Imaging Microbial Diversity – Gary Borisy, Jessica Mark Welch, Mitchell Sogin

Written by Jessica Mark Welch

The human body contains some of the most densely-colonized microbial habitats on earth, and humans can be considered meta-organisms with both microbial and human components.  Next-generation sequencing technology and metagenomics have revolutionized our understanding of the microbial parts of ourselves, but these sequencing-based analyses begin with homogenizing the samples and destroying fine-scale spatial information about the structure of the microbial community.  A major gap in our understanding of microbial communities is the lack of information about their spatial organization on the scale experienced by the average microbe, namely the scale of microns to hundreds of microns.  Characterizing the structure of microbial communities at this scale will likely lead to the identification of key interrelationships among different types of microbes or between specific microbes and the host, leading to a greater understanding of the function of the communities and the ways these communities affect the health of their host.

The Imaging Microbial Diversity (IMD) group at the Bay Paul Center is contributing to a deeper understanding of microbial communities using a recently developed CLASI-FISH (Combinatorial Labeling and Spectral Imaging – Fluorescence in situ Hybridization) strategy for the simultaneous identification of many microbial taxa in a single microscopic image.  Using fluorescent probes that hybridize to the ribosomal RNA of particular groups of microbes, and using many probes simultaneously so as to identify most of the cells in an image, they are gaining a far more detailed picture than previously possible of the fine-scale arrangement of microbes in human-associated communities, beginning with the communities that inhabit the human mouth and, using a mouse model, communities that inhabit the human gut.

In the past year the IMD group has discovered strikingly complex structures in human dental plaque (see figure).  Although structures called “corn cobs” have been seen in plaque since the 1970s, they were thought to be composed of just two taxa:  a long filamentous cell, usually of the genus Corynebacterium, surrounded by spherical Streptococcus cells.  Using CLASI-FISH the IMD group has discovered more complex corn cobs, composed of an additional layer of cells clinging to the Streptococcus cells, and they have discovered a second type of corn cob in which cells of the genus Porphyromonas surround the central Corynebacterium filament.  The two types of corn cob are found immediately adjacent to each other or even share the same filament.  These results point out the existence of previously unknown spatial relationships among microbes living on our teeth, and suggest that future work should focus on discovering why these taxa adopt a close relationship and what the significance of this interaction might be.

Complex “corn cobs” in dental plaque.  Plaque was collected from the surface of a volunteer’s tooth using a toothpick.  The plaque was then embedded in acrylic resin and sectioned to 2 microns thickness.  FISH was performed on the plaque using probes for Corynebacterium (magenta), Streptococcus (green), Aggregatibacter (orange), and Porphyromonas (blue).  Each tiny dot is an individual bacterial cell.  The Streptococcus cells form “corn cobs” surrounding Corynebacterium filaments, and Aggregatibacter cells surround some of the Streptococcus corn cobs.  Porphyromonas cells also form corn cobs around Corynebacterium filaments.

Complex “corn cobs” in dental plaque. Plaque was collected from the surface of a volunteer’s tooth using a toothpick. The plaque was then embedded in acrylic resin and sectioned to 2 microns thickness. FISH was performed on the plaque using probes for Corynebacterium (magenta), Streptococcus (green), Aggregatibacter (orange), and Porphyromonas (blue). Each tiny dot is an individual bacterial cell. The Streptococcus cells form “corn cobs” surrounding Corynebacterium filaments, and Aggregatibacter cells surround some of the Streptococcus corn cobs. Porphyromonas cells also form corn cobs around Corynebacterium filaments.

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