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Three‐Dimensional Quantitative Imaging of Native Microbiota Distribution in the Gut
Author(s) -
Wang Wei,
Zhang Ni,
Du Yahui,
Gao Juan,
Li Min,
Lin Liyuan,
Czajkowsky Daniel M.,
Li Xiaowei,
Yang Chaoyong,
Shao Zhifeng
Publication year - 2021
Publication title -
angewandte chemie international edition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.831
H-Index - 550
eISSN - 1521-3773
pISSN - 1433-7851
DOI - 10.1002/anie.202010921
Subject(s) - biology , gut flora , bacteria , host (biology) , small intestine , microbiology and biotechnology , computational biology , ecology , genetics , biochemistry
Owing to the challenges to acquire detailed spatial information of gut bacteria in situ, three‐dimensional (3D) microbiota distributions in the gut remain largely uncharted. Here, we propose a tissue clearing‐based and D‐amino acid labeling‐facilitated (TiDaL) strategy that combines a novel microbiota in vivo labeling protocol, CUBIC‐based tissue clearing and whole‐mount tissue imaging, to achieve 3D imaging of indigenous gut microbiota. We demonstrate high‐resolution 3D acquisition of their biogeography in different gut sections, and present quantitative spatial details in relation to the host epithelium. We unexpectedly observe microbiota in the small intestine crypts, which were thought to be bacteria‐free. Significant bacterial overgrowth in the first two‐thirds of the small intestine is detected in an enteritis model. We expect that this quantitative 3D imaging strategy for native gut microbiota will provide insightful information into the host–microbiota interactions.