Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface

Ellen G Avery; Lea-Maxie Haag; Victoria McParland; Sarah M Kedziora; Gabriel J Zigra; Daniela S Valdes; Marieluise Kirchner; Oliver Popp; Sabrina Geisberger; Olivia Nonn; Tine V Karlsen; Gabriele N'Diaye; Alex Yarritu; Hendrik Bartolomaeus; Theda U P Bartolomaeus; Nurana A Tagiyeva; Moritz I Wimmer; Nadine Haase; Yiming D Zhang; Andreas Wilhelm; Gerald Grütz; Olav Tenstad; Nicola Wilck; Sofia K Forslund; Robert Klopfleisch; Anja A Kühl; Raja Atreya; Stefan Kempa; Philipp Mertins; Britta Siegmund; Helge Wiig; Dominik N Müller

doi:10.1093/cvr/cvae267

Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface

Cardiovasc Res. 2025 Jan 10:cvae267. doi: 10.1093/cvr/cvae267. Online ahead of print.

Authors

Ellen G Avery^{1

2

3

4

5}, Lea-Maxie Haag^{6

7}, Victoria McParland^{1

2

3}, Sarah M Kedziora^{1

2

3

4}, Gabriel J Zigra⁶, Daniela S Valdes^{1

2

3

4}, Marieluise Kirchner^{8

9}, Oliver Popp⁹, Sabrina Geisberger^{1

10}, Olivia Nonn^{1

2

3

4}, Tine V Karlsen¹¹, Gabriele N'Diaye^{2

3}, Alex Yarritu^{1

2

3

4}, Hendrik Bartolomaeus^{1

2

3

4}, Theda U P Bartolomaeus^{1

2

3

4}, Nurana A Tagiyeva^{1

2

3

4}, Moritz I Wimmer^{1

2

3

12}, Nadine Haase^{1

2

3

4}, Yiming D Zhang^{1

10}, Andreas Wilhelm¹³, Gerald Grütz¹³, Olav Tenstad¹¹, Nicola Wilck^{1

2

3

4

14}, Sofia K Forslund^{1

2

3

4}, Robert Klopfleisch¹⁵, Anja A Kühl^{6

16}, Raja Atreya¹⁷, Stefan Kempa^{1

10}, Philipp Mertins^{8

9}, Britta Siegmund⁶, Helge Wiig¹¹, Dominik N Müller^{1

2

3

4}

Affiliations

¹ Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
² Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.
³ Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
⁴ DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.
⁵ Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
⁶ Department for Medicine (Gastroenterology, Infectious Diseases, Rheumatology) Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany.
⁷ Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, Berlin 10117, Germany.
⁸ Core Unit Proteomics, Berlin Institute of Health at Charite-Universitätsmedizin Berlin, Berlin, Germany.
⁹ Proteomics Platform, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
¹⁰ Integrative Proteomics and Metabolomics Platform, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
¹¹ Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen N-5009, Norway.
¹² Faculty of Medicine, Universität Tübingen, Tübingen, Germany.
¹³ CheckImmune GmbH, BerlinBioCube, Robert-Rössle Str. 10, Berlin 13125, Germany.
¹⁴ Medizinische Klinik mit Schwerpunkt Nephrologie und Internistische Intensivmedizin, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany.
¹⁵ Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
¹⁶ Charité-Universitätsmedizin Berlin, Corporate Member of Freie Univeristät Berlin and Humboldt Universität zu Berlin, iPATH, Berlin, Berlin, Germany.
¹⁷ Department of Medicine 1, Friedrich-Alexander University, Erlangen, Germany.

PMID: 39804196
DOI: 10.1093/cvr/cvae267

Abstract

Aims: The gastrointestinal (GI) tract is composed of distinct sub-regions, which exhibit segment-specific differences in microbial colonization and (patho)physiological characteristics. Gut microbes can be collectively considered as an active endocrine organ. Microbes produce metabolites, which can be taken up by the host and can actively communicate with the immune cells in the gut lamina propria with consequences for cardiovascular health. Variation in bacterial load and composition along the GI tract may influence the mucosal microenvironment and thus be reflected its interstitial fluid (IF). Characterization of the segment-specific microenvironment is challenging and largely unexplored because of lack of available tools.

Methods and results: Here, we developed methods, namely tissue centrifugation and elution, to collect IF from the mucosa of different intestinal segments. These methods were first validated in rats and mice, and the tissue elution method was subsequently translated for use in humans. These new methods allowed us to quantify microbiota-derived metabolites, mucosa-derived cytokines, and proteins at their site-of-action. Quantification of short-chain fatty acids showed enrichment in the colonic IF. Metabolite and cytokine analyses revealed differential abundances within segments, often significantly increased compared to plasma, and proteomics revealed that proteins annotated to the extracellular phase were site-specifically identifiable in IF. Lipopolysaccharide injections in rats showed significantly higher ileal IL-1β levels in IF compared to the systemic circulation, suggesting the potential of local as well as systemic effect.

Conclusion: Collection of IF from defined segments and the direct measurement of mediators at the site-of-action in rodents and humans bypasses the limitations of indirect analysis of faecal samples or serum, providing direct insight into this understudied compartment.

Keywords: Fluid isolation; Humans; Interstitial fluid; Intestinal microenvironment; Intestine; Microbiome; Rodents.

Abstract

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