Metabolic fluorine labeling and hotspot imaging of dynamic gut microbiota in mice

Real-time localization and microbial activity information of indigenous gut microbiota over an extended period of time remains a challenge with existing visualizing methods. Here, we report a metabolic fluorine labeling (MEFLA)-based strategy for monitoring the dynamic gut microbiota via 19F magnetic resonance imaging (19F MRI). In situ labeling of different microbiota subgroups is achieved by using a panel of peptidoglycan-targeting MEFLA probes containing 19F atoms of different chemical shifts, and subsequent real-time in vivo imaging is accomplished by multiplexed hotspot 19F MRI with high sensitivity and unlimited penetration. Using this method, we realize extended visualization (>24 hours) of native gut microbes located at different intestinal sec-tions and semiquantitative analysis of their metabolic dynamics modulated by various conditions, such as the host death and different beta-lactam antibiotics. Our strategy holds great potential for noninvasive and real-time assessing of the metabolic activities and locations of the highly dynamic gut microbiota.

Automated summary

In this study, a metabolic fluorine labeling (MEFLA)-based strategy using 19F MRI is proposed for monitoring the dynamic gut microbiota. Different microbiota subgroups are labeled in situ using a panel of peptidoglycan-targeting MEFLA probes with 19F atoms of different chemical shifts. Real-time in vivo imaging is then achieved using multiplexed hotspot 19F MRI. The strategy allows for extended visualization and semiquantitative analysis of the metabolic dynamics of gut microbiota located at different intestinal sections.