程应用于无菌和人类微生物群定殖的小鼠，我们证明从饮食中消除微生物可利用碳水化合物（MACs）会导致远端结肠黏液变薄、微生物与上皮细胞的距离增加以及炎症标志物REG3β的表达升高。对微生物与微生物之间距离的测量表明，缺乏MAC的饮食会改变单系空间聚类。此外，我们量化了幽门螺杆菌相对于宿主有丝分裂祖细胞侵入小鼠胃腺的情况，说明了这种方法的通用性。
