Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging

December 7th, 2012 @   - 

Valm, Alex M., Jessica L. Mark Welch, Christopher W. Rieken, Yuko Hasegawa, Mitchell L. Sogin, Rudolf Oldenbourg, Floyd E. Dewhirst, and Gary G. Borisy

(USA) 108: 4152-4157

Bacteria in nature live not as isolated cells, but as members of a community in which many different kinds of bacteria live intermingled in complex associations. The spatial arrangement of bacteria is important because bacteria that are close to each other can exchange DNA, including antibiotic resistance genes, can signal to each other, and can cooperate in digesting complex substrates. Until now, methods for visualizing the spatial organization of microbial communities could reveal only two to three different kinds of bacteria at once. In this paper, MBL-Brown graduate student Alex Valm and his colleagues in the Bay Paul Center developed a method for visualizing and differentiating 15 different kinds of microbes simultaneously. They applied this method to analyze spatial relationships of bacteria in human dental plaque, a microbial biofilm found in the human mouth. Further application of this method may lead to a better understanding of the way oral microbial communities function, with the goal of discovering ways to prevent periodontitis and dental caries. Bay Paul Center scientists Jessica Mark Welch and Gary Borisy and graduate student Yuko Hasegawa plan to apply the method to analyze spatial structure in other microbial communities, such as those in the human gut and, potentially, to microbial communities in soil or on surfaces in the environment.

Interactions of bacterial cells in human dental plaque.  Plaque was collected using dental floss and was embedded in plastic resin, sectioned, hybridized with fluorescent probes targeting 15 groups (genera or families) of oral bacteria, and imaged using the Zeiss 780 laser scanning confocal microscope.  Each small dot or rod is a single bacterial cell.  Bacteria hybridizing to 6 different probes are seen in this image:  Pasteurellaceae (dark orange), Streptococcus (yellow), Actinomyces (magenta), Porphyromonas (green), Neisseriaceae (blue), and Fusobacterium (peach).  Several kinds of corncob structures, in which dot-like cells surround a central filament, can be seen in the upper part of the image, including multilayer corncobs in which the filament is surrounded by Streptococcus (inner ring) and Pasteurellaceae (outer ring), as well as single-layer corncobs composed of Porphyromonas and of Neisseriaceae.  Photo credit:  Blair Rossetti.


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