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. 2020 Aug 5;10:396. doi: 10.3389/fcimb.2020.00396

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Copyright © 2020 Kvich, Burmølle, Bjarnsholt and Lichtenberg.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Methods for detecting bacteria from a biopsy. (Top left) Biopsy is homogenized with a tissue dissociator and grown on agar plates. This method is cheap and quick but is very unspecific and the risk of false negative results is high. In addition, spatial structure is lost. (Bottom left) Biopsy is homogenized with a tissue dissociator and DNA is extracted and sequenced. With molecular tools it is possible to find all species present in the biopsy, but all spatial structure is lost. (Right) The spatial structure is retained with imaging techniques such as confocal or electron microscopy where the tissue is sectioned into thin slices. But due to the relatively small area/volume that can be imaged, the risk of not finding the bacteria is high.