Visualizing the Microbes in the Human Mouth

Microbes are social organisms, living in biofilms all over the planet— including, inside your mouth. The very first bacteria were discovered there, and it is now know that the human mouth contains upwards of 600 different species.

CLASI-FISH Proof of principle with E. coli. (A-D) Details from images of a mixture of 28 different combinatorially labeled E. coli. (A) and (C) are raw spectral images in which the color at each pixel corresponds to a merge of all eight fluorophore channels after unmixing. (B) and (D) are segmented images of the same fields of view as in (A) and (C) respectively. The color of each segmented cell corresponds to one of 28 different label-types; each label type is assigned an arbitrary color. Bar in (a,b) = 50 µm, bar in (c,d) = 15 µm. Previously published in PNAS

Researchers around the world are working to chart the “human biome” (the sum of all of the organisms in and on the human body and their genomes) and Dr. Alex Valm and his colleagues at Brown University and the Woods Hole Marine Biological Lab have made a major step forward. In order to observe microbes in the human mouth at the systems level— a structure that has never before been observed— they developed CLASI-FISH, or Combinatorial Labeling and Spectral Imaging - Fluorescence In Situ Hybridization.

In traditional spectral imaging, the colored wavelengths of the different bacteria overlap, meaning that only six different species are identifiable in a single image. With CLASI-FISH, Dr. Valm and his colleagues were able to see 15 different species of microbes in a single image, unveiling structures that have never been seen before.

“Statistically significant inter-taxon associations were observed,” said Dr. Valm during his mini-symposium last night at the ASCB Annual Meeting.

The next step is to increase the number of distinguishable microbes in a single image to over a hundred, which will not only help researchers see the structure of the biofilm in the human mouth in even greater detail, it will help in all types of microbial research.

The only question left is, do we really want to know what’s growing in and on our bodies in that much detail?