Jessica Mark Welch Receives Grant to Develop Microbiome Imaging Technology

The photos are dazzling: Multiple kinds of bacteria, fluorescently color coded, forming intricate, organized assemblages inside human dental plaque. These vivid images by MBL scientist Jessica Mark Welch and colleagues, published last year, offered our first glimpses of the spatial structure of the mouth microbiome -- what one headline called “The Forest in Your Mouth.”

Mark Welch has now received a grant from the National Science Foundation (NSF) to adapt this microbiome imaging technology, which she co-developed with Gary Borisy of the Forsyth Institute and others, to environments other than the human mouth, including the vertebrate gut and on marine organisms and surfaces.

“Other investigators have started applying our technology to studying the mouth microbiome, and that is relatively straightforward to do. But it’s difficult to get the technology up and running in other systems,” Mark Welch says. “This grant will allow us to pioneer the technology in other environments, to make it easier for other people to adopt.”

“Hedgehog” structures of bacteria in dental plaque. MBL scientist Jessica Mark Welch has received a grant to expand this imaging technology to study microbiomes in other environments. Credit: Jessica Mark Welch et al., PNAS.1522149113

Their imaging technology uses fluorescent probes that selectively bind to the bacterial types present such that the bacteria’s spatial organization is preserved, relative to each other and to the host organism.

Mark Welch will use fish to develop a set of probes and protocols for visualizing the spatial microbiome in the vertebrate gut. She will also collaborate with others to adapt the technology for studying microbiomes on marine surfaces including kelp, oyster shells, and marine plastic debris.

“My hypothesis is that there is a similar enough set of microbiota on marine surfaces that I can design a set of probes that will be useful for many specimens in that environment,” Mark Welch says. “I suspect the same for a broad set of vertebrate guts.”

The award to Mark Welch is one of ten grants for plant and animal microbiome and phenomics research that the NSF recently announced.

Mark Welch is a member of the The Microbiome Center, a research collaboration between the University of Chicago, the Marine Biological Laboratory, and Argonne National Laboratory to advance understanding of the identity and function of microbes across all environments.