A major limitation of current methods of gut microbiota analysis (16S rRNA amplicon sequencing and metagenomics) is that preparing the bacterial DNA for sequencing destroys the fine spatial organization of the sample. Researchers have limited tools for 3-dimensional visualization of the anaerobic commensal bacteria in a living host.

Geva-Zatorsky, et al. recently reported that they used metabolic oligosaccharide engineering and click chemistry to tag several commensal bacteria, including Bacteroides fragilis, with a fluorescent marker and observe its activity in a host. Importantly, the method is bio-orthogonal: the compounds involved in tagging were sufficiently small and nonreactive that they did not interfere with processes of interest. The fluorescent labeling method was used for a variety of commensals, as well as one aerobic pathogen (Staphylococcus aureus).

The researchers investigated how B. fragilis distributed and colonized along a host’s intestine, and how it competed for a niche after co-administration with several different species of bacteria. This strategy gives researchers a new way to visualize microbial colonization and host-microbe interactions in real time.


Geva-Zatorsky N, et al. (2015) In vivo imaging and tracking of host–microbiota interactions via metabolic labeling of gut anaerobic bacteria. Nature Medicine doi:10.1038/nm.3929