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Spatial organization of intestinal microbiota in health and disease

Alexander Swidsinski, MD
Vera Loening-Baucke, MD
Section Editor
J Thomas Lamont, MD
Deputy Editor
Shilpa Grover, MD, MPH, AGAF


The alimentary tract represents an interface between the external environment and the body. Within it exists a complex polymicrobial ecology that interacts with the internal and external environment and has an important influence on health and disease.

The properties of isolated microorganisms do not explain how the polymicrobial community functions or why its organisms can grow under conditions that should be deadly to them [1]. An understanding of how microorganisms interact with each other, their host, and the luminal contents is expanding rapidly.

A major advance in understanding the function of the intestinal microbiota has been the development of techniques that permit a detailed assessment of the composition of the flora and its distribution throughout the alimentary tract. One of the methods to visualize single bacterial species within complex communities is called ribosomal RNA fluorescence in situ hybridization (FISH).

Each bacterium possesses tens of thousands of ribosomes, each of which includes a copy of the bacterial RNA. Some of the regions of the ribosomal RNA are strain-specific, others are universal for groups, domains, or even kingdoms. Synthetically produced oligonucleotides that are complementary to sequences of interest can be labeled with fluorescent dye and added to samples containing bacteria. These oligonucleotides, called FISH probes, hybridize with RNA of bacterial ribosomes. Bacteria can be visualized with the microscope directly without additional enhancement because of the high number of ribosomes within each bacterium [2,3].

The names of the FISH probes described in this topic review are based on abbreviations of probeBase online resource for rRNA-targeted oligonucleotide probes [4].

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Literature review current through: Nov 2017. | This topic last updated: Sep 05, 2017.
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