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Metabolic Labeling of Peptidoglycan with NIR-II Dye Enables in vivo Imaging of Gut Microbiota.

Deepening our understanding of mammalian gut microbiota has been greatly hampered by the lack of a facile, real-time and in vivo bacterial imaging method. To address this unmet need in microbial visualization, we herein report the development of a second near-infrared (NIR-II)-based method for in vivo imaging of gut bacteria. Using D-propargylglycine in gavage and then click reaction with an azide-containing NIR-II dye, gut microbiota of a donor mouse was strongly labeled with NIR-II fluorescence on their peptidoglycan. The bacteria could be readily visualized in recipient mouse gut with high spatial resolution and deep tissue penetration under NIR irradiation. We then adopted this chemical strategy to image different bacterial species, which expanded its applicability in microbiology. Moreover, by employing this method, we found that the biogeography of gut microbiota was dramatically affected by host's gastrointestinal motilities. The NIR-II-based metabolic labeling strategy reported here, to our knowledge, provides the first protocol for facile in vivo visualization of gut microbiota within deep tissues, and offers an instrumental tool for deciphering the complex biology of these gut "dark matters".