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Liu Y, Wang Y, Wei F, Chai L, Wang H. Gut microbiota-bile acid crosstalk contributes to intestinal damage after nitrate exposure in Bufo gargarizans tadpoles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173795. [PMID: 38851338 DOI: 10.1016/j.scitotenv.2024.173795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Bile acids (BAs) are amphipathic steroid acids whose production and diversity depend on both host and microbial metabolism. Nitrate (NO3-) is a widespread pollutant in aquatic ecosystems, which can cause rapid changes in microbial community structure and function. However, the effect of gut microbiota reshaped by nitrate‑nitrogen (NO3-N) on BAs profiles remains unclarified. To test this, intestinal targeted BAs metabolomics and fecal metagenomic sequencing were performed on Bufo gargarizans tadpoles treated with different concentrations of NO3-N. NO3-N exposure induced a reduction in the abundance of microbiota with bile acid-inducible enzymes (BAIs) and/or hydroxysteroid dehydrogenases (HSDHs), thus inhibiting the conversion of primary BAs to secondary BAs. Inhibition of BAs biotransformation decreased protective hydrophilic BAs (UDCA) and increased toxic hydrophobic BAs (CA and CDCA), which may contribute to intestinal histopathological damage. Moreover, we found that NO3-N treatment increased microbial virulence factors and decreased Glycoside hydrolases, further highlighting the deleterious risk of NO3-N. Overall, this study shed light on the complex interactions of NO3-N, gut microbiota, and BAs, and emphasized the hazardous effects of NO3-N pollution on the health of amphibians.
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Affiliation(s)
- Ying Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Yaxi Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Fei Wei
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an 710054, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.
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2
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Ng DZW, Low A, Tan AJH, Ong JH, Kwa WT, Lee JWJ, Chan ECY. Ex vivo metabolism kinetics of primary to secondary bile acids via a physiologically relevant human faecal microbiota model. Chem Biol Interact 2024; 399:111140. [PMID: 38992765 DOI: 10.1016/j.cbi.2024.111140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Bile acids (BA) are synthesized in the human liver and undergo metabolism by host gut bacteria. In diseased states, gut microbial dysbiosis may lead to high primary unconjugated BA concentrations and significant perturbations to secondary BA. Hence, it is important to understand the microbial-mediated formation kinetics of secondary bile acids using physiologically relevant ex vivo human faecal microbiota models. Here, we optimized an ex vivo human faecal microbiota model to recapitulate the metabolic kinetics of primary unconjugated BA and applied it to investigate the formation kinetics of novel secondary BA metabolites and their sequential pathways. We demonstrated (1) first-order depletion of primary BA, cholic acid (CA) and chenodeoxycholic acid (CDCA), under non-saturable conditions and (2) saturable Michaelis-Menten kinetics for secondary BA metabolite formation with increasing substrate concentration. Notably, relatively lower Michaelis constants (Km) were associated with the formation of deoxycholic acid (DCA, 14.3 μM) and lithocholic acid (LCA, 140 μM) versus 3-oxo CA (>1000 μM), 7-keto DCA (443 μM) and 7-keto LCA (>1000 μM), thereby recapitulating clinically observed saturation of 7α-dehydroxylation relative to oxidation of primary BA. Congruently, metagenomics revealed higher relative abundance of functional genes related to the oxidation pathway as compared to the 7α-dehydroxylation pathway. In addition, we demonstrated gut microbial-mediated hyocholic acid (HCA) and hyodeoxycholic acid (HDCA) formation from CDCA. In conclusion, we optimized a physiologically relevant ex vivo human faecal microbiota model to investigate gut microbial-mediated metabolism of primary BA and present a novel gut microbial-catalysed two-step pathway from CDCA to HCA and, subsequently, HDCA.
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Affiliation(s)
- Daniel Zhi Wei Ng
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore
| | - Adrian Low
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Amanda Jia Hui Tan
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore
| | - Jia Hui Ong
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore
| | - Wit Thun Kwa
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Jonathan Wei Jie Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore; Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, E7, 15 Kent Ridge Crescent, Singapore, 119276, Singapore; Division of Gastroenterology & Hepatology, Department of Medicine, National University Hospital, Singapore.
| | - Eric Chun Yong Chan
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore.
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3
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Cheng W, Zhu N, Wang J, Yang R. A role of gut microbiota metabolites in HLA-E and NKG2 blockage immunotherapy against tumors: new insights for clinical application. Front Immunol 2024; 15:1331518. [PMID: 39229258 PMCID: PMC11368731 DOI: 10.3389/fimmu.2024.1331518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 07/16/2024] [Indexed: 09/05/2024] Open
Abstract
One of major breakthroughs in immunotherapy against tumor is from blocking immune checkpoint molecules on tumor and reactive T cells. The development of CTLA-4 and PD-1 blockage antibodies has triggered to search for additional effective therapeutic strategies. This causes recent findings that blocking the interaction of checkpoint molecule NKG2A in NK and CD8 T cells with HLA-E in tumors is effective in defensing tumors. Interestingly, gut microbiota also affects this immune checkpoint immunotherapy against tumor. Gut microbiota such as bacteria can contribute to the regulation of host immune response and homeostasis. They not only promote the differentiation and function of immunosuppressive cells but also the inflammatory cells through the metabolites such as tryptophan (Trp) and bile acid (BA) metabolites as well as short chain fatty acids (SCFAs). These gut microbiota metabolites (GMMs) educated immune cells can affect the differentiation and function of effective CD8 and NK cells. Notably, these metabolites also directly affect the activity of CD8 and NK cells. Furthermore, the expression of CD94/NKG2A in the immune cells and/or their ligand HLA-E in the tumor cells is also regulated by gut microbiota associated immune factors. These findings offer new insights for the clinical application of gut microbiota in precise and/or personalized treatments of tumors. In this review, we will discuss the impacts of GMMs and GMM educated immune cells on the activity of effective CD8 and NK cells and the expression of CD94/NKG2A in immune cells and/or their ligand HLA-E in tumor cells.
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Affiliation(s)
- Wenyue Cheng
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Ningning Zhu
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Juanjuan Wang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Rongcun Yang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
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4
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Chen Y, Chaudhari SN, Harris DA, Roberts CF, Moscalu A, Mathur V, Zhao L, Tavakkoli A, Devlin AS, Sheu EG. A small intestinal bile acid modulates the gut microbiome to improve host metabolic phenotypes following bariatric surgery. Cell Host Microbe 2024; 32:1315-1330.e5. [PMID: 39043190 PMCID: PMC11332993 DOI: 10.1016/j.chom.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/27/2024] [Accepted: 06/20/2024] [Indexed: 07/25/2024]
Abstract
Bariatric surgical procedures such as sleeve gastrectomy (SG) provide effective type 2 diabetes (T2D) remission in human patients. Previous work demonstrated that gastrointestinal levels of the bacterial metabolite lithocholic acid (LCA) are decreased after SG in mice and humans. Here, we show that LCA worsens glucose tolerance and impairs whole-body metabolism. We also show that taurodeoxycholic acid (TDCA), which is the only bile acid whose concentration increases in the murine small intestine post-SG, suppresses the bacterial bile acid-inducible (bai) operon and production of LCA both in vitro and in vivo. Treatment of diet-induced obese mice with TDCA reduces LCA levels and leads to microbiome-dependent improvements in glucose handling. Moreover, TDCA abundance is decreased in small intestinal tissue from T2D patients. This work reveals that TDCA is an endogenous inhibitor of LCA production and suggests that TDCA may contribute to the glucoregulatory effects of bariatric surgery.
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Affiliation(s)
- Yingjia Chen
- Laboratory for Surgical and Metabolic Research, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Snehal N Chaudhari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David A Harris
- Laboratory for Surgical and Metabolic Research, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Cullen F Roberts
- Laboratory for Surgical and Metabolic Research, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Andrei Moscalu
- Laboratory for Surgical and Metabolic Research, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vasundhara Mathur
- Laboratory for Surgical and Metabolic Research, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lei Zhao
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ali Tavakkoli
- Laboratory for Surgical and Metabolic Research, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - A Sloan Devlin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Eric G Sheu
- Laboratory for Surgical and Metabolic Research, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA.
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5
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Wei X, Yao C, He X, Li J, Wang Y, Wang C, Chen Q, Ma X, Guo DA. Biotransformation of chenodeoxycholic acid by human intestinal fungi and the agonistic effects on FXR. PHYTOCHEMISTRY 2024; 224:114162. [PMID: 38797255 DOI: 10.1016/j.phytochem.2024.114162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Bile acids play a vital role in modulating host metabolism, with chenodeoxycholic acid (CDCA) standing out as a primary bile acid that naturally activates farnesoid X receptor (FXR). In this study, we investigated the microbial transformations of CDCA by seven human intestinal fungal species. Our findings revealed that hydroxylation and dehydrogenation were the most prevalent metabolic pathways. Incubation of CDCA with Rhizopus microspores (PT2906) afforded eight undescribed compounds (6-13) alongside five known analogs (1-5) which were elucidated by HRESI-MS and NMR data. Notably, compounds 8, 12 and 13 exhibited an inhibitory effect on FXR in contrast to the FXR activation observed with CDCA in vitro assays. This study shone a light on the diverse transformations of CDCA by intestinal fungi, unveiling potential modulators of FXR activity with implications for host metabolism.
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Affiliation(s)
- Xuemei Wei
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Changliang Yao
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xin He
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiayuan Li
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yulu Wang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chao Wang
- College of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Xiaochi Ma
- College of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, 116044, China.
| | - De-An Guo
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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6
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Lee MH, Nuccio SP, Mohanty I, Hagey LR, Dorrestein PC, Chu H, Raffatellu M. How bile acids and the microbiota interact to shape host immunity. Nat Rev Immunol 2024:10.1038/s41577-024-01057-x. [PMID: 39009868 DOI: 10.1038/s41577-024-01057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/17/2024]
Abstract
Bile acids are increasingly appearing in the spotlight owing to their novel impacts on various host processes. Similarly, there is growing attention on members of the microbiota that are responsible for bile acid modifications. With recent advances in technology enabling the discovery and continued identification of microbially conjugated bile acids, the chemical complexity of the bile acid landscape in the body is increasing at a rapid pace. In this Review, we summarize our current understanding of how bile acids and the gut microbiota interact to modulate immune responses during homeostasis and disease, with a particular focus on the gut.
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Affiliation(s)
- Michael H Lee
- Division of Host-Microbe Systems and Therapeutics, Department of Paediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sean-Paul Nuccio
- Division of Host-Microbe Systems and Therapeutics, Department of Paediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Hiutung Chu
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Paediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA.
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7
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Kim S, Seo SU, Kweon MN. Gut microbiota-derived metabolites tune host homeostasis fate. Semin Immunopathol 2024; 46:2. [PMID: 38990345 PMCID: PMC11239740 DOI: 10.1007/s00281-024-01012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/15/2024] [Indexed: 07/12/2024]
Abstract
The gut microbiota, housing trillions of microorganisms within the gastrointestinal tract, has emerged as a critical regulator of host health and homeostasis. Through complex metabolic interactions, these microorganisms produce a diverse range of metabolites that substantially impact various physiological processes within the host. This review aims to delve into the intricate relationships of gut microbiota-derived metabolites and their influence on the host homeostasis. We will explore how these metabolites affect crucial aspects of host physiology, including metabolism, mucosal integrity, and communication among gut tissues. Moreover, we will spotlight the potential therapeutic applications of targeting these metabolites to restore and sustain host equilibrium. Understanding the intricate interplay between gut microbiota and their metabolites is crucial for developing innovative strategies to promote wellbeing and improve outcomes of chronic diseases.
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Affiliation(s)
- Seungil Kim
- Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine / Asan Medical Center, Seoul, Republic of Korea
- Digestive Diseases Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang-Uk Seo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Mi-Na Kweon
- Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine / Asan Medical Center, Seoul, Republic of Korea.
- Digestive Diseases Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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8
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Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. Nat Rev Gastroenterol Hepatol 2024; 21:493-516. [PMID: 38575682 DOI: 10.1038/s41575-024-00914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/06/2024]
Abstract
Bile acids regulate nutrient absorption and mitochondrial function, they establish and maintain gut microbial community composition and mediate inflammation, and they serve as signalling molecules that regulate appetite and energy homeostasis. The observation that there are hundreds of bile acids, especially many amidated bile acids, necessitates a revision of many of the classical descriptions of bile acids and bile acid enzyme functions. For example, bile salt hydrolases also have transferase activity. There are now hundreds of known modifications to bile acids and thousands of bile acid-associated genes, especially when including the microbiome, distributed throughout the human body (for example, there are >2,400 bile salt hydrolases alone). The fact that so much of our genetic and small-molecule repertoire, in both amount and diversity, is dedicated to bile acid function highlights the centrality of bile acids as key regulators of metabolism and immune homeostasis, which is, in large part, communicated via the gut microbiome.
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Affiliation(s)
- Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Celeste Allaband
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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9
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Li XJ, Fang C, Zhao RH, Zou L, Miao H, Zhao YY. Bile acid metabolism in health and ageing-related diseases. Biochem Pharmacol 2024; 225:116313. [PMID: 38788963 DOI: 10.1016/j.bcp.2024.116313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Bile acids (BAs) have surpassed their traditional roles as lipid solubilizers and regulators of BA homeostasis to emerge as important signalling molecules. Recent research has revealed a connection between microbial dysbiosis and metabolism disruption of BAs, which in turn impacts ageing-related diseases. The human BAs pool is primarily composed of primary BAs and their conjugates, with a smaller proportion consisting of secondary BAs. These different BAs exert complex effects on health and ageing-related diseases through several key nuclear receptors, such as farnesoid X receptor and Takeda G protein-coupled receptor 5. However, the underlying molecular mechanisms of these effects are still debated. Therefore, the modulation of signalling pathways by regulating synthesis and composition of BAs represents an interesting and novel direction for potential therapies of ageing-related diseases. This review provides an overview of synthesis and transportion of BAs in the healthy body, emphasizing its dependence on microbial community metabolic capacity. Additionally, the review also explores how ageing and ageing-related diseases affect metabolism and composition of BAs. Understanding BA metabolism network and the impact of their nuclear receptors, such as farnesoid X receptor and G protein-coupled receptor 5 agonists, paves the way for developing therapeutic agents for targeting BA metabolism in various ageing-related diseases, such as metabolic disorder, hepatic injury, cardiovascular disease, renal damage and neurodegenerative disease.
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Affiliation(s)
- Xiao-Jun Li
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China; Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, No.13, Shi Liu Gang Road, Haizhu District, Guangzhou, Guangdong 510315, China
| | - Chu Fang
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China
| | - Rui-Hua Zhao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China
| | - Liang Zou
- School of Food and Bioengineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, Sichuan 610106, China
| | - Hua Miao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China.
| | - Ying-Yong Zhao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China; National Key Laboratory of Kidney Diseases, First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Beijing 100853, China.
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10
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Marroncini G, Naldi L, Martinelli S, Amedei A. Gut-Liver-Pancreas Axis Crosstalk in Health and Disease: From the Role of Microbial Metabolites to Innovative Microbiota Manipulating Strategies. Biomedicines 2024; 12:1398. [PMID: 39061972 PMCID: PMC11273695 DOI: 10.3390/biomedicines12071398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
The functions of the gut are closely related to those of many other organs in the human body. Indeed, the gut microbiota (GM) metabolize several nutrients and compounds that, once released in the bloodstream, can reach distant organs, thus influencing the metabolic and inflammatory tone of the host. The main microbiota-derived metabolites responsible for the modulation of endocrine responses are short-chain fatty acids (SCFAs), bile acids and glucagon-like peptide 1 (GLP-1). These molecules can (i) regulate the pancreatic hormones (insulin and glucagon), (ii) increase glycogen synthesis in the liver, and (iii) boost energy expenditure, especially in skeletal muscles and brown adipose tissue. In other words, they are critical in maintaining glucose and lipid homeostasis. In GM dysbiosis, the imbalance of microbiota-related products can affect the proper endocrine and metabolic functions, including those related to the gut-liver-pancreas axis (GLPA). In addition, the dysbiosis can contribute to the onset of some diseases such as non-alcoholic steatohepatitis (NASH)/non-alcoholic fatty liver disease (NAFLD), hepatocellular carcinoma (HCC), and type 2 diabetes (T2D). In this review, we explored the roles of the gut microbiota-derived metabolites and their involvement in onset and progression of these diseases. In addition, we detailed the main microbiota-modulating strategies that could improve the diseases' development by restoring the healthy balance of the GLPA.
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Affiliation(s)
- Giada Marroncini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy; (G.M.); (L.N.)
| | - Laura Naldi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy; (G.M.); (L.N.)
| | - Serena Martinelli
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), 50139 Florence, Italy
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11
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Han L, Pendleton A, Singh A, Xu R, Scott SA, Palma JA, Diebold P, Malarney KP, Brito IL, Chang PV. Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases. Cell Chem Biol 2024:S2451-9456(24)00210-1. [PMID: 38889717 DOI: 10.1016/j.chembiol.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/25/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024]
Abstract
The gut microbiome possesses numerous biochemical enzymes that biosynthesize metabolites that impact human health. Bile acids comprise a diverse collection of metabolites that have important roles in metabolism and immunity. The gut microbiota-associated enzyme that is responsible for the gateway reaction in bile acid metabolism is bile salt hydrolase (BSH), which controls the host's overall bile acid pool. Despite the critical role of these enzymes, the ability to profile their activities and substrate preferences remains challenging due to the complexity of the gut microbiota, whose metaproteome includes an immense diversity of protein classes. Using a systems biochemistry approach employing activity-based probes, we have identified gut microbiota-associated BSHs that exhibit distinct substrate preferences, revealing that different microbes contribute to the diversity of the host bile acid pool. We envision that this chemoproteomic approach will reveal how secondary bile acid metabolism controlled by BSHs contributes to the etiology of various inflammatory diseases.
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Affiliation(s)
- Lin Han
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Adarsh Singh
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Raymond Xu
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Samantha A Scott
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Jaymee A Palma
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Peter Diebold
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA; Cornell Center for Immunology, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853, USA
| | - Pamela V Chang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA; Cornell Center for Immunology, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853, USA; Cornell Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853, USA.
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12
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Nie Q, Luo X, Wang K, Ding Y, Jia S, Zhao Q, Li M, Zhang J, Zhuo Y, Lin J, Guo C, Zhang Z, Liu H, Zeng G, You J, Sun L, Lu H, Ma M, Jia Y, Zheng MH, Pang Y, Qiao J, Jiang C. Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway. Cell 2024; 187:2717-2734.e33. [PMID: 38653239 DOI: 10.1016/j.cell.2024.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 02/05/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
Abstract
The gut microbiota has been found to play an important role in the progression of metabolic dysfunction-associated steatohepatitis (MASH), but the mechanisms have not been established. Here, by developing a click-chemistry-based enrichment strategy, we identified several microbial-derived bile acids, including the previously uncharacterized 3-succinylated cholic acid (3-sucCA), which is negatively correlated with liver damage in patients with liver-tissue-biopsy-proven metabolic dysfunction-associated fatty liver disease (MAFLD). By screening human bacterial isolates, we identified Bacteroides uniformis strains as effective producers of 3-sucCA both in vitro and in vivo. By activity-based protein purification and identification, we identified an enzyme annotated as β-lactamase in B. uniformis responsible for 3-sucCA biosynthesis. Furthermore, we found that 3-sucCA is a lumen-restricted metabolite and alleviates MASH by promoting the growth of Akkermansia muciniphila. Together, our data offer new insights into the gut microbiota-liver axis that may be leveraged to augment the management of MASH.
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Affiliation(s)
- Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; State Key Laboratory of Food Science and Resources, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Kai Wang
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Shumi Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China
| | - Qixiang Zhao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Meng Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jinxin Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Yingying Zhuo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Chenghao Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Huiying Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Guangyi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jie You
- Department of Thyroid Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lulu Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China
| | - Yanxing Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China.
| | - Ming-Hua Zheng
- MAFLD Research Center, Department of Hepatology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Key Laboratory of Diagnosis and Treatment for the Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China; Translational Medicine Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China.
| | - Yanli Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Jie Qiao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
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13
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Han L, Xu R, Conwell AN, Takahashi S, Parasar B, Chang PV. Bile Salt Hydrolase Activity-Based Probes for Monitoring Gut Microbial Bile Acid Metabolism. Chembiochem 2024; 25:e202300821. [PMID: 38564329 PMCID: PMC11102598 DOI: 10.1002/cbic.202300821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/17/2024] [Accepted: 04/01/2024] [Indexed: 04/04/2024]
Abstract
Bile acids are bioactive metabolites that are biotransformed into secondary bile acids by the gut microbiota, a vast consortium of microbes that inhabit the intestines. The first step in intestinal secondary bile acid metabolism is carried out by a critical enzyme, bile salt hydrolase (BSH), that catalyzes the gateway reaction that precedes all subsequent microbial metabolism of these important metabolites. As gut microbial metabolic activity is difficult to probe due to the complex nature of the gut microbiome, approaches are needed to profile gut microbiota-associated enzymes such as BSH. Here, we develop a panel of BSH activity-based probes (ABPs) to determine how changes in diurnal rhythmicity of gut microbiota-associated metabolism affects BSH activity and substrate preference. This panel of covalent probes enables determination of BSH activity and substrate specificity from multiple gut anerobic bacteria derived from the human and mouse gut microbiome. We found that both gut microbiota-associated BSH activity and substrate preference is rhythmic, likely due to feeding patterns of the mice. These results indicate that this ABP-based approach can be used to profile changes in BSH activity in physiological and disease states that are regulated by circadian rhythms.
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Affiliation(s)
- Lin Han
- Department of Chemistry and Chemical Biology
| | - Raymond Xu
- Department of Microbiology and Immunology
| | | | | | | | - Pamela V Chang
- Department of Chemistry and Chemical Biology
- Department of Microbiology and Immunology
- Cornell Center for Immunology
- Cornell Institute of Host-Microbe Interactions and Disease
- Cornell Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853
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14
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Ridlon JM, Gaskins HR. Another renaissance for bile acid gastrointestinal microbiology. Nat Rev Gastroenterol Hepatol 2024; 21:348-364. [PMID: 38383804 DOI: 10.1038/s41575-024-00896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2024] [Indexed: 02/23/2024]
Abstract
The field of bile acid microbiology in the gastrointestinal tract is going through a current rebirth after a peak of activity in the late 1970s and early 1980s. This renewed activity is a result of many factors, including the discovery near the turn of the century that bile acids are potent signalling molecules and technological advances in next-generation sequencing, computation, culturomics, gnotobiology, and metabolomics. We describe the current state of the field with particular emphasis on questions that have remained unanswered for many decades in both bile acid synthesis by the host and metabolism by the gut microbiota. Current knowledge of established enzymatic pathways, including bile salt hydrolase, hydroxysteroid dehydrogenases involved in the oxidation and epimerization of bile acid hydroxy groups, the Hylemon-Bjӧrkhem pathway of bile acid C7-dehydroxylation, and the formation of secondary allo-bile acids, is described. We cover aspects of bile acid conjugation and esterification as well as evidence for bile acid C3-dehydroxylation and C12-dehydroxylation that are less well understood but potentially critical for our understanding of bile acid metabolism in the human gut. The physiological consequences of bile acid metabolism for human health, important caveats and cautionary notes on experimental design and interpretation of data reflecting bile acid metabolism are also explored.
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Affiliation(s)
- Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Advanced Study, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Biomedical and Translational Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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15
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Liu Y, Cheng YY, Thompson J, Zhou Z, Vivas EI, Warren MF, Rey FE, Anantharaman K, Venturelli OS. Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.10.523442. [PMID: 37986770 PMCID: PMC10659395 DOI: 10.1101/2023.01.10.523442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The arginine dihydrolase pathway (arc operon) present in a subset of diverse human gut species enables arginine catabolism. This specialized metabolic pathway can alter environmental pH and nitrogen availability, which in turn could shape gut microbiota inter-species interactions. By exploiting synthetic control of gene expression, we investigated the role of the arc operon in probiotic Escherichia coli Nissle 1917 on human gut community assembly and health-relevant metabolite profiles in vitro and in the murine gut. By stabilizing environmental pH, the arc operon reduced variability in community composition across different initial pH perturbations. The abundance of butyrate producing bacteria were altered in response to arc operon activity and butyrate production was enhanced in a physiologically relevant pH range. While the presence of the arc operon altered community dynamics, it did not impact production of short chain fatty acids. Dynamic computational modeling of pH-mediated interactions reveals the quantitative contribution of this mechanism to community assembly. In sum, our framework to quantify the contribution of molecular pathways and mechanism modalities on microbial community dynamics and functions could be applied more broadly.
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Affiliation(s)
- Yiyi Liu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
- Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew F. Warren
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | | | - Ophelia S. Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
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16
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Han L, Pendleton A, Singh A, Xu R, Scott SA, Palma JA, Diebold P, Malarney KP, Brito IL, Chang PV. Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587558. [PMID: 38617281 PMCID: PMC11014516 DOI: 10.1101/2024.04.01.587558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The gut microbiome possesses numerous biochemical enzymes that biosynthesize metabolites that impact human health. Bile acids comprise a diverse collection of metabolites that have important roles in metabolism and immunity. The gut microbiota-associated enzyme that is responsible for the gateway reaction in bile acid metabolism is bile salt hydrolase (BSH), which controls the host's overall bile acid pool. Despite the critical role of these enzymes, the ability to profile their activities and substrate preferences remains challenging due to the complexity of the gut microbiota, whose metaproteome includes an immense diversity of protein classes. Using a systems biochemistry approach employing activity-based probes, we have identified gut microbiota-associated BSHs that exhibit distinct substrate preferences, revealing that different microbes contribute to the diversity of the host bile acid pool. We envision that this chemoproteomic approach will reveal how secondary bile acid metabolism controlled by BSHs contributes to the etiology of various inflammatory diseases.
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Affiliation(s)
- Lin Han
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | | | - Adarsh Singh
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Raymond Xu
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
| | - Samantha A Scott
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
| | - Jaymee A Palma
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853
| | - Peter Diebold
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853
| | - Pamela V Chang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853
- Cornell Center for Innovative Proteomics, Cornell University, Ithaca, NY 14853
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17
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Ay Ü, Leníček M, Haider RS, Classen A, van Eijk H, Koelfat KV, van der Kroft G, Neumann UP, Hoffmann C, Bolm C, Olde Damink SW, Schaap FG. Microbially conjugated bile salts found in human bile activate the bile salt receptors TGR5 and FXR. Hepatol Commun 2024; 8:e0383. [PMID: 38517202 PMCID: PMC10962891 DOI: 10.1097/hc9.0000000000000383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/06/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Bile salts of hepatic and microbial origin mediate interorgan cross talk in the gut-liver axis. Here, we assessed whether the newly discovered class of microbial bile salt conjugates (MBSCs) activate the main host bile salt receptors (Takeda G protein-coupled receptor 5 [TGR5] and farnesoid X receptor [FXR]) and enter the human systemic and enterohepatic circulation. METHODS N-amidates of (chenodeoxy) cholic acid and leucine, tyrosine, and phenylalanine were synthesized. Receptor activation was studied in cell-free and cell-based assays. MBSCs were quantified in mesenteric and portal blood and bile of patients undergoing pancreatic surgery. RESULTS MBSCs were activating ligands of TGR5 as evidenced by recruitment of Gsα protein, activation of a cAMP-driven reporter, and diminution of lipopolysaccharide-induced cytokine release from macrophages. Intestine-enriched and liver-enriched FXR isoforms were both activated by MBSCs, provided that a bile salt importer was present. The affinity of MBSCs for TGR5 and FXR was not superior to host-derived bile salt conjugates. Individual MBSCs were generally not detected (ie, < 2.5 nmol/L) in human mesenteric or portal blood, but Leu-variant and Phe-variant were readily measurable in bile, where MBSCs comprised up to 213 ppm of biliary bile salts. CONCLUSIONS MBSCs activate the cell surface receptor TGR5 and the transcription factor FXR and are substrates for intestinal (apical sodium-dependent bile acid transporter) and hepatic (Na+ taurocholate co-transporting protein) transporters. Their entry into the human circulation is, however, nonsubstantial. Given low systemic levels and a surplus of other equipotent bile salt species, the studied MBSCs are unlikely to have an impact on enterohepatic TGR5/FXR signaling in humans. The origin and function of biliary MBSCs remain to be determined.
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Affiliation(s)
- Ümran Ay
- Department of General, Visceral and Transplant Surgery, University Hospital Aachen, Aachen, Germany
| | - Martin Leníček
- Institute of Medical Biochemistry and Laboratory Diagnostics, Faculty General Hospital and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Raphael S. Haider
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, Jena, Germany
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen’s Medical Center, University of Nottingham, Nottingham, United Kingdom
- Center of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Midlands, United Kingdom
| | - Arno Classen
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Hans van Eijk
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Kiran V.K. Koelfat
- Department of General, Visceral and Transplant Surgery, University Hospital Aachen, Aachen, Germany
| | - Gregory van der Kroft
- Department of General, Visceral and Transplant Surgery, University Hospital Aachen, Aachen, Germany
| | - Ulf. P. Neumann
- Department of General, Visceral and Transplant Surgery, University Hospital Aachen, Aachen, Germany
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Carsten Hoffmann
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, Jena, Germany
| | - Carsten Bolm
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Steven W.M. Olde Damink
- Department of General, Visceral and Transplant Surgery, University Hospital Aachen, Aachen, Germany
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Frank G. Schaap
- Department of General, Visceral and Transplant Surgery, University Hospital Aachen, Aachen, Germany
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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18
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Mohanty I, Mannochio-Russo H, Schweer JV, El Abiead Y, Bittremieux W, Xing S, Schmid R, Zuffa S, Vasquez F, Muti VB, Zemlin J, Tovar-Herrera OE, Moraïs S, Desai D, Amin S, Koo I, Turck CW, Mizrahi I, Kris-Etherton PM, Petersen KS, Fleming JA, Huan T, Patterson AD, Siegel D, Hagey LR, Wang M, Aron AT, Dorrestein PC. The underappreciated diversity of bile acid modifications. Cell 2024; 187:1801-1818.e20. [PMID: 38471500 DOI: 10.1016/j.cell.2024.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/30/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.
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Affiliation(s)
- Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Joshua V Schweer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium
| | - Shipei Xing
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, Vancouver, BC, Canada
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Felipe Vasquez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Valentina B Muti
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, USA; Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Omar E Tovar-Herrera
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Dhimant Desai
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - Shantu Amin
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - Imhoi Koo
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Christoph W Turck
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Kraepelinstrasse 2-10, Munich 80804, Germany; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Penny M Kris-Etherton
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Kristina S Petersen
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jennifer A Fleming
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, Vancouver, BC, Canada
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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19
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Gentry EC, Collins SL, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu HH, Zuffa S, Yan T, Avila-Pacheco J, Plichta DR, Aron AT, Wang M, Jarmusch AK, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland BS, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish CB, Xavier RJ, Chu H, Baker ES, Patterson AD, Knight R, Siegel D, Dorrestein PC. Reverse metabolomics for the discovery of chemical structures from humans. Nature 2024; 626:419-426. [PMID: 38052229 PMCID: PMC10849969 DOI: 10.1038/s41586-023-06906-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
Determining the structure and phenotypic context of molecules detected in untargeted metabolomics experiments remains challenging. Here we present reverse metabolomics as a discovery strategy, whereby tandem mass spectrometry spectra acquired from newly synthesized compounds are searched for in public metabolomics datasets to uncover phenotypic associations. To demonstrate the concept, we broadly synthesized and explored multiple classes of metabolites in humans, including N-acyl amides, fatty acid esters of hydroxy fatty acids, bile acid esters and conjugated bile acids. Using repository-scale analysis1,2, we discovered that some conjugated bile acids are associated with inflammatory bowel disease (IBD). Validation using four distinct human IBD cohorts showed that cholic acids conjugated to Glu, Ile/Leu, Phe, Thr, Trp or Tyr are increased in Crohn's disease. Several of these compounds and related structures affected pathways associated with IBD, such as interferon-γ production in CD4+ T cells3 and agonism of the pregnane X receptor4. Culture of bacteria belonging to the Bifidobacterium, Clostridium and Enterococcus genera produced these bile amidates. Because searching repositories with tandem mass spectrometry spectra has only recently become possible, this reverse metabolomics approach can now be used as a general strategy to discover other molecules from human and animal ecosystems.
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Affiliation(s)
- Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Stephanie L Collins
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA
| | - Allison K Stewart
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | | | - Hsueh-Han Lu
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Tingting Yan
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Fuhua Hao
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Mashette Syrkin-Nikolau
- Division of Gastroenterology, Department of Pediatrics, Rady Children's Hospital University of California San Diego, La Jolla, CA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Brigid S Boland
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Amy Hemperly
- Division of Gastroenterology, Department of Pediatrics, Rady Children's Hospital University of California San Diego, La Jolla, CA, USA
| | - Niels Vande Casteele
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
- CU-UCSD, Center for Mucosal Immunology, Allergy and Vaccine Development, University of California, San Diego, La Jolla, California, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
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20
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Liu C, Du MX, Xie LS, Wang WZ, Chen BS, Yun CY, Sun XW, Luo X, Jiang Y, Wang K, Jiang MZ, Qiao SS, Sun M, Cui BJ, Huang HJ, Qu SP, Li CK, Wu D, Wang LS, Jiang C, Liu HW, Liu SJ. Gut commensal Christensenella minuta modulates host metabolism via acylated secondary bile acids. Nat Microbiol 2024; 9:434-450. [PMID: 38233647 DOI: 10.1038/s41564-023-01570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/29/2023] [Indexed: 01/19/2024]
Abstract
A strong correlation between gut microbes and host health has been observed in numerous gut metagenomic cohort studies. However, the underlying mechanisms governing host-microbe interactions in the gut remain largely unknown. Here we report that the gut commensal Christensenella minuta modulates host metabolism by generating a previously undescribed class of secondary bile acids with 3-O-acylation substitution that inhibit the intestinal farnesoid X receptor. Administration of C. minuta alleviated features of metabolic disease in high fat diet-induced obese mice associated with a significant increase in these acylated bile acids, which we refer to as 3-O-acyl-cholic acids. Specific knockout of intestinal farnesoid X receptor in mice counteracted the beneficial effects observed in their wild-type counterparts. Finally, we showed that 3-O-acyl-CAs were prevalent in healthy humans but significantly depleted in patients with type 2 diabetes. Our findings indicate a role for C. minuta and acylated bile acids in metabolic diseases.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Meng-Xuan Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Li-Sheng Xie
- College of Life Science, Hebei University, Baoding, P. R. China
| | - Wen-Zhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Bao-Song Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Chu-Yu Yun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Yu Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Shan-Shan Qiao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Min Sun
- The Second Hospital of Shandong University, Jinan, P. R. China
| | - Bao-Juan Cui
- The Second Hospital of Shandong University, Jinan, P. R. China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | | | | | - Dalei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Lu-Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China.
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, P. R. China.
| | - Hong-Wei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
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21
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Rimal B, Collins SL, Tanes CE, Rocha ER, Granda MA, Solanki S, Hoque NJ, Gentry EC, Koo I, Reilly ER, Hao F, Paudel D, Singh V, Yan T, Kim MS, Bittinger K, Zackular JP, Krausz KW, Desai D, Amin S, Coleman JP, Shah YM, Bisanz JE, Gonzalez FJ, Vanden Heuvel JP, Wu GD, Zemel BS, Dorrestein PC, Weinert EE, Patterson AD. Bile salt hydrolase catalyses formation of amine-conjugated bile acids. Nature 2024; 626:859-863. [PMID: 38326609 PMCID: PMC10881385 DOI: 10.1038/s41586-023-06990-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
Abstract
Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect host-mediated metabolic processes1-6; however, the bacterial gene(s) responsible for their production remain unknown. Herein, we report that bile salt hydrolase (BSH) possesses dual functions in bile acid metabolism. Specifically, we identified a previously unknown role for BSH as an amine N-acyltransferase that conjugates amines to bile acids, thus forming bacterial bile acid amidates (BBAAs). To characterize this amine N-acyltransferase BSH activity, we used pharmacological inhibition of BSH, heterologous expression of bsh and mutants in Escherichia coli and bsh knockout and complementation in Bacteroides fragilis to demonstrate that BSH generates BBAAs. We further show in a human infant cohort that BBAA production is positively correlated with the colonization of bsh-expressing bacteria. Lastly, we report that in cell culture models, BBAAs activate host ligand-activated transcription factors including the pregnane X receptor and the aryl hydrocarbon receptor. These findings enhance our understanding of how gut bacteria, through the promiscuous actions of BSH, have a significant role in regulating the bile acid metabolic network.
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Affiliation(s)
- Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Stephanie L Collins
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ceylan E Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edson R Rocha
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Megan A Granda
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Sumeet Solanki
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Nushrat J Hoque
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Imhoi Koo
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Erin R Reilly
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Fuhua Hao
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Devendra Paudel
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, USA
| | - Vishal Singh
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, USA
| | - Tingting Yan
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Min Soo Kim
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristopher W Krausz
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dhimant Desai
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - Shantu Amin
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - James P Coleman
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Jordan E Bisanz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- One Health Microbiome Center, Huck Life Sciences Institute, University Park, PA, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John P Vanden Heuvel
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
- INDIGO Biosciences, Inc., State College, PA, USA
| | - Gary D Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Babette S Zemel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA.
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
- One Health Microbiome Center, Huck Life Sciences Institute, University Park, PA, USA.
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22
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Guzior DV, Okros M, Shivel M, Armwald B, Bridges C, Fu Y, Martin C, Schilmiller AL, Miller WM, Ziegler KM, Sims MD, Maddens ME, Graham SF, Hausinger RP, Quinn RA. Bile salt hydrolase acyltransferase activity expands bile acid diversity. Nature 2024; 626:852-858. [PMID: 38326608 DOI: 10.1038/s41586-024-07017-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
Bile acids (BAs) are steroid detergents in bile that contribute to the absorption of fats and fat-soluble vitamins while shaping the gut microbiome because of their antimicrobial properties1-4. Here we identify the enzyme responsible for a mechanism of BA metabolism by the gut microbiota involving amino acid conjugation to the acyl-site of BAs, thus producing a diverse suite of microbially conjugated bile acids (MCBAs). We show that this transformation is mediated by acyltransferase activity of bile salt hydrolase (bile salt hydrolase/transferase, BSH/T). Clostridium perfringens BSH/T rapidly performed acyl transfer when provided various amino acids and taurocholate, glycocholate or cholate, with an optimum at pH 5.3. Amino acid conjugation by C. perfringens BSH/T was diverse, including all proteinaceous amino acids except proline and aspartate. MCBA production was widespread among gut bacteria, with strain-specific amino acid use. Species with similar BSH/T amino acid sequences had similar conjugation profiles and several bsh/t alleles correlated with increased conjugation diversity. Tertiary structure mapping of BSH/T followed by mutagenesis experiments showed that active site structure affects amino acid selectivity. These MCBA products had antimicrobial properties, where greater amino acid hydrophobicity showed greater antimicrobial activity. Inhibitory concentrations of MCBAs reached those measured natively in the mammalian gut. MCBAs fed to mice entered enterohepatic circulation, in which liver and gallbladder concentrations varied depending on the conjugated amino acid. Quantifying MCBAs in human faecal samples showed that they reach concentrations equal to or greater than secondary and primary BAs and were reduced after bariatric surgery, thus supporting MCBAs as a significant component of the BA pool that can be altered by changes in gastrointestinal physiology. In conclusion, the inherent acyltransferase activity of BSH/T greatly diversifies BA chemistry, creating a set of previously underappreciated metabolites with the potential to affect the microbiome and human health.
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Affiliation(s)
- Douglas V Guzior
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology, Genetics & Immunology, Michigan State University, East Lansing, MI, USA
| | - Maxwell Okros
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Madison Shivel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Bruin Armwald
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Christopher Bridges
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology, Genetics & Immunology, Michigan State University, East Lansing, MI, USA
| | - Yousi Fu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Christian Martin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Anthony L Schilmiller
- Mass Spectrometry and Metabolomics Core, Michigan State University, East Lansing, MI, USA
| | - Wendy M Miller
- Corewell Health, William Beaumont University Hospital, Royal Oak, MI, USA
- Oakland University, William Beaumont School of Medicine, Rochester, MI, USA
| | - Kathryn M Ziegler
- Corewell Health, William Beaumont University Hospital, Royal Oak, MI, USA
- Oakland University, William Beaumont School of Medicine, Rochester, MI, USA
| | - Matthew D Sims
- Corewell Health, William Beaumont University Hospital, Royal Oak, MI, USA
- Oakland University, William Beaumont School of Medicine, Rochester, MI, USA
| | - Michael E Maddens
- Corewell Health, William Beaumont University Hospital, Royal Oak, MI, USA
- Oakland University, William Beaumont School of Medicine, Rochester, MI, USA
| | - Stewart F Graham
- Corewell Health, William Beaumont University Hospital, Royal Oak, MI, USA
- Oakland University, William Beaumont School of Medicine, Rochester, MI, USA
- Beaumont Research Institute, Royal Oak, MI, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology, Genetics & Immunology, Michigan State University, East Lansing, MI, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
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23
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Roach J, Mital R, Haffner JJ, Colwell N, Coats R, Palacios HM, Liu Z, Godinho JLP, Ness M, Peramuna T, McCall LI. Microbiome metabolite quantification methods enabling insights into human health and disease. Methods 2024; 222:81-99. [PMID: 38185226 DOI: 10.1016/j.ymeth.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.
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Affiliation(s)
- Jarrod Roach
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Rohit Mital
- Department of Biology, University of Oklahoma
| | - Jacob J Haffner
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Nathan Colwell
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Randy Coats
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Horvey M Palacios
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Zongyuan Liu
- Department of Chemistry and Biochemistry, University of Oklahoma
| | | | - Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma; Department of Chemistry and Biochemistry, San Diego State University.
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24
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Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RDC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 2024; 9:336-345. [PMID: 38316926 PMCID: PMC10847041 DOI: 10.1038/s41564-023-01575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024]
Abstract
microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Andres M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Sara L Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula C Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Matthew F Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Daniel Alvarado-Villalobos
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, MD, USA
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Nyon, Switzerland
| | | | - Berenike C Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Daniel Petras
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department for Metabolomics, Kiel University, Kiel, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- King's College London, London, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | | | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jerry J Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Hector H F Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sidnee E Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
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25
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Wang D, Ye A, Jiang N. The role of bacteria in gallstone formation. Folia Microbiol (Praha) 2024; 69:33-40. [PMID: 38252338 DOI: 10.1007/s12223-024-01131-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Gallstones are a prevalent biliary system disorder that is particularly common in women. They can lead to various complications, such as biliary colic, infection, cholecystitis, and even gallbladder cancer. However, the etiology of gallstones remains incompletely understood. The significant role of bacteria in gallstone formation has been demonstrated in recent studies. Certain bacteria not only influence bile composition and the gallbladder environment but also actively participate in stone formation by producing enzymes such as β-glucuronidase and mucus. Therefore, this review aimed to analyze the mechanisms involving the types and quantities of bacteria involved in gallstone formation, providing valuable references for understanding the etiology and clinical treatment of gallstones.
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Affiliation(s)
- Danfeng Wang
- Health Management (Physical Examination) Section of Hubei Third People's Hospital Affiliated to Jianghan University, Wuhan, 430034, People's Republic of China
| | - Aihui Ye
- Wuchang District Shouyilu Street Community Health Service Center, Wuhan, 430061, People's Republic of China
| | - Ni Jiang
- Health Management (Physical Examination) Section of Hubei Third People's Hospital Affiliated to Jianghan University, Wuhan, 430034, People's Republic of China.
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26
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Mullowney MW, Fiebig A, Schnizlein MK, McMillin M, Rose AR, Koval J, Rubin D, Dalal S, Sogin ML, Chang EB, Sidebottom AM, Crosson S. Microbially catalyzed conjugation of GABA and tyramine to bile acids. J Bacteriol 2024; 206:e0042623. [PMID: 38174933 PMCID: PMC10810215 DOI: 10.1128/jb.00426-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Bile acids (BAs) are cholesterol-derived molecules that aid in digestion and nutrient absorption, regulate host metabolic processes, and influence physiology of the gut microbiota. Both the host and its microbiome contribute to enzymatic modifications that shape the chemical diversity of BAs in the gut. Several bacterial species have been reported to conjugate standard amino acids to BAs, but it was not known if bacteria conjugate BAs to other amine classes. Here, we show that Bacteroides fragilis strain P207, isolated from a bacterial bloom in the J-pouch of a patient with ulcerative colitis pouchitis, conjugates standard amino acids and the neuroactive amines γ-aminobutyric acid (GABA) and tyramine to deoxycholic acid. We extended this analysis to other human gut isolates and identified species that are competent to conjugate GABA and tyramine to primary and secondary BAs, and further identified diverse BA-GABA and BA-tyramine amides in human stool. A longitudinal metabolomic analysis of J-pouch contents of the patient from whom B. fragilis P207 was isolated revealed highly reduced levels of secondary bile acids and a shifting BA amide profile before, during, and after onset of pouchitis, including temporal changes in several BA-GABA amides. Treatment of pouchitis with ciprofloxacin was associated with a marked reduction of nearly all BA amides in the J-pouch. Our study expands the known repertoire of conjugated bile acids produced by bacteria to include BA conjugates to GABA and tyramine and demonstrates that these molecules are present in the human gut. IMPORTANCE BAs are modified in multiple ways by host enzymes and the microbiota to produce a chemically diverse set of molecules that assist in the digestive process and impact many physiological functions. This study reports the discovery of bacterial species that conjugate the neuroactive amines, GABA and tyramine, to primary and secondary BAs. We further present evidence that BA-GABA and BA-tyramine conjugates are present in the human gut, and document a shifting BA-GABA profile in a human pouchitis patient before, during, and after inflammation and antibiotic treatment. GABA and tyramine are common metabolic products of the gut microbiota and potent neuroactive molecules. GABA- and tyramine-conjugated BAs may influence receptor-mediated regulatory mechanisms of humans and their gut microbes, and absorption of these molecules and their entry into enterohepatic circulation may impact host physiology at distal tissue sites. This study defines new conjugated bile acids in the human gut.
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Affiliation(s)
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Amber R. Rose
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Jason Koval
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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27
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Joyce SA, Clarke DJ. Microbial metabolites as modulators of host physiology. Adv Microb Physiol 2024; 84:83-133. [PMID: 38821635 DOI: 10.1016/bs.ampbs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.
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Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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McMillan AS, Foley MH, Perkins CE, Theriot CM. Loss of Bacteroides thetaiotaomicron bile acid-altering enzymes impacts bacterial fitness and the global metabolic transcriptome. Microbiol Spectr 2024; 12:e0357623. [PMID: 38018975 PMCID: PMC10783122 DOI: 10.1128/spectrum.03576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Recent work on bile salt hydrolases (BSHs) in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it are not well understood. In this study, we set out to define if and how Bacteroides thetaiotaomicron (B. theta) uses its BSHs and hydroxysteroid dehydrogenase to modify bile acids to provide a fitness advantage for itself in vitro and in vivo. Genes encoding bile acid-altering enzymes were able to impact how B. theta responds to nutrient limitation in the presence of bile acids, specifically carbohydrate metabolism, affecting many polysaccharide utilization loci. This suggests that B. theta may be able to shift its metabolism, specifically its ability to target different complex glycans including host mucin, when it comes into contact with specific bile acids in the gut.
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Affiliation(s)
- Arthur S. McMillan
- Department of Biological Sciences, Genetics Program, College of Science, North Carolina State University, Raleigh, North Carolina, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Matthew H. Foley
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Caroline E. Perkins
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Casey M. Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Correa Lopes B, Chen CC, Sung CH, Ishii PE, Medina LFDC, Gaschen FP, Suchodolski JS, Pilla R. Correlation between Peptacetobacter hiranonis, the baiCD Gene, and Secondary Bile Acids in Dogs. Animals (Basel) 2024; 14:216. [PMID: 38254385 PMCID: PMC10812727 DOI: 10.3390/ani14020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Bile acid metabolism is a key pathway modulated by intestinal microbiota. Peptacetobacter (Clostridium) hiranonis has been described as the main species responsible for the conversion of primary into secondary fecal unconjugated bile acids (fUBA) in dogs. This multi-step biochemical pathway is encoded by the bile acid-inducible (bai) operon. We aimed to assess the correlation between P. hiranonis abundance, the abundance of one specific gene of the bai operon (baiCD), and secondary fUBA concentrations. In this retrospective study, 133 fecal samples were analyzed from 24 dogs. The abundances of P. hiranonis and baiCD were determined using qPCR. The concentration of fUBA was measured by gas chromatography-mass spectrometry. The baiCD abundance exhibited a strong positive correlation with secondary fUBA (ρ = 0.7377, 95% CI (0.6461, 0.8084), p < 0.0001). Similarly, there was a strong correlation between P. hiranonis and secondary fUBA (ρ = 0.6658, 95% CI (0.5555, 0.7532), p < 0.0001). Animals displaying conversion of fUBA and lacking P. hiranonis were not observed. These results suggest P. hiranonis is the main converter of primary to secondary bile acids in dogs.
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Affiliation(s)
- Bruna Correa Lopes
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Chih-Chun Chen
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Chi-Hsuan Sung
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Patricia Eri Ishii
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Luis Fernando da Costa Medina
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Frederic P. Gaschen
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
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30
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Calton CM, Carothers K, Ramamurthy S, Jagadish N, Phanindra B, Garcia A, Viswanathan VK, Halpern MD. Clostridium scindens exacerbates experimental necrotizing enterocolitis via upregulation of the apical sodium-dependent bile acid transporter. Am J Physiol Gastrointest Liver Physiol 2024; 326:G25-G37. [PMID: 37933481 PMCID: PMC11208032 DOI: 10.1152/ajpgi.00102.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in premature infants. Evidence indicates that bile acid homeostasis is disrupted during NEC: ileal bile acid levels are elevated in animals with experimental NEC, as is expression of the apical sodium-dependent bile acid transporter (Asbt). In addition, bile acids, which are synthesized in the liver, are extensively modified by the gut microbiome, including via the conversion of primary bile acids to more cytotoxic secondary forms. We hypothesized that the addition of bile acid-modifying bacteria would increase susceptibility to NEC in a neonatal rat model of the disease. The secondary bile acid-producing species Clostridium scindens exacerbated both incidence and severity of NEC. C. scindens upregulated the bile acid transporter Asbt and increased levels of intraenterocyte bile acids. Treatment with C. scindens also altered bile acid profiles and increased hydrophobicity of the ileal intracellular bile acid pool. The ability of C. scindens to enhance NEC requires bile acids, as pharmacological sequestration of ileal bile acids protects animals from developing disease. These findings indicate that bile acid-modifying bacteria can contribute to NEC pathology and provide additional evidence for the role of bile acids in the pathophysiology of experimental NEC.NEW & NOTEWORTHY Necrotizing enterocolitis (NEC), a life-threatening gastrointestinal emergency in premature infants, is characterized by dysregulation of bile acid homeostasis. We demonstrate that administering the secondary bile acid-producing bacterium Clostridium scindens enhances NEC in a neonatal rat model of the disease. C. scindens-enhanced NEC is dependent on bile acids and driven by upregulation of the ileal bile acid transporter Asbt. This is the first report of bile acid-modifying bacteria exacerbating experimental NEC pathology.
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Affiliation(s)
- Christine M Calton
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - Katelyn Carothers
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States
| | - Shylaja Ramamurthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States
| | - Neha Jagadish
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - Bhumika Phanindra
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - Anett Garcia
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - V K Viswanathan
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States
| | - Melissa D Halpern
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
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Pan Y, Zhang H, Li M, He T, Guo S, Zhu L, Tan J, Wang B. Novel approaches in IBD therapy: targeting the gut microbiota-bile acid axis. Gut Microbes 2024; 16:2356284. [PMID: 38769683 PMCID: PMC11110704 DOI: 10.1080/19490976.2024.2356284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and recurrent condition affecting the gastrointestinal tract. Disturbed gut microbiota and abnormal bile acid (BA) metabolism are notable in IBD, suggesting a bidirectional relationship. Specifically, the diversity of the gut microbiota influences BA composition, whereas altered BA profiles can disrupt the microbiota. IBD patients often exhibit increased primary bile acid and reduced secondary bile acid concentrations due to a diminished bacteria population essential for BA metabolism. This imbalance activates BA receptors, undermining intestinal integrity and immune function. Consequently, targeting the microbiota-BA axis may rectify these disturbances, offering symptomatic relief in IBD. Here, the interplay between gut microbiota and bile acids (BAs) is reviewed, with a particular focus on the role of gut microbiota in mediating bile acid biotransformation, and contributions of the gut microbiota-BA axis to IBD pathology to unveil potential novel therapeutic avenues for IBD.
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Affiliation(s)
- Yinping Pan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Haojie Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Tingjing He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Sihao Guo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological & Chemical engineering, Chongqing University of Education, Chongqing, PR China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
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32
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McMillan AS, Theriot CM. Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics. Gut Microbes 2024; 16:2393766. [PMID: 39224076 PMCID: PMC11376424 DOI: 10.1080/19490976.2024.2393766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Clostridioides difficile is a major nosocomial pathogen, causing significant morbidity and mortality worldwide. Antibiotic usage, a major risk factor for Clostridioides difficile infection (CDI), disrupts the gut microbiota, allowing C. difficile to proliferate and cause infection, and can often lead to recurrent CDI (rCDI). Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as effective treatments for rCDI and aim to restore colonization resistance provided by a healthy gut microbiota. However, much is still unknown about the mechanisms mediating their success. Bile acids, extensively modified by gut microbes, affect C. difficile's germination, growth, and toxin production while also shaping the gut microbiota and influencing host immune responses. Additionally, microbial interactions, such as nutrient competition and cross-feeding, contribute to colonization resistance against C. difficile and may contribute to the success of microbiota-focused therapeutics. Bile acids as well as other microbial mediated interactions could have implications for other diseases being treated with microbiota-focused therapeutics. This review focuses on the intricate interplay between bile acid modifications, microbial ecology, and host responses with a focus on C. difficile, hoping to shed light on how to move forward with the development of new microbiota mediated therapeutic strategies to combat rCDI and other intestinal diseases.
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Affiliation(s)
- Arthur S McMillan
- Genetics Program, Department of Biological Sciences, College of Science, North Carolina State University, Raleigh, NC, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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33
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Zhang H, Xie Y, Cao F, Song X. Gut microbiota-derived fatty acid and sterol metabolites: biotransformation and immunomodulatory functions. Gut Microbes 2024; 16:2382336. [PMID: 39046079 PMCID: PMC11271093 DOI: 10.1080/19490976.2024.2382336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/26/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
Commensal microorganisms in the human gut produce numerous metabolites by using small molecules derived from the host or diet as precursors. Host or dietary lipid molecules are involved in energy metabolism and maintaining the structural integrity of cell membranes. Notably, gut microbes can convert these lipids into bioactive signaling molecules through their biotransformation and synthesis pathways. These microbiota-derived lipid metabolites can affect host physiology by influencing the body's immune and metabolic processes. This review aims to summarize recent advances in the microbial transformation and host immunomodulatory functions of these lipid metabolites, with a special focus on fatty acids and steroids produced by our gut microbiota.
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Affiliation(s)
- Haohao Zhang
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yadong Xie
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Fei Cao
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xinyang Song
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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34
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Sun H, Su X, Liu Y, Li G, Du Q. Roseburia intestinalis relieves intrahepatic cholestasis of pregnancy through bile acid/FXR-FGF15 in rats. iScience 2023; 26:108392. [PMID: 38025767 PMCID: PMC10679810 DOI: 10.1016/j.isci.2023.108392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Previous research has demonstrated significant differences in intestinal flora between pregnant women with intrahepatic cholestasis of pregnancy (ICP) and healthy pregnant women. The objective of our study is to identify the key bacteria involved in ICP rats and explore the underlying mechanism. We established an ICP rat model and collected rat feces for metagenomic sequencing and found that Roseburia intestinalis (R.I) is the key bacteria in ICP. Transplantation of R.I improved phenotypes associated with ICP through the bile acid/farnesoid X receptor-fibroblast growth factor 15 (FXR-FGF15) signaling pathway. We used the FXR antagonist Z-Guggulsterone (Z-Gu) to verify the key role of FXR in ICP and found that Z-Gu reversed the benefits of R.I on ICP rats. Our research highlights the important role of intestinal flora in the pathogenesis of ICP and provides a novel approach for its treatment.
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Affiliation(s)
- Hanxiang Sun
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xiujuan Su
- Clinical Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yang Liu
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Guohua Li
- Department of Reproductive Immunology, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Qiaoling Du
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
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35
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Mullowney MW, Fiebig A, Schnizlein MK, McMillin M, Rose AR, Koval J, Rubin D, Dalal S, Sogin ML, Chang EB, Sidebottom AM, Crosson S. Microbially-catalyzed conjugation of GABA and tyramine to bile acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559407. [PMID: 37808758 PMCID: PMC10557584 DOI: 10.1101/2023.09.25.559407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Bile acids (BAs) are cholesterol-derived molecules that aid in digestion and nutrient absorption, regulate host metabolic processes, and influence physiology of the gut microbiota. Both the host and its microbiome contribute to enzymatic modifications that shape the chemical diversity of BAs in the gut. Several bacterial species have been reported to conjugate standard amino acids to BAs, but it was not known if bacteria conjugate BAs to other amine classes. Here, we show that Bacteroides fragilis strain P207, isolated from a bacterial bloom in the J-pouch of a patient with ulcerative colitis (UC) pouchitis, conjugates standard amino acids and the neuroactive amines γ-aminobutyric acid (GABA) and tyramine to deoxycholic acid. We extended this analysis to other human gut isolates and identified species that are competent to conjugate GABA and tyramine to primary and secondary BAs, and further identified diverse BA-GABA and BA-tyramine amides in human stool. A longitudinal metabolomic analysis of J-pouch contents of the patient from whom B. fragilis P207 was isolated revealed highly reduced levels of secondary bile acids and a shifting BA amide profile before, during, and after onset of pouchitis, including temporal changes in several BA-GABA amides. Treatment of pouchitis with ciprofloxacin was associated with a marked reduction of nearly all BA amides in the J-pouch. Our study expands the known repertoire of conjugated bile acids produced by bacteria to include BA conjugates to GABA and tyramine and demonstrates that these molecules are present in the human gut.
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Affiliation(s)
- Michael W Mullowney
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Amber R Rose
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Jason Koval
- Department of Medicine, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - David Rubin
- Department of Medicine, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | | | - Eugene B Chang
- Department of Medicine, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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36
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Malarney KP, Chang PV. Electrostatic Interactions Dictate Bile Salt Hydrolase Substrate Preference. Biochemistry 2023; 62:3076-3084. [PMID: 37883888 PMCID: PMC10727128 DOI: 10.1021/acs.biochem.3c00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The human intestines are colonized by trillions of microbes, comprising the gut microbiota, which produce diverse small molecule metabolites and modify host metabolites, such as bile acids, that regulate host physiology. Biosynthesized in the liver, bile acids are conjugated with glycine or taurine and secreted into the intestines, where gut microbial bile salt hydrolases (BSHs) deconjugate the amino acid to produce unconjugated bile acids that serve as precursors for secondary bile acid metabolites. Among these include a recently discovered class of microbially conjugated bile acids (MCBAs), wherein alternative amino acids are conjugated onto bile acids. To elucidate the metabolic potential of MCBAs, we performed detailed kinetic studies to investigate the preference of BSHs for host-conjugated bile acids and MCBAs. We identified a BSH that exhibits positive cooperativity uniquely for MCBAs containing an aromatic side chain. Further molecular modeling and phylogenetic analyses indicated that the BSH preference for aromatic MCBAs is due to a substrate-specific cation-π interaction and is predicted to be widespread among human gut microbial BSHs.
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Affiliation(s)
- Kien P. Malarney
- Department of Microbiology, Cornell University, 930 Campus Road, Ithaca, NY 14853, United States
| | - Pamela V. Chang
- Department of Microbiology and Immunology, Cornell University, 930 Campus Road, Ithaca, NY 14853, United States; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States; Cornell Center for Immunology, Cornell University, Ithaca, NY 14853, United States; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, 930 Campus Road, Ithaca, NY 14853, United States
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37
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Ma Y, Cao Y, Song X, Xu W, Luo Z, Shan J, Zhou J. Integration of semi-empirical MS/MS library with characteristic features for the annotation of novel amino acid-conjugated bile acids. Analyst 2023; 148:5380-5389. [PMID: 37743718 DOI: 10.1039/d3an01237a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Recently, amino acids other than glycine and taurine were found to be conjugated with bile acids by the gut microbiome in mouse and human. As potential diagnostic markers for inflammatory bowel disease and farnesoid X receptor agonists, their physiological effects and mechanisms, however, remain to be elucidated. A tool for the rapid and comprehensive annotation of such new metabolites is required. Thus, we developed a semi-empirical MS/MS library for bile acids conjugated with 18 common amino acids, including alanine, arginine, asparagine, aspartate, glutamine, glutamate, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine. To investigate their fragmentation rules, these amino acids were chemically conjugated with lithocholic acid, deoxycholic acid, and cholic acid, and their accurate-mass MS/MS spectra were acquired. The common fragmentation patterns from the amino acid moieties were combined with 10 general bile acid skeletons to generate a semi-empirical MS/MS library of 180 structures. Software named BAFinder 2.0 was developed to combine the semi-empirical library in negative mode and the characteristic fragments in positive mode for automatic unknown identification. As a proof of concept, this workflow was applied to the LC-MS/MS analysis of the feces of human, beagle dogs, and rats. In total, 171 common amino acid-conjugated bile acids were annotated and 105 of them were confirmed with the retention times of synthesized compounds. To explore other potential bile acid conjugates, user-defined small molecules were in-silico conjugated with bile acids and searched in the fecal dataset. Four novel bile acid conjugates were discovered, including D-Ala-D-Ala, Lys(iso)-Gly, L-2-aminobutyric acid, and ornithine.
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Affiliation(s)
- Yan Ma
- National Institute of Biological Sciences, Beijing, Beijing 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Yang Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China.
| | - Xiaocui Song
- National Institute of Biological Sciences, Beijing, Beijing 102206, China.
| | - Weichen Xu
- Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zichen Luo
- Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jinjun Shan
- Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jingjie Zhou
- The Affiliated Jiangyin Hospital of Nanjing University of Chinese Medicine, Jiangyin 214400, China
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38
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Stewart AK, Foley MH, Dougherty MK, McGill SK, Gulati AS, Gentry EC, Hagey LR, Dorrestein PC, Theriot CM, Dodds JN, Baker ES. Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems. Anal Chem 2023; 95:15357-15366. [PMID: 37796494 PMCID: PMC10613829 DOI: 10.1021/acs.analchem.3c03057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Bile acids play key roles in nutrient uptake, inflammation, signaling, and microbiome composition. While previous bile acid analyses have primarily focused on profiling 5 canonical primary and secondary bile acids and their glycine and taurine amino acid-bile acid (AA-BA) conjugates, recent studies suggest that many other microbial conjugated bile acids (or MCBAs) exist. MCBAs are produced by the gut microbiota and serve as biomarkers, providing information about early disease onset and gut health. Here we analyzed 8 core bile acids synthetically conjugated with 22 proteinogenic and nonproteogenic amino acids totaling 176 MCBAs. Since many of the conjugates were isomeric and only 42 different m/z values resulted from the 176 MCBAs, a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) was used for their separation. Their molecular characteristics were then used to create an in-house extended bile acid library for a combined total of 182 unique compounds. Additionally, ∼250 rare bile acid extracts were also assessed to provide additional resources for bile acid profiling and identification. This library was then applied to healthy mice dosed with antibiotics and humans having fecal microbiota transplantation (FMT) to assess the MCBA presence and changes in the gut before and after each perturbation.
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Affiliation(s)
- Allison K Stewart
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Matthew H Foley
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Michael K Dougherty
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States
| | - Sarah K McGill
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States
| | - Ajay S Gulati
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lee R Hagey
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, California 92093, United States
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology and Pediatrics, University of California at San Diego, La Jolla, California 92093, United States
| | - Casey M Theriot
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - James N Dodds
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27607, United States
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27607, United States
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Cao Y, Ibrahim KS, Li X, Wong A, Wu Y, Yu XD, Zhou X, Tan Z, He Z, Craft JA, Shu X. Chinese medicine, Qijudihuang pill, mediates cholesterol metabolism and regulates gut microbiota in high-fat diet-fed mice, implications for age-related macular degeneration. Front Immunol 2023; 14:1274401. [PMID: 37901244 PMCID: PMC10602650 DOI: 10.3389/fimmu.2023.1274401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/21/2023] [Indexed: 10/31/2023] Open
Abstract
Background Traditional Chinese Medicines have been used for thousands of years but without any sound empirical basis. One such preparation is the Qijudihuang pill (QP), a mixture of eight herbs, that has been used in China for the treatment of various conditions including age-related macular degeneration (AMD), the most common cause of blindness in the aged population. In order to explain the mechanism behind the effect of QP, we used an AMD model of high-fat diet (HFD) fed mice to investigate cholesterol homeostasis, oxidative stress, inflammation and gut microbiota. Methods Mice were randomly divided into three groups, one group was fed with control diet (CD), the other two groups were fed with high-fat-diet (HFD). One HFD group was treated with QP, both CD and the other HFD groups were treated with vehicles. Tissue samples were collected after the treatment. Cholesterol levels in retina, retinal pigment epithelium (RPE), liver and serum were determined using a commercial kit. The expression of enzymes involved in cholesterol metabolism, inflammation and oxidative stress was measured with qRT-PCR. Gut microbiota was analyzed using 16S rRNA sequencing. Results In the majority of the lipid determinations, analytes were elevated by HFD but this was reversed by QP. Cholesterol metabolism including the enzymes of bile acid (BA) formation was suppressed by HFD but again this was reversed by QP. BAs play a major role in signaling between host and microbiome and this is disrupted by HFD resulting in major changes in the composition of colonic bacterial communities. Associated with these changes are predictions of the metabolic pathway complexity and abundance of individual pathways. These concerned substrate breakdowns, energy production and the biosynthesis of pro-inflammatory factors but were changed back to control characteristics by QP. Conclusion We propose that the ability of QP to reverse these HFD-induced effects is related to mechanisms acting to lower cholesterol level, oxidative stress and inflammation, and to modulate gut microbiota.
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Affiliation(s)
- Yanqun Cao
- Pu Ai Medical School, Shaoyang University, Shaoyang, Hunan, China
| | - Khalid S. Ibrahim
- Department of Biological and Biomedical Sciences , Glasgow Caledonian University, Glasgow, United Kingdom
- Department of Biology, Faculty of Science, University of Zakho, Zakho, Iraq
| | - Xing Li
- Pu Ai Medical School, Shaoyang University, Shaoyang, Hunan, China
| | - Aileen Wong
- Department of Biological and Biomedical Sciences , Glasgow Caledonian University, Glasgow, United Kingdom
| | - Yi Wu
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Xu-Dong Yu
- Pu Ai Medical School, Shaoyang University, Shaoyang, Hunan, China
| | - Xinzhi Zhou
- Department of Biological and Biomedical Sciences , Glasgow Caledonian University, Glasgow, United Kingdom
| | - Zhoujin Tan
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhiming He
- Pu Ai Medical School, Shaoyang University, Shaoyang, Hunan, China
| | - John A. Craft
- Department of Biological and Biomedical Sciences , Glasgow Caledonian University, Glasgow, United Kingdom
| | - Xinhua Shu
- Pu Ai Medical School, Shaoyang University, Shaoyang, Hunan, China
- Department of Biological and Biomedical Sciences , Glasgow Caledonian University, Glasgow, United Kingdom
- Department of Vision Science , Glasgow Caledonian University, Glasgow, United Kingdom
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40
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Tang H, Zha Z, Tan Y, Li Y, Jiao Y, Yang B, Xiong Q, Yin H, Wang H. Extraction and characterization of polysaccharide from fermented mycelia of Coriolus versicolor and its efficacy for treating nonalcoholic fatty liver disease. Int J Biol Macromol 2023; 248:125951. [PMID: 37499724 DOI: 10.1016/j.ijbiomac.2023.125951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 07/09/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023]
Abstract
Coriolus versicolor, a popular traditional Chinese medicinal herb, is widely used in China to treat spleen and liver diseases; however, the beneficial effects of C. versicolor polysaccharides (CVPs) on nonalcoholic fatty liver disease (NAFLD) remain elusive. Herein we isolated and purified a novel CVP (molecular weight, 17,478 Da) from fermented mycelium powder. This CVP was composed of mannose, galacturonic acid, glucose, galactose, xylose, and fucose at a molar ratio of 22:1:8:15:10:3. Methylation, gas chromatography-mass spectrometry, and nuclear magnetic resonance analyses indicated that the CVP backbone consisted of →1)-β-D-Man-(6,4→1)-α-D-Gal-(3→1)-α-D-Man-(4→1)-α-D-Gal-(6→, with branches of →1)-α-D-Glc-(6→1)-α-D-Man-(4,3→1)-β-D-Xyl-(2→1)-β-D-Glc on the O-6 position of →1)-β-D-Man-(6,4→ of the main chain. The secondary branches linked to the O-4 position of →1)-α-D-Man-(4,3→ with the chain of →1)-α-D-Fuc-(4→1)-α-D-Man. Further, CVP treatment alleviated the symptoms of NAFLD in an HFD-induced mice model. CVP altered gut microbiota, predominantly suppressing microbes associated with bile acids both in the serum and cecal contents. In vitro data showed that CVP reduced HFD-induced hyperlipidemia via farnesoid X receptor. Our results improve our understanding of the mechanisms underlying the cholesterol- and lipid-lowering effects of CVP and indicate that CVP is a promising candidate for NAFLD therapy.
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Affiliation(s)
- Huiling Tang
- Department of Scientific Research Office, Jiangsu Food & Pharmaceutical Science College, Huai'an 223003, People's Republic of China
| | - Zhengqi Zha
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yanfang Tan
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yuan Li
- Department of Scientific Research Office, Jiangsu Food & Pharmaceutical Science College, Huai'an 223003, People's Republic of China
| | - Yuzhi Jiao
- Department of Scientific Research Office, Jiangsu Food & Pharmaceutical Science College, Huai'an 223003, People's Republic of China
| | - Baowei Yang
- Department of Scientific Research Office, Jiangsu Food & Pharmaceutical Science College, Huai'an 223003, People's Republic of China
| | - Qingping Xiong
- Jiangsu Key Laboratory of Regional Resource Exploitation and Medicinal Research, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Hongping Yin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
| | - Hang Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
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Ridlon JM, Daniel SL, Gaskins HR. The Hylemon-Björkhem pathway of bile acid 7-dehydroxylation: history, biochemistry, and microbiology. J Lipid Res 2023; 64:100392. [PMID: 37211250 PMCID: PMC10382948 DOI: 10.1016/j.jlr.2023.100392] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023] Open
Abstract
Bile acids are detergents derived from cholesterol that function to solubilize dietary lipids, remove cholesterol from the body, and act as nutrient signaling molecules in numerous tissues with functions in the liver and gut being the best understood. Studies in the early 20th century established the structures of bile acids, and by mid-century, the application of gnotobiology to bile acids allowed differentiation of host-derived "primary" bile acids from "secondary" bile acids generated by host-associated microbiota. In 1960, radiolabeling studies in rodent models led to determination of the stereochemistry of the bile acid 7-dehydration reaction. A two-step mechanism was proposed, which we have termed the Samuelsson-Bergström model, to explain the formation of deoxycholic acid. Subsequent studies with humans, rodents, and cell extracts of Clostridium scindens VPI 12708 led to the realization that bile acid 7-dehydroxylation is a result of a multi-step, bifurcating pathway that we have named the Hylemon-Björkhem pathway. Due to the importance of hydrophobic secondary bile acids and the increasing measurement of microbial bai genes encoding the enzymes that produce them in stool metagenome studies, it is important to understand their origin.
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Affiliation(s)
- Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA; Center for Advanced Study, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
| | - Steven L Daniel
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Biomedical and Translational Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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42
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McMillan AS, Foley MH, Perkins CE, Theriot CM. Loss of Bacteroides thetaiotaomicron bile acid altering enzymes impact bacterial fitness and the global metabolic transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546749. [PMID: 37425690 PMCID: PMC10327073 DOI: 10.1101/2023.06.27.546749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Bacteroides thetaiotaomicron (B. theta) is a Gram-negative gut bacterium that encodes enzymes that alter the bile acid pool in the gut. Primary bile acids are synthesized by the host liver and are modified by gut bacteria. B. theta encodes two bile salt hydrolases (BSHs), as well as a hydroxysteroid dehydrogenase (HSDH). We hypothesize that B. theta modifies the bile acid pool in the gut to provide a fitness advantage for itself. To investigate each gene's role, different combinations of genes encoding bile acid altering enzymes (bshA, bshB, and hsdhA) were knocked out by allelic exchange, including a triple KO. Bacterial growth and membrane integrity assays were done in the presence and absence of bile acids. To explore if B. theta's response to nutrient limitation changes due to the presence of bile acid altering enzymes, RNASeq analysis of WT and triple KO strains in the presence and absence of bile acids was done. WT B. theta is more sensitive to deconjugated bile acids (CA, CDCA, and DCA) compared to the triple KO, which also decreased membrane integrity. The presence of bshB is detrimental to growth in conjugated forms of CDCA and DCA. RNA-Seq analysis also showed bile acid exposure impacts multiple metabolic pathways in B. theta, but DCA significantly increases expression of many genes in carbohydrate metabolism, specifically those in polysaccharide utilization loci or PULs, in nutrient limited conditions. This study suggests that bile acids B. theta encounters in the gut may signal the bacteria to increase or decrease its utilization of carbohydrates. Further study looking at the interactions between bacteria, bile acids, and the host may inform rationally designed probiotics and diets to ameliorate inflammation and disease. Importance Recent work on BSHs in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it is not well understood. In this study we set out to define if and how B. theta uses its BSHs and HSDH to modify bile acids to provide a fitness advantage for itself in vitro and in vivo. Genes encoding bile acid altering enzymes were able to impact how B. theta responds to nutrient limitation in the presence of bile acids, specifically carbohydrate metabolism, affecting many polysaccharide utilization loci (PULs). This suggests that B. theta may be able to shift its metabolism, specifically its ability to target different complex glycans including host mucin, when it comes into contact with specific bile acids in the gut. This work will aid in our understanding of how to rationally manipulate the bile acid pool and the microbiota to exploit carbohydrate metabolism in the context of inflammation and other GI diseases.
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Affiliation(s)
- Arthur S. McMillan
- Genetics Program, Department of Biological Sciences, College of Science
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Matthew H. Foley
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Caroline E. Perkins
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Casey M. Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
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Kalecký K, Bottiglieri T. Targeted metabolomic analysis in Parkinson's disease brain frontal cortex and putamen with relation to cognitive impairment. NPJ Parkinsons Dis 2023; 9:84. [PMID: 37270646 PMCID: PMC10239505 DOI: 10.1038/s41531-023-00531-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 05/22/2023] [Indexed: 06/05/2023] Open
Abstract
We performed liquid chromatography tandem mass spectrometry analysis with the targeted metabolomic kit Biocrates MxP Quant 500, in human brain cortex (Brodmann area 9) and putamen, to reveal metabolic changes characteristic of Parkinson's disease (PD) and PD-related cognitive decline. This case-control study involved 101 subjects (33 PD without dementia, 32 PD with dementia (cortex only), 36 controls). We found changes associated with PD, cognitive status, levodopa levels, and disease progression. The affected pathways include neurotransmitters, bile acids, homocysteine metabolism, amino acids, TCA cycle, polyamines, β-alanine metabolism, fatty acids, acylcarnitines, ceramides, phosphatidylcholines, and several microbiome-derived metabolites. Previously reported levodopa-related homocysteine accumulation in cortex still best explains the dementia status in PD, which can be modified by dietary supplementation. Further investigation is needed to reveal the exact mechanisms behind this pathological change.
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Affiliation(s)
- Karel Kalecký
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76712, USA.
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, 75204, USA.
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
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Su X, Gao Y, Yang R. Gut microbiota derived bile acid metabolites maintain the homeostasis of gut and systemic immunity. Front Immunol 2023; 14:1127743. [PMID: 37256134 PMCID: PMC10225537 DOI: 10.3389/fimmu.2023.1127743] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/07/2023] [Indexed: 06/01/2023] Open
Abstract
Bile acids (BAs) as cholesterol-derived molecules play an essential role in some physiological processes such as nutrient absorption, glucose homeostasis and regulation of energy expenditure. They are synthesized in the liver as primary BAs such as cholic acid (CA), chenodeoxycholic acid (CDCA) and conjugated forms. A variety of secondary BAs such as deoxycholic acid (DCA) and lithocholic acid (LCA) and their derivatives is synthesized in the intestine through the involvement of various microorganisms. In addition to essential physiological functions, BAs and their metabolites are also involved in the differentiation and functions of innate and adaptive immune cells such as macrophages (Macs), dendritic cells (DCs), myeloid derived suppressive cells (MDSCs), regulatory T cells (Treg), Breg cells, T helper (Th)17 cells, CD4 Th1 and Th2 cells, CD8 cells, B cells and NKT cells. Dysregulation of the BAs and their metabolites also affects development of some diseases such as inflammatory bowel diseases. We here summarize recent advances in how BAs and their metabolites maintain gut and systemic homeostasis, including the metabolism of the BAs and their derivatives, the role of BAs and their metabolites in the differentiation and function of immune cells, and the effects of BAs and their metabolites on immune-associated disorders.
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Affiliation(s)
- Xiaomin Su
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Yunhuan Gao
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Rongcun Yang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
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45
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Quinn RA, Martin C, Guzior DV. A multi-omic trip through the human gut. Nat Metab 2023; 5:720-721. [PMID: 37165175 DOI: 10.1038/s42255-023-00773-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
| | - Christian Martin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Douglas V Guzior
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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Folz J, Culver RN, Morales JM, Grembi J, Triadafilopoulos G, Relman DA, Huang KC, Shalon D, Fiehn O. Human metabolome variation along the upper intestinal tract. Nat Metab 2023; 5:777-788. [PMID: 37165176 PMCID: PMC10229427 DOI: 10.1038/s42255-023-00777-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/03/2023] [Indexed: 05/12/2023]
Abstract
Most processing of the human diet occurs in the small intestine. Metabolites in the small intestine originate from host secretions, plus the ingested exposome1 and microbial transformations. Here we probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy male and female participants. For this, we use a non-invasive, ingestible sampling device to collect and analyse 274 intestinal samples and 60 corresponding stool homogenates by combining five mass spectrometry assays2,3 and 16S rRNA sequencing. We identify 1,909 metabolites, including sulfonolipids and fatty acid esters of hydroxy fatty acids (FAHFA) lipids. We observe that stool and intestinal metabolomes differ dramatically. Food metabolites display trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites account for the largest inter-individual differences. Notably, two individuals who had taken antibiotics within 6 months before sampling show large variation in levels of bioactive FAHFAs and sulfonolipids and other microbially related metabolites. From inter-individual variation, we identify Blautia species as a candidate to be involved in FAHFA metabolism. In conclusion, non-invasive, in vivo sampling of the human small intestine and ascending colon under physiological conditions reveals links between diet, host and microbial metabolism.
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Affiliation(s)
- Jacob Folz
- West Coast Metabolomics Center, University of California, Davis, CA, USA
| | - Rebecca Neal Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jessica Grembi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, CA, USA.
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Shalon D, Culver RN, Grembi JA, Folz J, Treit PV, Shi H, Rosenberger FA, Dethlefsen L, Meng X, Yaffe E, Aranda-Díaz A, Geyer PE, Mueller-Reif JB, Spencer S, Patterson AD, Triadafilopoulos G, Holmes SP, Mann M, Fiehn O, Relman DA, Huang KC. Profiling the human intestinal environment under physiological conditions. Nature 2023; 617:581-591. [PMID: 37165188 PMCID: PMC10191855 DOI: 10.1038/s41586-023-05989-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2023] [Indexed: 05/12/2023]
Abstract
The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.
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Affiliation(s)
| | - Rebecca Neal Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Jessica A Grembi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob Folz
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - Peter V Treit
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Florian A Rosenberger
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Les Dethlefsen
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Eitan Yaffe
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B Mueller-Reif
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Sean Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - George Triadafilopoulos
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA
- Silicon Valley Neurogastroenterology and Motility Center, Mountain View, CA, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA.
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA.
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Collins SL, Stine JG, Bisanz JE, Okafor CD, Patterson AD. Bile acids and the gut microbiota: metabolic interactions and impacts on disease. Nat Rev Microbiol 2023; 21:236-247. [PMID: 36253479 DOI: 10.1038/s41579-022-00805-x] [Citation(s) in RCA: 210] [Impact Index Per Article: 210.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/08/2022]
Abstract
Despite decades of bile acid research, diverse biological roles for bile acids have been discovered recently due to developments in understanding the human microbiota. As additional bacterial enzymes are characterized, and the tools used for identifying new bile acids become increasingly more sensitive, the repertoire of bile acids metabolized and/or synthesized by bacteria continues to grow. Additionally, bile acids impact microbiome community structure and function. In this Review, we highlight how the bile acid pool is manipulated by the gut microbiota, how it is dependent on the metabolic capacity of the bacterial community and how external factors, such as antibiotics and diet, shape bile acid composition. It is increasingly important to understand how bile acid signalling networks are affected in distinct organs where the bile acid composition differs, and how these networks impact infectious, metabolic and neoplastic diseases. These advances have enabled the development of therapeutics that target imbalances in microbiota-associated bile acid profiles.
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Affiliation(s)
- Stephanie L Collins
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Jonathan G Stine
- Division of Gastroenterology and Hepatology, Department of Medicine, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA
- Department of Public Health Sciences, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA
- Penn State Health Liver Center, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Jordan E Bisanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, USA.
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA.
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49
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Foley MH, Walker ME, Stewart AK, O'Flaherty S, Gentry EC, Patel S, Beaty VV, Allen G, Pan M, Simpson JB, Perkins C, Vanhoy ME, Dougherty MK, McGill SK, Gulati AS, Dorrestein PC, Baker ES, Redinbo MR, Barrangou R, Theriot CM. Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. Nat Microbiol 2023; 8:611-628. [PMID: 36914755 PMCID: PMC10066039 DOI: 10.1038/s41564-023-01337-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/08/2023] [Indexed: 03/16/2023]
Abstract
Bile acids (BAs) mediate the crosstalk between human and microbial cells and influence diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate selectivity and impact on C. difficile remain elusive. Here we survey the diversity of BSHs in the gut commensals Lactobacillaceae, which are commonly used as probiotics, and other members of the human gut microbiome. We structurally pinpoint a loop that predicts BSH preferences for either glycine or taurine substrates. BSHs with varying specificities were shown to restrict C. difficile spore germination and growth in vitro and colonization in pre-clinical in vivo models of CDI. Furthermore, BSHs reshape the pool of microbial conjugated bile acids (MCBAs) in the murine gut, and these MCBAs can further restrict C. difficile virulence in vitro. The recognition of conjugated BAs by BSHs defines the resulting BA pool, including the expansive MCBAs. This work provides insights into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile.
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Affiliation(s)
- Matthew H Foley
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Morgan E Walker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison K Stewart
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shakshi Patel
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Violet V Beaty
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Garrison Allen
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Joshua B Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caroline Perkins
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Molly E Vanhoy
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Michael K Dougherty
- Department of Pediatrics, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah K McGill
- Department of Pediatrics, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ajay S Gulati
- Department of Pediatrics, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Departments of Biochemistry and Biophysics, and Microbiology and Immunology, and the Integrated Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Casey M Theriot
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
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50
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Murali A, Giri V, Zickgraf FM, Ternes P, Cameron HJ, Sperber S, Haake V, Driemert P, Kamp H, Funk-Weyer D, Sturla SJ, Rietjens IMCM, van Ravenzwaay B. Connecting Gut Microbial Diversity with Plasma Metabolome and Fecal Bile Acid Changes Induced by the Antibiotics Tobramycin and Colistin Sulfate. Chem Res Toxicol 2023; 36:598-616. [PMID: 36972423 DOI: 10.1021/acs.chemrestox.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The diversity of microbial species in the gut has a strong influence on health and development of the host. Further, there are indications that the variation in expression of gut bacterial metabolic enzymes is less diverse than the taxonomic profile, underlying the importance of microbiome functionality, particularly from a toxicological perspective. To address these relationships, the gut bacterial composition of Wistar rats was altered by a 28 day oral treatment with the antibiotics tobramycin or colistin sulfate. On the basis of 16S marker gene sequencing data, tobramycin was found to cause a strong reduction in the diversity and relative abundance of the microbiome, whereas colistin sulfate had only a marginal impact. Associated plasma and fecal metabolomes were characterized by targeted mass spectrometry-based profiling. The fecal metabolome of tobramycin-treated animals had a high number of significant alterations in metabolite levels compared to controls, particularly in amino acids, lipids, bile acids (BAs), carbohydrates, and energy metabolites. The accumulation of primary BAs and significant reduction of secondary BAs in the feces indicated that the microbial alterations induced by tobramycin inhibit bacterial deconjugation reactions. The plasma metabolome showed less, but still many alterations in the same metabolite groups, including reductions in indole derivatives and hippuric acid, and furthermore, despite marginal effects of colistin sulfate treatment, there were nonetheless systemic alterations also in BAs. Aside from these treatment-based differences, we also uncovered interindividual differences particularly centering on the loss of Verrucomicrobiaceae in the microbiome, but with no apparent associated metabolite alterations. Finally, by comparing the data set from this study with metabolome alterations in the MetaMapTox database, key metabolite alterations were identified as plasma biomarkers indicative of altered gut microbiomes resulting from a wide activity spectrum of antibiotics.
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Affiliation(s)
| | - Varun Giri
- BASF SE, Ludwigshafen am Rhein 67056, Rheinland-Pfalz, Germany
| | | | - Philipp Ternes
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Hunter James Cameron
- BASF Corporation Computational Biology (RTP), Research Triangle Park, 3500 Paramount Parkway, Morrisvile, North Carolina 27560, United States
| | - Saskia Sperber
- BASF SE, Ludwigshafen am Rhein 67056, Rheinland-Pfalz, Germany
| | - Volker Haake
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Peter Driemert
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Hennicke Kamp
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | | | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zurich CH 8092, Switzerland
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