1
|
Harris DMM, Szymczak S, Schuchardt S, Labrenz J, Tran F, Welz L, Graßhoff H, Zirpel H, Sümbül M, Oumari M, Engelbogen N, Junker R, Conrad C, Thaçi D, Frey N, Franke A, Weidinger S, Hoyer B, Rosenstiel P, Waschina S, Schreiber S, Aden K. Tryptophan degradation as a systems phenomenon in inflammation - an analysis across 13 chronic inflammatory diseases. EBioMedicine 2024; 102:105056. [PMID: 38471395 PMCID: PMC10943670 DOI: 10.1016/j.ebiom.2024.105056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Chronic inflammatory diseases (CIDs) are systems disorders that affect diverse organs including the intestine, joints and skin. The essential amino acid tryptophan (Trp) can be broken down to various bioactive derivatives important for immune regulation. Increased Trp catabolism has been observed in some CIDs, so we aimed to characterise the specificity and extent of Trp degradation as a systems phenomenon across CIDs. METHODS We used high performance liquid chromatography and targeted mass spectrometry to assess the serum and stool levels of Trp and Trp derivatives. Our retrospective study incorporates both cross-sectional and longitudinal components, as we have included a healthy population as a reference and there are also multiple observations per patient over time. FINDINGS We found reduced serum Trp levels across the majority of CIDs, and a prevailing negative relationship between Trp and systemic inflammatory marker C-reactive protein (CRP). Notably, serum Trp was low in several CIDs even in the absence of measurable systemic inflammation. Increases in the kynurenine-to-Trp ratio (Kyn:Trp) suggest that these changes result from increased degradation along the kynurenine pathway. INTERPRETATION Increases in Kyn:Trp indicate the kynurenine pathway as a major route for CID-related Trp metabolism disruption and the specificity of the network changes indicates excessive Trp degradation relative to other proteogenic amino acids. Our results suggest that increased Trp catabolism is a common metabolic occurrence in CIDs that may directly affect systemic immunity. FUNDING This work was supported by the DFG Cluster of Excellence 2167 "Precision medicine in chronic inflammation" (KA, SSchr, PR, BH, SWa), the BMBF (e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, the e:Med Network iTREAT 01ZX2202A, and GUIDE-IBD 031L0188A), EKFS (2020_EKCS.11, KA), DFG RU5042 (PR, KA), and Innovative Medicines Initiative 2 Joint Undertakings ("Taxonomy, Treatments, Targets and Remission", 831434, "ImmUniverse", 853995, "BIOMAP", 821511).
Collapse
Affiliation(s)
- Danielle M M Harris
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany; Institute for Human Nutrition and Food Science, Division Nutriinformatics, Kiel University, Kiel, Germany
| | - Silke Szymczak
- Institute of Medical Biometry and Statistics, University of Lübeck, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Sven Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hanover, Germany
| | - Johannes Labrenz
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lina Welz
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany; Institute for Human Nutrition and Food Science, Division Nutriinformatics, Kiel University, Kiel, Germany
| | - Hanna Graßhoff
- Department of Rheumatology University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Henner Zirpel
- Comprehensive Center for Inflammation Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Melike Sümbül
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Mhmd Oumari
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nils Engelbogen
- Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ralf Junker
- Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Claudio Conrad
- Department of Internal Medicine I, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Diamant Thaçi
- Comprehensive Center for Inflammation Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Norbert Frey
- Department of Medicine III: Cardiology, Angiology, and Pneumology, Heidelberg University, Heidelberg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Bimba Hoyer
- Department of Internal Medicine I, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Division Nutriinformatics, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| |
Collapse
|
2
|
Starke S, Harris DMM, Zimmermann J, Schuchardt S, Oumari M, Frank D, Bang C, Rosenstiel P, Schreiber S, Frey N, Franke A, Aden K, Waschina S. Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability. ISME J 2023; 17:2370-2380. [PMID: 37891427 PMCID: PMC10689445 DOI: 10.1038/s41396-023-01537-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and function of the human gut microbiome remain poorly understood. This study performed the first systematic analysis of the distribution of amino acid auxotrophies in the human gut microbiome using a combined metabolomic, metagenomic, and metabolic modeling approach. Results showed that amino acid auxotrophies are ubiquitous in the colon microbiome, with tryptophan auxotrophy being the most common. Auxotrophy frequencies were higher for those amino acids that are also essential to the human host. Moreover, a higher overall abundance of auxotrophies was associated with greater microbiome diversity and stability, and the distribution of auxotrophs was found to be related to the human host's metabolome, including trimethylamine oxide, small aromatic acids, and secondary bile acids. Thus, our results suggest that amino acid auxotrophies are important factors contributing to microbiome ecology and host-microbiome metabolic interactions.
Collapse
Affiliation(s)
- Svenja Starke
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany
| | - Danielle M M Harris
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Johannes Zimmermann
- Zoological Institute, Research Group Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hanover, Germany
| | - Mhmd Oumari
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Derk Frank
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Hamburg, Kiel, Lübeck, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Hamburg, Kiel, Lübeck, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Silvio Waschina
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany.
| |
Collapse
|
3
|
Parsons CV, Harris DMM, Patten CL. Regulation of indole-3-acetic acid biosynthesis by branched-chain amino acids in Enterobacter cloacae UW5. FEMS Microbiol Lett 2015; 362:fnv153. [PMID: 26347301 DOI: 10.1093/femsle/fnv153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 01/22/2023] Open
Abstract
The soil bacterium Enterobacter cloacae UW5 produces the rhizosphere signaling molecule indole-3-acetic acid (IAA) via the indolepyruvate pathway. Expression of indolepyruvate decarboxylase, a key pathway enzyme encoded by ipdC, is upregulated by the transcription factor TyrR in response to aromatic amino acids. Some members of the TyrR regulon may also be controlled by branched-chain amino acids and here we show that expression from the ipdC promoter and production of IAA are downregulated by valine, leucine and isoleucine. Regulation of the IAA synthesis pathway by both aromatic and branched-chain amino acids suggests a broader role for this pathway in bacterial physiology, beyond plant interactions.
Collapse
Affiliation(s)
- Cassandra V Parsons
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Danielle M M Harris
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Cheryl L Patten
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| |
Collapse
|