Millions of chemical and biochemical reactions, in which the gut microbes are involved, occur constantly in our intestines, and yet our knowledge of these processes is still far from sufficient. The products of these reactions can profoundly affect us, either as metabolites absorbed into the circulation, epitopes interacting with the immune system, or chemical compounds affecting our nervous system. Elucidating these reactions and processes will help to better understand the symbiotic and antagonistic relationships between us and our close neighbors, which have been co-evolving with us for millions of years. To this end, we pioneer new chemical tools and strategies that are suitable for directly probing gut microbes on a microbiomics level. Currently, we have a chemical arsenal containing nearly thirty probes that are designed for various aspects of gut microbiota research, and this collection will continue to expand. By integrating these chemical tools with advanced imaging, bioinformatic and multi-omics analysis, we hope to bring new insights of the microbial “dark matter” in our gut, via this “chemical microbiomics” approach.
Microbiome Atlas (microbiome-atlas.com) is an open-access fluorescence imaging collection of gut bacterial growth and divisions. This database contains the fluorescence images of gut bacteria obtained via the integrative use of STAMP (in vivo sequential tagging with fluorescent D-amino acid-based probes) and FISH staining. Currently, 63 bacterial species/genus are deposited, including 33 species and 3 genera from human, 12 species and 15 genera from mouse, and 15 species from rat gut microbiota. For each species/genus, high quality fluorescence images are included together with the corresponding FISH sequences and cell sizes information.
We also have a list of chemical probes suitable for microbiota labeling. These probes, designed for in vivo labeling uses and targeting different subgroups of microbes, are mostly developed in Prof. Wei Wang’s laboratory affiliated to Fudan Microbione Center for gut microbiota. These chemical tools, most of which are fluorescently modified, can facilitate the imaging, monitoring and studying of the specific microbes of interests. Their functioning mechanism, labeling protocols and targeting microbial groups are detailed. They are currently available to the public from FMC on request, and will be commercially available soon.
