In vivo imaging and tracking of host–microbiota interactions via metabolic labeling of gut anaerobic bacteria

Abstract

The intestine is densely populated by anaerobic commensal bacteria. These microorganisms shape immune system development, but our understanding of host–commensal interactions is hampered by a lack of tools for studying the anaerobic intestinal environment. We applied metabolic oligosaccharide engineering and bioorthogonal click-chemistry to label various commensal anaerobes, including Bacteroides fragilis, a common and immunologically important commensal. We studied the dissemination of B. fragilis following acute peritonitis, and characterized the interactions of the intact microbe and its polysaccharide components in myeloid and B cell lineages. The distribution and colonization of labeled B. fragilis along the intestine can be assessed, as well as niche competition following coadministration of multiple species of the microbiota. Nine additional anaerobic commensals (both gram-negative and gram-positive) from three phyla common in the gut—Bacteroidetes, Firmicutes, and Proteobacteria—and five families and one aerobic pathogen (Staphylococcus aureus) were also fluorescently labeled. This strategy permits visualization of the anaerobic microbial niche by various methods, including intravital two-photon microscopy and non-invasive whole-body imaging, and an approach to study microbial colonization and host–microbe interactions in real-time.

Development of Rare Bacterial Monosaccharide Analogs for Metabolic Glycan Labeling in Pathogenic Bacteria

“…In contrast, Western blot and flow cytometry analyses revealed that the azidosugar peracetylated N -azidoacetylgalactosamine (Ac 4 GalNAz), 43 an analog of N -acetylgalactosamine, was robustly displayed in B. fragilis surface glycans (Figure 5B,C; Supplementary Figure 4B); this result is consistent with a recent demonstration by Kasper and co-workers that Ac 4 GalNAz is processed into polysaccharide A in B. fragilis . 44 These data indicate that, though it is possible to incorporate azides into B. fragilis surface glycans, such incorporation is negligible with the rare bacterial monosaccharide analogs reported here. Thus, narrow range antibiotics based on differential incorporation of azides onto the surface of pathogenic but not symbiotic bacteria may be possible.…”

Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome

“…Our platform for rapid modification of Bacteroides with strong and predictable expression adds to an emerging palette of tools (Earle et al, 2015; Geva-Zatorsky et al, 2015; Goodman et al, 2009; Koropatkin et al, 2008; Mimee et al, 2015) that can synergize to add new dimensions to our understanding of gut ecology. At one extreme, our data reveals new facets of Bacteroides promoter architecture providing an example of how our high throughput strain generation can yield basic molecular insight (Figure 4A).…”

Gut microbiota, metabolites and host immunity

“…Although much remains to be understood about microbial spatial distribution and the factors influencing microbial community organization, this imaging and analysis approach provides a new way to investigate host–microbiota interactions. The second study 32 used (MOE) and (BCC) in combination with whole-body imaging to label and track bacteria in vivo . Combining these techniques enabled researchers to track the distribution of a symbiotic bacterium along the intestinal tract, its ability to compete with other species and its interaction with host cells.…”