Mark Welch, J. Lab

Jessica Mark Welch Laboratory / Imaging Microbial Diversity

J_MarkWelchJessica Mark Welch
Associate Research Scientist
p: 508 289 7180
f: 508 457 4727


Bacteria in nature live in complex, multi-species communities in which bacterial cells that are in close proximity can exchange metabolic products and signals. The Imaging Microbial Diversity group is using fluorescence microscopy to gain new information about the micron-scale arrangement of microbes in natural communities, including human-associated microbial communities, to discover how the bacterial community is structured. We employ fluorescence spectral imaging, with which the spectrum of emitted fluorescence can be recorded from each pixel or object in the field of view, and we have developed a technique called “combinatorial imaging,” in which we use combinations of fluorophore-labeled oligonucleotide probes so as to increase greatly the number of different taxa of bacteria that can be identified in a single image. The group is a collaboration between Dr. Jessica Mark Welch of the MBL’s Bay Paul Center and Dr. Gary Borisy and Mr. Blair Rossetti at the Forsyth Institute.


Combinatorial Imaging of the Oral Microbiome

The human oral microbiome consists of more than 500 bacterial species. In collaboration with Gary Borisy and Floyd Dewhirst of the Forsyth Institute, we are developing sets of fluorescently-labeled oligonucleotide probes targeting most of the genera and higher-order taxa in the Human Oral Microbiome Database (HOMD). We are employing these probes to examine the structure of natural and artificial oral biofilms and facilitate the study of oral microbial communities.


Combinatorial Imaging of Gut Microbes in Gnotobiotic Mice

We are also investigating the microbes of the gut, using a mouse model. In collaboration with Jeffrey Gordon of Washington University,we are applying the spectral imaging technique to germ-free mice that have been colonized with model microbial communities. By examining thin sections of small intestine, large intestine, and cecum, we are studying the distribution of 15 bacterial taxa as a first step in understanding the functional roles of these bacteria in mammalian digestion, metabolism, and immune system function.





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