Single-cell microbiota phenotyping reveals distinct disease and therapy-associated signatures in Crohn’s disease
Lisa Budzinski,
Gi-Ung Kang,
René Riedel,
Toni Sempert,
Leonie Lietz,
René Maier,
Janine Büttner,
Bettina Bochow,
Marcell T. Tordai,
Aayushi Shah,
Amro Abbas,
Tanisha Momtaz,
Jannike L. Krause,
Robin Kempkens,
Katrin Lehman,
Gitta A. Heinz,
Anne E. Benken,
Stefanie Bartsch,
Kathleen Necke,
Ute Hoffmann,
Mir-Farzin Mashreghi,
Robert Biesen,
Tilmann Kallinich,
Tobias Alexander,
Bosse Jessen,
Carl Weidinger,
Britta Siegmund,
Andreas Radbruch,
Anja Schirbel,
Benjamin Moser,
Hyun-Dong Chang
Affiliations
Lisa Budzinski
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Gi-Ung Kang
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
René Riedel
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Toni Sempert
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Leonie Lietz
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
René Maier
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Janine Büttner
Department of Hepatology and Gastroenterology, Campus Charité Mitte, Charité, Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Bettina Bochow
Department of Hepatology and Gastroenterology, Campus Charité Mitte, Charité, Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Marcell T. Tordai
Department of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Aayushi Shah
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Amro Abbas
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Tanisha Momtaz
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Jannike L. Krause
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Robin Kempkens
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Katrin Lehman
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Gitta A. Heinz
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Anne E. Benken
Department of Rheumatology, Campus Charité Mitte, Charité – Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Stefanie Bartsch
Department of Paediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité Campus Virchow, Charité Universitätsmedizin Berlin, Berlin, Germany
Kathleen Necke
Department of Paediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité Campus Virchow, Charité Universitätsmedizin Berlin, Berlin, Germany
Ute Hoffmann
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Mir-Farzin Mashreghi
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Robert Biesen
Department of Rheumatology, Campus Charité Mitte, Charité – Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Tilmann Kallinich
Department of Paediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité Campus Virchow, Charité Universitätsmedizin Berlin, Berlin, Germany
Tobias Alexander
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Bosse Jessen
Department of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Carl Weidinger
Department of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Britta Siegmund
Department of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Andreas Radbruch
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
Anja Schirbel
Department of Hepatology and Gastroenterology, Campus Charité Mitte, Charité, Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Benjamin Moser
Department of Hepatology and Gastroenterology, Campus Charité Mitte, Charité, Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
Hyun-Dong Chang
German Rheumatology Research Centre Berlin – A Leibniz Institute, Berlin, Germany
IgA-coated fractions of the intestinal microbiota of Crohn’s disease (CD) patients have been shown to contain taxa that hallmark the compositional dysbiosis in CD microbiomes. However, the correlation between other cellular properties of intestinal bacteria and disease has not been explored further, especially for features that are not directly driven by the host immune-system, e.g. the expression of surface sugars by bacteria. By sorting and sequencing IgA-coated and lectin-stained fractions from CD patients microbiota and healthy controls, we found that lectin-stained bacteria were distinct from IgA-coated bacteria, but still displayed specific differences between CD and healthy controls. To exploit the discriminatory potential of both, immunoglobulin coated bacteria and the altered surface sugar expression of bacteria in CD, we developed a multiplexed single cell-based analysis approach for intestinal microbiota. By multi-parameter microbiota flow cytometry (mMFC) we characterized the intestinal microbiota of 55 CD patients and 44 healthy controls for 11-parameters in total, comprising host-immunoglobulin coating and the presence of distinct surface sugar moieties. The data were analyzed by machine-learning to assess disease-specific marker patterns in the microbiota phenotype. mMFC captured detailed characteristics of CD microbiota and identified patterns to classify CD patients. In addition, we identified phenotypic signatures in the CD microbiota which not only reflected remission after 6 weeks of anti-TNF treatment, but were also able to predict remission before the start of an adalimumab treatment course in a pilot study. We here present the proof-of-concept demonstrating that multi-parameter single-cell bacterial phenotyping by mMFC could be a novel tool with high translational potential to expand current microbiome investigations by phenotyping of bacteria to identify disease- and therapy-associated cellular alterations and to reveal novel target properties of bacteria for functional assays and therapeutic approaches.
