University of Oulu

Peñate-Medina, O., Tower, R.J., Peñate-Medina, T. et al. Universal membrane-labeling combined with expression of Katushka far-red fluorescent protein enables non-invasive dynamic and longitudinal quantitative 3D dual-color fluorescent imaging of multiple bacterial strains in mouse intestine. BMC Microbiol 19, 167 (2019).

Universal membrane-labeling combined with expression of Katushka far-red fluorescent protein enables non-invasive dynamic and longitudinal quantitative 3D dual-color fluorescent imaging of multiple bacterial strains in mouse intestine

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Author: Peñate-Medina, Oula1; Tower, Robert J.1; Peñate-Medina, Tuula1;
Organizations: 1Molecular Imaging North Competence Center, Section Biomedical Imaging, Department of Radiology and Neuroradiology, University Hospital Schleswig-Holstein, Am Botanischen Garten 14, 24118, Kiel, Germany
2Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
3Cleft Palate and Craniofacial Centre, Department of Plastic Surgery, Helsinki University Hospital, Helsinki University Central Hospital, Topeliuksenkatu 5, 00029, Helsinki, Finland
4Päijät-Häme Joint Authority for Health and Wellbeing, Department of Oral and Maxillo-Facial Surgery, Keskussairaalankatu 7, 15850, Lahti, Finland
5Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4E, 00029, Helsinki, Finland
6Division of Periodontology, Department of Dental Medicine, Karolinska Institutet, Alfreds Nobels Alle 8, Huddinge, 14104, Stockholm, Sweden
7Department of Bacteriology and Immunology and Immunobiology Research Program, Faculty of Medicine, University of Helsinki, Haartmaninkatu 2, 00014, Helsinki, Finland
8Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöberginkatu 2, 00014, Helsinki, Finland
9Laboratory of Microbiology, Wageningen University, Wageningen, 6708 PB, The Netherlands
10Biocenter Oulu & Cancer and Translational Medicine Research Unit, University of Oulu, Aapistie 5, 90220, Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 3.4 MB)
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Language: English
Published: Springer Nature, 2019
Publish Date: 2020-04-20


Background: The human gastrointestinal (GI) tract microbiota has been a subject of intense research throughout the 3rd Millennium. Now that a general picture about microbiota composition in health and disease is emerging, questions about factors determining development of microbiotas with specific community structures will be addressed. To this end, usage of murine models for colonization studies remains crucial. Optical in vivo imaging of either bioluminescent or fluorescent bacteria is the basis for non-invasive detection of intestinal colonization of bacteria. Although recent advances in in vivo fluorescence imaging have overcome many limitations encountered in bioluminescent imaging of intestinal bacteria, such as requirement for live cells, high signal attenuation and 2D imaging, the method is still restricted to bacteria for which molecular cloning tools are available.

Results: Here, we present usage of a lipophilic fluorescent dye together with Katushka far-red fluorescent protein to establish a dual-color in vivo imaging system to monitor GI transit of different bacterial strains, suitable also for strains resistant to genetic labeling. Using this system, we were able to distinguish two different E. coli strains simultaneously and show their unique transit patterns. Combined with fluorescence molecular tomography, these distinct strains could be spatially and temporally resolved and quantified in 3D.

Conclusions: Developed novel method for labeling microbes and identify their passage both temporally and spatially in vivo makes now possible to monitor all culturable bacterial strains, also those that are resistant to conventional genetic labeling.

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Series: BMC microbiology
ISSN: 1471-2180
ISSN-E: 1471-2180
ISSN-L: 1471-2180
Volume: 19
Article number: 167
DOI: 10.1186/s12866-019-1538-z
Type of Publication: A1 Journal article – refereed
Field of Science: 1183 Plant biology, microbiology, virology
Funding: This work was funded by the Academy of Finland grant number 299749.
Academy of Finland Grant Number: 299749
Detailed Information: 299749 (Academy of Finland Funding decision)
Copyright information: © The Author(s). 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.