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Mohamed ME, Saqr A, Staley C, Onyeaghala G, Teigen L, Dorr CR, Remmel RP, Guan W, Oetting WS, Matas AJ, Israni AK, Jacobson PA. Pharmacomicrobiomics: Immunosuppressive Drugs and Microbiome Interactions in Transplantation. Transplantation 2024; 108:1895-1910. [PMID: 38361239 PMCID: PMC11327386 DOI: 10.1097/tp.0000000000004926] [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] [Indexed: 02/17/2024]
Abstract
The human microbiome is associated with human health and disease. Exogenous compounds, including pharmaceutical products, are also known to be affected by the microbiome, and this discovery has led to the field of pharmacomicobiomics. The microbiome can also alter drug pharmacokinetics and pharmacodynamics, possibly resulting in side effects, toxicities, and unanticipated disease response. Microbiome-mediated effects are referred to as drug-microbiome interactions (DMI). Rapid advances in the field of pharmacomicrobiomics have been driven by the availability of efficient bacterial genome sequencing methods and new computational and bioinformatics tools. The success of fecal microbiota transplantation for recurrent Clostridioides difficile has fueled enthusiasm and research in the field. This review focuses on the pharmacomicrobiome in transplantation. Alterations in the microbiome in transplant recipients are well documented, largely because of prophylactic antibiotic use, and the potential for DMI is high. There is evidence that the gut microbiome may alter the pharmacokinetic disposition of tacrolimus and result in microbiome-specific tacrolimus metabolites. The gut microbiome also impacts the enterohepatic recirculation of mycophenolate, resulting in substantial changes in pharmacokinetic disposition and systemic exposure. The mechanisms of these DMI and the specific bacteria or communities of bacteria are under investigation. There are little or no human DMI data for cyclosporine A, corticosteroids, and sirolimus. The available evidence in transplantation is limited and driven by small studies of heterogeneous designs. Larger clinical studies are needed, but the potential for future clinical application of the pharmacomicrobiome in avoiding poor outcomes is high.
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Affiliation(s)
- Moataz E Mohamed
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | - Abdelrahman Saqr
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | | | - Guillaume Onyeaghala
- Hennepin Healthcare Research Institute, Minneapolis, MN
- Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Levi Teigen
- Department of Food Science and Nutrition, University of Minnesota, St Paul, MN
| | - Casey R Dorr
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
- Hennepin Healthcare Research Institute, Minneapolis, MN
- Department of Medicine, University of Minnesota, Minneapolis, MN
- Department of Medicine, Hennepin Healthcare, Minneapolis, MN
| | - Rory P Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN
| | - Ajay K Israni
- Hennepin Healthcare Research Institute, Minneapolis, MN
- Department of Medicine, Hennepin Healthcare, Minneapolis, MN
- Department of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
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2
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Favaron A, Abdalla Y, McCoubrey LE, Nandiraju LP, Shorthouse D, Gaisford S, Basit AW, Orlu M. Exploring the interactions of JAK inhibitor and S1P receptor modulator drugs with the human gut microbiome: Implications for colonic drug delivery and inflammatory bowel disease. Eur J Pharm Sci 2024; 200:106845. [PMID: 38971433 DOI: 10.1016/j.ejps.2024.106845] [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: 05/15/2024] [Revised: 06/24/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The gut microbiota is a complex ecosystem, home to hundreds of bacterial species and a vast repository of enzymes capable of metabolising a wide range of pharmaceuticals. Several drugs have been shown to affect negatively the composition and function of the gut microbial ecosystem. Janus Kinase (JAK) inhibitors and Sphingosine-1-phosphate (S1P) receptor modulators are drugs recently approved for inflammatory bowel disease through an immediate release formulation and would potentially benefit from colonic targeted delivery to enhance the local drug concentration at the diseased site. However, their impact on the human gut microbiota and susceptibility to bacterial metabolism remain unexplored. With the use of calorimetric, optical density measurements, and metagenomics next-generation sequencing, we show that JAK inhibitors (tofacitinib citrate, baricitinib, filgotinib) have a minor impact on the composition of the human gut microbiota, while ozanimod exerts a significant antimicrobial effect, leading to a prevalence of the Enterococcus genus and a markedly different metabolic landscape when compared to the untreated microbiota. Moreover, ozanimod, unlike the JAK inhibitors, is the only drug subject to enzymatic degradation by the human gut microbiota sourced from six healthy donors. Overall, given the crucial role of the gut microbiome in health, screening assays to investigate the interaction of drugs with the microbiota should be encouraged for the pharmaceutical industry as a standard in the drug discovery and development process.
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Affiliation(s)
- Alessia Favaron
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Youssef Abdalla
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Laura E McCoubrey
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | | | - David Shorthouse
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Simon Gaisford
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Abdul W Basit
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom.
| | - Mine Orlu
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom.
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3
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Maryam, Rehman MU, Hussain I, Tayara H, Chong KT. A graph neural network approach for predicting drug susceptibility in the human microbiome. Comput Biol Med 2024; 179:108729. [PMID: 38955124 DOI: 10.1016/j.compbiomed.2024.108729] [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: 04/22/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 07/04/2024]
Abstract
Recent studies have illuminated the critical role of the human microbiome in maintaining health and influencing the pharmacological responses of drugs. Clinical trials, encompassing approximately 150 drugs, have unveiled interactions with the gastrointestinal microbiome, resulting in the conversion of these drugs into inactive metabolites. It is imperative to explore the field of pharmacomicrobiomics during the early stages of drug discovery, prior to clinical trials. To achieve this, the utilization of machine learning and deep learning models is highly desirable. In this study, we have proposed graph-based neural network models, namely GCN, GAT, and GINCOV models, utilizing the SMILES dataset of drug microbiome. Our primary objective was to classify the susceptibility of drugs to depletion by gut microbiota. Our results indicate that the GINCOV surpassed the other models, achieving impressive performance metrics, with an accuracy of 93% on the test dataset. This proposed Graph Neural Network (GNN) model offers a rapid and efficient method for screening drugs susceptible to gut microbiota depletion and also encourages the improvement of patient-specific dosage responses and formulations.
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Affiliation(s)
- Maryam
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Mobeen Ur Rehman
- Khalifa University Center for Autonomous Robotic Systems (KUCARS), Khalifa University, United Arab Emirates
| | - Irfan Hussain
- Khalifa University Center for Autonomous Robotic Systems (KUCARS), Khalifa University, United Arab Emirates
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea.
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea; Advances Electronics and Information Research Centre, Jeonbuk National University, Jeonju, 54896, South Korea.
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4
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Deng MS, Huang STZ, Xu YN, Shao L, Wang ZG, Chen LJ, Huang WH. In vivo pharmacokinetics of ginsenoside compound K mediated by gut microbiota. PLoS One 2024; 19:e0307286. [PMID: 39178246 PMCID: PMC11343376 DOI: 10.1371/journal.pone.0307286] [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] [Received: 12/16/2023] [Accepted: 07/03/2024] [Indexed: 08/25/2024] Open
Abstract
Ginsenoside Compound K (GCK) is the main metabolite of natural protopanaxadiol ginsenosides with diverse pharmacological effects. Gut microbiota contributes to the biotransformation of GCK, while the effect of gut microbiota on the pharmacokinetics of GCK in vivo remains unclear. To illustrate the role of gut microbiota in GCK metabolism in vivo, a systematic investigation of the pharmacokinetics of GCK in specific pathogen free (SPF) and pseudo-germ-free (pseudo-GF) rats were conducted. Pseudo-GF rats were treated with non-absorbable antibiotics. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was validated for the quantification of GCK in rat plasma. Compared with SPF rats, the plasma concentration of GCK significantly increased after the gut microbiota depleted. The results showed that GCK absorption slowed down, Tmax delayed by 3.5 h, AUC0-11 increased by 1.3 times, CLz/F decreased by 0.6 times in pseudo-GF rats, and Cmax was 1.6 times higher than that of normal rats. The data indicated that gut microbiota played an important role in the pharmacokinetics of GCK in vivo.
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Affiliation(s)
- Ming-Si Deng
- Department of Stomatology, the Third Xiangya Hospital of Central South University, Central South University, Changsha, China
- Department of Orthodontics, Changsha Stomatological Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Su-tian-zi Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Ya-Ni Xu
- Department of Orthodontics, Changsha Stomatological Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Li Shao
- Department of Pharmacognosy, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zheng-Guang Wang
- Department of Spinal Surgery, the Third Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Liang-Jian Chen
- Department of Stomatology, the Third Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Wei-Hua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- FuRong Laboratory, Changsha, Hunan, China
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Kuo J, Uzunovic J, Jacobson A, Dourado M, Gierke S, Rajendram M, Keilberg D, Mar J, Stekol E, Curry J, Verstraete S, Lund J, Liang Y, Tamburini FB, Omattage NS, Masureel M, Rutherford ST, Hackos DH, Tan MW, Byrd AL, Keir ME, Skippington E, Storek KM. Toxigenic Clostridium perfringens Isolated from At-Risk Paediatric Inflammatory Bowel Disease Patients. J Crohns Colitis 2024; 18:985-1001. [PMID: 38267224 PMCID: PMC11302968 DOI: 10.1093/ecco-jcc/jjae016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/22/2023] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND AND AIMS This study aimed to identify microbial drivers of inflammatory bowel disease [IBD], by investigating mucosal-associated bacteria and their detrimental products in IBD patients. METHODS We directly cultured bacterial communities from mucosal biopsies from paediatric gastrointestinal patients and examined for pathogenicity-associated traits. Upon identifying Clostridium perfringens as toxigenic bacteria present in mucosal biopsies, we isolated strains and further characterized toxicity and prevalence. RESULTS Mucosal biopsy microbial composition differed from corresponding stool samples. C. perfringens was present in eight of nine patients' mucosal biopsies, correlating with haemolytic activity, but was not present in all corresponding stool samples. Large IBD datasets showed higher C. perfringens prevalence in stool samples of IBD adults [18.7-27.1%] versus healthy controls [5.1%]. In vitro, C. perfringens supernatants were toxic to cell types beneath the intestinal epithelial barrier, including endothelial cells, neuroblasts, and neutrophils, while the impact on epithelial cells was less pronounced, suggesting C. perfringens may be particularly damaging when barrier integrity is compromised. Further characterization using purified toxins and genetic insertion mutants confirmed perfringolysin O [PFO] toxin was sufficient for toxicity. Toxin RNA signatures were found in the original patient biopsies by PCR, suggesting intestinal production. C. perfringens supernatants also induced activation of neuroblast and dorsal root ganglion neurons in vitro, suggesting C. perfringens in inflamed mucosal tissue may directly contribute to abdominal pain, a frequent IBD symptom. CONCLUSIONS Gastrointestinal carriage of certain toxigenic C. perfringens may have an important pathogenic impact on IBD patients. These findings support routine monitoring of C. perfringens and PFO toxins and potential treatment in patients.
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Affiliation(s)
- James Kuo
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Jasmina Uzunovic
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Amanda Jacobson
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA, USA
| | - Michelle Dourado
- Department of Neuroscience, Genentech Inc., South San Francisco, CA, USA
| | - Sarah Gierke
- Department of Pathology, Genentech Inc., South San Francisco, CA, USA
| | - Manohary Rajendram
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Daniela Keilberg
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Jordan Mar
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech Inc., South San Francisco, CA, USA
| | - Emily Stekol
- Department of Pediatrics, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA, 94158, USA
| | - Joanna Curry
- Department of Pediatrics, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA, 94158, USA
| | - Sofia Verstraete
- Department of Pediatrics, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA, 94158, USA
| | - Jessica Lund
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Yuxin Liang
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Fiona B Tamburini
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech Inc., South San Francisco, CA, USA
| | - Natalie S Omattage
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - David H Hackos
- Department of Neuroscience, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Allyson L Byrd
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Mary E Keir
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech Inc., South San Francisco, CA, USA
| | - Elizabeth Skippington
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
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6
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Haange SB, Riesbeck S, Aldehoff AS, Engelmann B, Jensen Pedersen K, Castaneda-Monsalve V, Rolle-Kampczyk U, von Bergen M, Jehmlich N. Chemical mixture effects on the simplified human intestinal microbiota: Assessing xenobiotics at environmentally realistic concentrations. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134683. [PMID: 38820745 DOI: 10.1016/j.jhazmat.2024.134683] [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: 03/12/2024] [Revised: 05/07/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024]
Abstract
The microbial community present in our intestines is pivotal for converting indigestible substances into vital nutrients and signaling molecules such as short-chain fatty acids (SCFAs). These compounds have considerable influence over our immune system and the development of diverse human diseases. However, ingested environmental contaminants, known as xenobiotics, can upset the delicate balance of the microbial gut community and enzymatic processes, consequently affecting the host organism. In our study, we employed an in vitro bioreactor model system based on the simplified human microbiome model (SIHUMIx) to investigate the direct effects of specific xenobiotics, such as perfluorooctanoic acid (PFOA), perfluorohexanoic acid (PFHxA) and perfluorobutanoic acid (PFBA) or bisphenol S (BPS) and bisphenol F (BPF), either individually or in combination, on the microbiota. We observed increased SCFA production, particularly acetate and butyrate, with PFAS exposure. Metaproteomics revealed pathway alterations across treatments, including changes in vitamin synthesis and fatty acid metabolism with BPX. This study underscores the necessity of assessing the combined effects of xenobiotics to better safeguard public health. It emphasizes the significance of considering adverse effects on the microbiome in the risk assessment of environmental chemicals.
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Affiliation(s)
- Sven-Bastiaan Haange
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Sarah Riesbeck
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Alix Sarah Aldehoff
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Beatrice Engelmann
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Kristian Jensen Pedersen
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Victor Castaneda-Monsalve
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany.
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7
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Nayak RR, Orellana DA. The impact of the human gut microbiome on the treatment of autoimmune disease. Immunol Rev 2024; 325:107-130. [PMID: 38864582 PMCID: PMC11338731 DOI: 10.1111/imr.13358] [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] [Indexed: 06/13/2024]
Abstract
Autoimmune (or rheumatic) diseases are increasing in prevalence but selecting the best therapy for each patient proceeds in trial-and-error fashion. This strategy can lead to ineffective therapy resulting in irreversible damage and suffering; thus, there is a need to bring the promise of precision medicine to patients with autoimmune disease. While host factors partially determine the therapeutic response to immunosuppressive drugs, these are not routinely used to tailor therapy. Thus, non-host factors likely contribute. Here, we consider the impact of the human gut microbiome in the treatment of autoimmunity. We propose that the gut microbiome can be manipulated to improve therapy and to derive greater benefit from existing therapies. We focus on the mechanisms by which the human gut microbiome impacts treatment response, provide a framework to interrogate these mechanisms, review a case study of a widely-used anti-rheumatic drug, and discuss challenges with studying multiple complex systems: the microbiome, the human immune system, and autoimmune disease. We consider open questions that remain in the field and speculate on the future of drug-microbiome-autoimmune disease interactions. Finally, we present a blue-sky vision for how the microbiome can be used to bring the promise of precision medicine to patients with rheumatic disease.
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Affiliation(s)
- Renuka R Nayak
- Rheumatology Division, Department of Medicine, University of California, San Francisco, California, USA
- Veterans Affairs Medical Center, San Francisco, California, USA
| | - Diego A Orellana
- Rheumatology Division, Department of Medicine, University of California, San Francisco, California, USA
- Veterans Affairs Medical Center, San Francisco, California, USA
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8
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Kim D, Nguyen TTM, Moon Y, Kim JM, Nam H, Cha DS, An YJ, de Guzman ACV, Park S. Time-Resolved Evaluation of L-Dopa Metabolism in Bacteria-Host Symbiotic System and the Effect on Parkinson's Molecular Pathology. SMALL METHODS 2024:e2400469. [PMID: 39058017 DOI: 10.1002/smtd.202400469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Indexed: 07/28/2024]
Abstract
The gut microbiome influences drug metabolism and therapeutic efficacy. Still, the lack of a general label-free approach for monitoring bacterial or host metabolic contribution hampers deeper insights. Here, a 2D nuclear magnetic resonance (NMR) approach is introduced that enables real-time monitoring of the metabolism of Levodopa (L-dopa), an anti-Parkinson drug, in both live bacteria and bacteria-host (Caenorhabditis elegans) symbiotic systems. The quantitative method reveals that discrete Enterococcus faecalis substrains produce different amounts of dopamine in live hosts, even though they are a single species and all have the Tyrosine decarboxylase (TyrDC) gene involved in L-dopa metabolism. The differential bacterial metabolic activity correlates with differing Parkinson's molecular pathology concerning alpha-synuclein aggregation as well as behavioral phenotypes. The gene's existence or expression is not an indicator of metabolic activity is also shown, underscoring the significance of quantitative metabolic estimation in vivo. This simple approach is widely adaptable to any chemical drug to elucidate pharmacomicrobiomic relationships and may help rapidly screen bacterial metabolic effects in drug development.
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Affiliation(s)
- Doyeon Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
| | - Tin Tin Manh Nguyen
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
| | - Yechan Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Mo Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
| | - Hoonsik Nam
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
| | - Dong Seok Cha
- College of Pharmacy Woosuk University, Jeonbuk, 55338, South Korea
| | - Yong Jin An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
| | - Arvie Camille V de Guzman
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
| | - Sunghyouk Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, South Korea
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9
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Carmody RN, Varady K, Turnbaugh PJ. Digesting the complex metabolic effects of diet on the host and microbiome. Cell 2024; 187:3857-3876. [PMID: 39059362 PMCID: PMC11309583 DOI: 10.1016/j.cell.2024.06.032] [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] [Received: 04/04/2024] [Revised: 06/08/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
The past 50 years of interdisciplinary research in humans and model organisms has delivered unprecedented insights into the mechanisms through which diet affects energy balance. However, translating these results to prevent and treat obesity and its associated diseases remains challenging. Given the vast scope of this literature, we focus this Review on recent conceptual advances in molecular nutrition targeting the management of energy balance, including emerging dietary and pharmaceutical interventions and their interactions with the human gut microbiome. Notably, multiple current dietary patterns of interest embrace moderate-to-high fat intake or prioritize the timing of eating over macronutrient intake. Furthermore, the rapid expansion of microbiome research findings has complicated multiple longstanding tenets of nutrition while also providing new opportunities for intervention. Continued progress promises more precise and reliable dietary recommendations that leverage our growing knowledge of the microbiome, the changing landscape of clinical interventions, and our molecular understanding of human biology.
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Affiliation(s)
- Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Krista Varady
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, IL, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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10
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Khojasteh SC, Argikar UA, Chatzopoulou M, Cheruzel L, Cho S, Dhaware D, Johnson KM, Kalgutkar AS, Liu J, Ma B, Maw H, Rowley JA, Seneviratne HK, Wang S. Biotransformation research advances - 2023 year in review. Drug Metab Rev 2024:1-33. [PMID: 38989688 DOI: 10.1080/03602532.2024.2370330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024]
Abstract
This annual review marks the eighth in the series starting with Baillie et al. (2016) Our objective is to explore and share articles which we deem influential and significant in the field of biotransformation. Its format is to highlight important aspects captured in synopsis followed by a commentary with relevant figure and references.
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Affiliation(s)
- S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Upendra A Argikar
- Non-clinical Development, Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - Maria Chatzopoulou
- Early Clinical Development and Translational Science, UCB Biopharma UK, Slough, UK
| | - Lionel Cheruzel
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Sungjoon Cho
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | | | - Kevin M Johnson
- Drug Metabolism and Pharmacokinetics, Inotiv, MD Heights, MO, USA
| | - Amit S Kalgutkar
- Medicine Design, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Joyce Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Bin Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Hlaing Maw
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc, Ridgefield, CT, USA
| | - Jessica A Rowley
- Early Clinical Development and Translational Science, UCB Biopharma UK, Slough, UK
| | - Herana Kamal Seneviratne
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
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Zhang Y, Zhao X, Zhang J, Zhang Y, Wei Y. Advancements in the impact of human microbiota and probiotics on leukemia. Front Microbiol 2024; 15:1423838. [PMID: 39021626 PMCID: PMC11251910 DOI: 10.3389/fmicb.2024.1423838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
The human gut microbiota is a complex ecosystem that plays a crucial role in promoting the interaction between the body and its environment. It has been increasingly recognized that the gut microbiota has diverse physiological functions. Recent studies have shown a close association between the gut microbiota and the development of certain tumors, including leukemia. Leukemia is a malignant clonal disease characterized by the uncontrolled growth of one or more types of blood cells, which is the most common cancer in children. The imbalance of gut microbiota is linked to the pathological mechanisms of leukemia. Probiotics, which are beneficial microorganisms that help maintain the balance of the host microbiome, play a role in regulating gut microbiota. Probiotics have the potential to assist in the treatment of leukemia and improve the clinical prognosis of leukemia patients. This study reviews the relationship between gut microbiota, probiotics, and the progression of leukemia based on current research. In addition, utilizing zebrafish leukemia models in future studies might reveal the specific mechanisms of their interactions, thereby providing new insights into the clinical treatment of leukemia. In conclusion, further investigation is still needed to fully understand the accurate role of microbes in leukemia.
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Affiliation(s)
| | | | | | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, School of Pharmaceutical Sciences, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital Zhengzhou Children’s Hospital, Zhengzhou University, Zhengzhou, China
| | - Yongjun Wei
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, School of Pharmaceutical Sciences, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital Zhengzhou Children’s Hospital, Zhengzhou University, Zhengzhou, China
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12
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Zhang Z, Wang K, Jiang C. Gut microbial-host-isozymes are new targets for diseases. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1525-1527. [PMID: 38644445 DOI: 10.1007/s11427-024-2551-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/28/2024] [Indexed: 04/23/2024]
Affiliation(s)
- Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, 100191, 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
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, 100191, 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
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, 100191, 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.
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13
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Long AR, Mortara EL, Mendoza BN, Fink EC, Sacco FX, Ciesla MJ, Stack TMM. Sequence similarity network analysis of drug- and dye-modifying azoreductase enzymes found in the human gut microbiome. Arch Biochem Biophys 2024; 757:110025. [PMID: 38740275 PMCID: PMC11295148 DOI: 10.1016/j.abb.2024.110025] [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: 04/06/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024]
Abstract
Drug metabolism by human gut microbes is often exemplified by azo bond reduction in the anticolitic prodrug sulfasalazine. Azoreductase activity is often found in incubations with cell cultures or ex vivo gut microbiome samples and contributes to the xenobiotic metabolism of drugs and food additives. Applying metagenomic studies to personalized medicine requires knowledge of the genes responsible for sulfasalazine and other drug metabolism, and candidate genes and proteins for drug modifications are understudied. A representative gut-abundant azoreductase from Anaerotignum lactatifermentan DSM 14214 efficiently reduces sulfasalazine and another drug, phenazopyridine, but could not reduce all azo-bonded drugs in this class. We used enzyme kinetics to characterize this enzyme for its NADH-dependent reduction of these drugs and food additives and performed computational docking to provide the groundwork for understanding substrate specificity in this family. We performed an analysis of the Flavodoxin-like fold InterPro family (IPR003680) by computing a sequence similarity network to classify distinct subgroups of the family and then performed chemically-guided functional profiling to identify proteins that are abundant in the NIH Human Microbiome Project dataset. This strategy aims to reduce the number of unique azoreductases needed to characterize one protein family in the diverse set of potential drug- and dye-modifying activities found in the human gut microbiome.
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Affiliation(s)
- Audrey R Long
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Emma L Mortara
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Brisa N Mendoza
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Emma C Fink
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Francis X Sacco
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Matthew J Ciesla
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Tyler M M Stack
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States.
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14
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Parthasarathy G, Malhi H, Bajaj JS. Therapeutic manipulation of the microbiome in liver disease. Hepatology 2024:01515467-990000000-00932. [PMID: 38922826 DOI: 10.1097/hep.0000000000000987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Myriad associations between the microbiome and various facets of liver physiology and pathology have been described in the literature. Building on descriptive and correlative sequencing studies, metagenomic studies are expanding our collective understanding of the functional and mechanistic role of the microbiome as mediators of the gut-liver axis. Based on these mechanisms, the functional activity of the microbiome represents an attractive, tractable, and precision medicine therapeutic target in several liver diseases. Indeed, several therapeutics have been used in liver disease even before their description as a microbiome-dependent approach. To bring successful microbiome-targeted and microbiome-inspired therapies to the clinic, a comprehensive appreciation of the different approaches to influence, collaborate with, or engineer the gut microbiome to coopt a disease-relevant function of interest in the right patient is key. Herein, we describe the various levels at which the microbiome can be targeted-from prebiotics, probiotics, synbiotics, and antibiotics to microbiome reconstitution and precision microbiome engineering. Assimilating data from preclinical animal models, human studies as well as clinical trials, we describe the potential for and rationale behind studying such therapies across several liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cirrhosis, HE as well as liver cancer. Lastly, we discuss lessons learned from previous attempts at developing such therapies, the regulatory framework that needs to be navigated, and the challenges that remain.
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Affiliation(s)
| | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
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15
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Jarmakiewicz-Czaja S, Gruszecka J, Filip R. The Diagnosis of Intestinal Fibrosis in Crohn's Disease-Present and Future. Int J Mol Sci 2024; 25:6935. [PMID: 39000043 PMCID: PMC11241173 DOI: 10.3390/ijms25136935] [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: 05/15/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Crohn's disease (CD) progresses with periods of remission and exacerbations. During exacerbations, chronic inflammation leads to tissue destruction. As a result, intestinal fibrosis may develop in response to the ongoing inflammatory process. Fibrosis in CD should be considered the result of the response of the intestinal wall (over) to the presence of inflammation in the deep structures of the intestinal wall. In the absence of ideal noninvasive methods, endoscopic evaluation in combination with biopsy, histopathological analysis, stool analysis, and blood analysis remains the gold standard for assessing both inflammation and fibrosis in CD. On the contrary, the ability to identify markers of intestinal fibrosis would help to develop new diagnostic and therapeutic methods to detect early stages of fibrosis. It is speculated that miRNAs may, in the future, become biomarkers for early noninvasive diagnosis in the treatment of intestinal fibrosis. The purpose of this review is to summarise existing diagnostic methods for Crohn's disease and present recent scientific reports on molecular testing.
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Affiliation(s)
| | - Jolanta Gruszecka
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Clinical Microbiology, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Gastroenterology with IBD Unit, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
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16
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Kyaw TS, Zhang C, Sandy M, Trepka K, Zhang S, Ramirez Hernandez LA, Ramirez L, Goh JJ, Yu K, Dimassa V, Bess EN, Brockert JG, Dumlao DS, Bisanz JE, Turnbaugh PJ. Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors. iScience 2024; 27:110122. [PMID: 38947502 PMCID: PMC11214321 DOI: 10.1016/j.isci.2024.110122] [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: 10/17/2022] [Revised: 04/17/2024] [Accepted: 05/24/2024] [Indexed: 07/02/2024] Open
Abstract
Drug efflux transporters are a major determinant of drug efficacy and toxicity. A canonical example is P-glycoprotein (P-gp), an efflux transporter that controls the intestinal absorption of diverse compounds. Despite a rich literature on the dietary and pharmaceutical compounds that impact P-gp activity, its sensitivity to gut microbial metabolites remains an open question. Surprisingly, we found that the cardiac drug-metabolizing gut Actinobacterium Eggerthella lenta increases drug absorption in mice. Experiments in cell culture revealed that E. lenta produces a soluble factor that post-translationally inhibits P-gp ATPase efflux activity. P-gp inhibition is conserved in the Eggerthellaceae family but absent in other Actinobacteria. Comparative genomics identified genes associated with P-gp inhibition. Finally, activity-guided biochemical fractionation coupled to metabolomics implicated a group of small polar metabolites with P-gp inhibitory activity. These results highlight the importance of considering the broader relevance of the gut microbiome for drug disposition beyond first-pass metabolism.
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Affiliation(s)
- Than S. Kyaw
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Chen Zhang
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Moriah Sandy
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Quantitative Metabolite Analysis Center, Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kai Trepka
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Shenwei Zhang
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Luis A. Ramirez Hernandez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Lorenzo Ramirez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Janice J.N. Goh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kristie Yu
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Vincent Dimassa
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Elizabeth N. Bess
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jacob G. Brockert
- Quantitative Metabolite Analysis Center, Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Darren S. Dumlao
- Quantitative Metabolite Analysis Center, Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jordan E. Bisanz
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Chan-Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA
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17
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Wu CY, Davis S, Saudagar N, Shah S, Zhao W, Stern A, Martel J, Ojcius D, Yang HC. Caenorhabditis elegans as a Convenient Animal Model for Microbiome Studies. Int J Mol Sci 2024; 25:6670. [PMID: 38928375 PMCID: PMC11203780 DOI: 10.3390/ijms25126670] [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: 04/18/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Microbes constitute the most prevalent life form on Earth, yet their remarkable diversity remains mostly unrecognized. Microbial diversity in vertebrate models presents a significant challenge for investigating host-microbiome interactions. The model organism Caenorhabditis elegans has many advantages for delineating the effects of host genetics on microbial composition. In the wild, the C. elegans gut contains various microbial species, while in the laboratory it is usually a host for a single bacterial species. There is a potential host-microbe interaction between microbial metabolites, drugs, and C. elegans phenotypes. This mini-review aims to summarize the current understanding regarding the microbiome in C. elegans. Examples using C. elegans to study host-microbe-metabolite interactions are discussed.
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Affiliation(s)
- Cheng-Yeu Wu
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.W.); (J.M.)
| | - Scott Davis
- Department of Endodontics, Arthur Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
| | - Neekita Saudagar
- Doctor of Dental Surgery Program, Arthur Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA; (N.S.); (S.S.); (W.Z.)
| | - Shrey Shah
- Doctor of Dental Surgery Program, Arthur Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA; (N.S.); (S.S.); (W.Z.)
| | - William Zhao
- Doctor of Dental Surgery Program, Arthur Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA; (N.S.); (S.S.); (W.Z.)
| | - Arnold Stern
- Grossman School of Medicine, New York University, New York, NY 10016, USA;
| | - Jan Martel
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.W.); (J.M.)
| | - David Ojcius
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.W.); (J.M.)
- Department of Biomedical Sciences, Arthur Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA
| | - Hung-Chi Yang
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu 30041, Taiwan
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18
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Trøseid M, Nielsen SD, Vujkovic-Cvijin I. Gut microbiome and cardiometabolic comorbidities in people living with HIV. MICROBIOME 2024; 12:106. [PMID: 38877521 PMCID: PMC11177534 DOI: 10.1186/s40168-024-01815-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Despite modern antiretroviral therapy (ART), people living with HIV (PLWH) have increased relative risk of inflammatory-driven comorbidities, including cardiovascular disease (CVD). The gut microbiome could be one of several driving factors, along with traditional risk factors and HIV-related risk factors such as coinfections, ART toxicity, and past immunodeficiency. RESULTS PLWH have an altered gut microbiome, even after adjustment for known confounding factors including sexual preference. The HIV-related microbiome has been associated with cardiometabolic comorbidities, and shares features with CVD-related microbiota profiles, in particular reduced capacity for short-chain fatty acid (SCFA) generation. Substantial inter-individual variation has so far been an obstacle for applying microbiota profiles for risk stratification. This review covers updated knowledge and recent advances in our understanding of the gut microbiome and comorbidities in PLWH, with specific focus on cardiometabolic comorbidities and inflammation. It covers a comprehensive overview of HIV-related and comorbidity-related dysbiosis, microbial translocation, and microbiota-derived metabolites. It also contains recent data from studies in PLWH on circulating metabolites related to comorbidities and underlying gut microbiota alterations, including circulating levels of the SCFA propionate, the histidine-analogue imidazole propionate, and the protective metabolite indole-3-propionic acid. CONCLUSIONS Despite recent advances, the gut microbiome and related metabolites are not yet established as biomarkers or therapeutic targets. The review gives directions for future research needed to advance the field into clinical practice, including promises and pitfalls for precision medicine. Video Abstract.
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Affiliation(s)
- Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Section for Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, Copenhagen Oe, 2100, Denmark
| | - Ivan Vujkovic-Cvijin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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19
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Ross PA, Xu W, Jalomo-Khayrova E, Bange G, Gumerov VM, Bradley PH, Sourjik V, Zhulin IB. Framework for exploring the sensory repertoire of the human gut microbiota. mBio 2024; 15:e0103924. [PMID: 38757952 PMCID: PMC11237719 DOI: 10.1128/mbio.01039-24] [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: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Bacteria sense changes in their environment and transduce signals to adjust their cellular functions accordingly. For this purpose, bacteria employ various sensors feeding into multiple signal transduction pathways. Signal recognition by bacterial sensors is studied mainly in a few model organisms, but advances in genome sequencing and analysis offer new ways of exploring the sensory repertoire of many understudied organisms. The human gut is a natural target of this line of study: it is a nutrient-rich and dynamic environment and is home to thousands of bacterial species whose activities impact human health. Many gut commensals are also poorly studied compared to model organisms and are mainly known through their genome sequences. To begin exploring the signals human gut commensals sense and respond to, we have designed a framework that enables the identification of sensory domains, prediction of signals that they recognize, and experimental verification of these predictions. We validate this framework's functionality by systematically identifying amino acid sensors in selected bacterial genomes and metagenomes, characterizing their amino acid binding properties, and demonstrating their signal transduction potential.IMPORTANCESignal transduction is a central process governing how bacteria sense and respond to their environment. The human gut is a complex environment with many living organisms and fluctuating streams of nutrients. One gut inhabitant, Escherichia coli, is a model organism for studying signal transduction. However, E. coli is not representative of most gut microbes, and signaling pathways in the thousands of other organisms comprising the human gut microbiota remain poorly understood. This work provides a foundation for how to explore signals recognized by these organisms.
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Affiliation(s)
- Patricia A. Ross
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Wenhao Xu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ekaterina Jalomo-Khayrova
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Patrick H. Bradley
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
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20
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de la Cuesta-Zuluaga J, Boldt L, Maier L. Response, resistance, and recovery of gut bacteria to human-targeted drug exposure. Cell Host Microbe 2024; 32:786-793. [PMID: 38870896 DOI: 10.1016/j.chom.2024.05.009] [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: 02/29/2024] [Revised: 04/03/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Survival strategies of human-associated microbes to drug exposure have been mainly studied in the context of bona fide pathogens exposed to antibiotics. Less well understood are the survival strategies of non-pathogenic microbes and host-associated commensal communities to the variety of drugs and xenobiotics to which humans are exposed. The lifestyle of microbial commensals within complex communities offers a variety of ways to adapt to different drug-induced stresses. Here, we review the responses and survival strategies employed by gut commensals when exposed to drugs-antibiotics and non-antibiotics-at the individual and community level. We also discuss the factors influencing the recovery and establishment of a new community structure following drug exposure. These survival strategies are key to the stability and resilience of the gut microbiome, ultimately influencing the overall health and well-being of the host.
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Affiliation(s)
- Jacobo de la Cuesta-Zuluaga
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany; M3-Research Center for Malignome, Metabolome and Microbiome, University of Tübingen, Tübingen, Germany
| | - Leonardo Boldt
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany; M3-Research Center for Malignome, Metabolome and Microbiome, University of Tübingen, Tübingen, Germany
| | - Lisa Maier
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany; M3-Research Center for Malignome, Metabolome and Microbiome, University of Tübingen, Tübingen, Germany.
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21
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He J, Liu X, Zhang J, Wang R, Cao X, Liu G. Gut microbiome-derived hydrolases-an underrated target of natural product metabolism. Front Cell Infect Microbiol 2024; 14:1392249. [PMID: 38915922 PMCID: PMC11194327 DOI: 10.3389/fcimb.2024.1392249] [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: 02/28/2024] [Accepted: 05/16/2024] [Indexed: 06/26/2024] Open
Abstract
In recent years, there has been increasing interest in studying gut microbiome-derived hydrolases in relation to oral drug metabolism, particularly focusing on natural product drugs. Despite the significance of natural product drugs in the field of oral medications, there is a lack of research on the regulatory interplay between gut microbiome-derived hydrolases and these drugs. This review delves into the interaction between intestinal microbiome-derived hydrolases and natural product drugs metabolism from three key perspectives. Firstly, it examines the impact of glycoside hydrolases, amide hydrolases, carboxylesterase, bile salt hydrolases, and epoxide hydrolase on the structure of natural products. Secondly, it explores how natural product drugs influence microbiome-derived hydrolases. Lastly, it analyzes the impact of interactions between hydrolases and natural products on disease development and the challenges in developing microbial-derived enzymes. The overarching goal of this review is to lay a solid theoretical foundation for the advancement of research and development in new natural product drugs and personalized treatment.
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Affiliation(s)
- Jiaxin He
- People’s Hospital of Ningxia Hui Autonomous Region, Pharmacy Department, Yinchuan, China
| | - Xiaofeng Liu
- People’s Hospital of Ningxia Hui Autonomous Region, Pharmacy Department, Yinchuan, China
| | - Junming Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Rong Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xinyuan Cao
- People’s Hospital of Ningxia Hui Autonomous Region, Pharmacy Department, Yinchuan, China
- Ningxia Medical University, School of Basic Medicine, Yinchuan, China
| | - Ge Liu
- Ningxia Medical University, School of Basic Medicine, Yinchuan, China
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22
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Trepka KR, Kidder WA, Kyaw TS, Olson CA, Upadhyay V, Noecker C, Stanfield D, Steiding P, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ. Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597471. [PMID: 38895199 PMCID: PMC11185696 DOI: 10.1101/2024.06.04.597471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Herein, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal study of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. 16S rRNA gene and metagenomic sequencing revealed significant shifts in gut microbial community structure during treatment with oral fluoropyrimidines, which was validated in an independent cohort. Gene abundance was also markedly changed by oral fluoropyrimidines, including an enrichment for the preTA operon, which is sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). Higher levels of preTA led to increased 5-FU depletion by the gut microbiota grown ex vivo. Germ-free and antibiotic-treated mice had increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA+ E. coli, or CRC patient stool with high preTA levels. preTA abundance was negatively associated with patient toxicities. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach is generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.
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Affiliation(s)
- Kai R. Trepka
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Wesley A. Kidder
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Than S. Kyaw
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Christine A. Olson
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Vaibhav Upadhyay
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Dalila Stanfield
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Paige Steiding
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Darren Dumlao
- Department of Gastroenterology, University of California San Francisco; San Francisco, USA
| | - Jessie A. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Matthew D. Stachler
- Department of Pathology, University of California San Francisco; San Francisco, USA
| | - Erin L. Van Blarigan
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco; San Francisco, USA
- Department of Urology, University of California San Francisco; San Francisco, USA
| | - Alan P. Venook
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Chloe E. Atreya
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
- Chan Zuckerberg Biohub-San Francisco; San Francisco, USA
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23
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Ruan Z, Chen K, Cao W, Meng L, Yang B, Xu M, Xing Y, Li P, Freilich S, Chen C, Gao Y, Jiang J, Xu X. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. Nat Commun 2024; 15:4694. [PMID: 38824157 PMCID: PMC11144243 DOI: 10.1038/s41467-024-49098-z] [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: 03/26/2022] [Accepted: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Weimiao Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Lei Meng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Chen Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Yanzheng Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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24
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Shi Y, Wei L, Jin F, Wang J, Cao H, Yang Y, Gao L. Colchicine disrupts bile acid metabolic homeostasis by affecting the enterohepatic circulation in mice. J Appl Toxicol 2024; 44:863-873. [PMID: 38311468 DOI: 10.1002/jat.4587] [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: 10/06/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/06/2024]
Abstract
Although the medicinal properties of colchicine (COL) have been widely known for centuries, its toxicity has been the subject of controversy. The narrow therapeutic window causes COL to induce gastrointestinal adverse effects even when taken at recommended doses, mainly manifested as nausea, vomiting, and diarrhea. However, the mechanism of COL-induced gastrointestinal toxic reactions remains obscure. In the present study, the mice were dosed with COL (2.5 mg/kg b.w./day) for a week to explore the effect of COL on bile acid metabolism and the mechanism of COL-induced diarrhea. The results showed that COL treatment affected liver biochemistry in mice, resulting in a significant down-regulation of the mRNA expression levels of bile acid biosynthesis regulators Cyp7a1, Cyp8b1, Cyp7b1, and Cyp27a1 in liver tissues. The mRNA expression levels of bile acid transporters Ntcp, Oatp1, Mrp2, Ibabp, Mrp3, Osta, and Ostb in liver and ileum tissues were also significantly down-regulated. In addition, COL treatment significantly inhibited the mRNA expression levels of Fxr and its downstream target genes Shp, Lrh1, and Fgf15 in liver and ileum tissues, affecting the feedback regulation of bile acid biosynthesis. More importantly, the inhibition of COL on bile acid transporters in ileal and hepatic tissues affected bile acid recycling in the ileum as well as their reuptake in the liver, leading to a significantly increased accumulation of bile acids in the colon, which may be an important cause of diarrhea. In conclusion, our study revealed that COL treatment affected bile acid biosynthesis and enterohepatic circulation, thereby disrupting bile acid metabolic homeostasis in mice.
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Affiliation(s)
- Yongpeng Shi
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Li Wei
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Gansu Provincial Hospital, Lanzhou, China
| | - Fang Jin
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Gansu Provincial Hospital, Lanzhou, China
| | - Ji Wang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hanwen Cao
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lan Gao
- School of Life Sciences, Lanzhou University, Lanzhou, China
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25
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De Filippis F, Valentino V, Sequino G, Borriello G, Riccardi MG, Pierri B, Cerino P, Pizzolante A, Pasolli E, Esposito M, Limone A, Ercolini D. Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome. Nat Commun 2024; 15:4482. [PMID: 38802370 PMCID: PMC11130323 DOI: 10.1038/s41467-024-48739-7] [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: 02/19/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
Environmental pollutants from different chemical families may reach the gut microbiome, where they can be metabolized and transformed. However, how our gut symbionts respond to the exposure to environmental pollution is still underexplored. In this observational, cohort study, we aim to investigate the influence of environmental pollution on the gut microbiome composition and potential activity by shotgun metagenomics. We select as a case study a population living in a highly polluted area in Campania region (Southern Italy), proposed as an ideal field for exposomic studies and we compare the fecal microbiome of 359 subjects living in areas with high, medium and low environmental pollution. We highlight changes in gut microbiome composition and functionality that were driven by pollution exposure. Subjects from highly polluted areas show higher blood concentrations of dioxin and heavy metals, as well as an increase in microbial genes related to degradation and/or resistance to these molecules. Here we demonstrate the dramatic effect that environmental xenobiotics have on gut microbial communities, shaping their composition and boosting the selection of strains with degrading capacity. The gut microbiome can be considered as a pivotal player in the environment-health interaction that may contribute to detoxifying toxic compounds and should be taken into account when developing risk assessment models. The study was registered at ClinicalTrials.gov with the identifier NCT05976126.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I, 40, Napoli, Italy
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, Portici, Italy
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
| | - Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
| | - Giorgia Borriello
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, Portici, Italy
| | | | - Biancamaria Pierri
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Pellegrino Cerino
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Antonio Pizzolante
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I, 40, Napoli, Italy
| | - Mauro Esposito
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Antonio Limone
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I, 40, Napoli, Italy.
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26
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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [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: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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27
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McCoubrey LE, Seegobin N, Sangfuang N, Moens F, Duyvejonck H, Declerck E, Dierick A, Marzorati M, Basit AW. The colon targeting efficacies of mesalazine medications and their impacts on the gut microbiome. J Control Release 2024; 369:630-641. [PMID: 38599548 DOI: 10.1016/j.jconrel.2024.04.016] [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: 01/21/2024] [Revised: 03/27/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Successful treatment of ulcerative colitis (UC) is highly dependent on several parameters, including dosing regimen and the ability to deliver drugs to the disease site. In this study two strategies for delivering mesalazine (5-aminosalicylic acid, 5-ASA) to the colon were compared in an advanced in vitro model of the human gastrointestinal (GI) tract, the SHIME® system. Herein, a prodrug strategy employing bacteria-mediated drug release (sulfasalazine, Azulfidine®) was evaluated alongside a formulation strategy that utilised pH and bacteria-mediated release (5-ASA, Octasa® 1600 mg). SHIME® experiments were performed simulating both the GI physiology and colonic microbiota under healthy and inflammatory bowel disease (IBD) conditions, to study the impact of the disease state and ileal pH variability on colonic 5-ASA delivery. In addition, the effects of the products on the colonic microbiome were investigated by monitoring bacterial growth and metabolites. Results demonstrated that both the prodrug and formulation approaches resulted in a similar percentage of 5-ASA recovery under healthy conditions. On the contrary, during experiments simulating the GI physiology and microbiome of IBD patients (the target population) the formulation strategy resulted in a higher proportion of 5-ASA delivery to the colonic region as compared to the prodrug approach (P < 0.0001). Interestingly, the two products had distinct effects on the synthesis of key bacterial metabolites, such as lactate and short chain fatty acids, which varied according to disease state and ileal pH variability. Further, both 5-ASA and sulfasalazine significantly reduced the growth of the faecal microbiota sourced from six healthy humans. The findings support that the approach selected for colonic drug delivery could significantly influence the effectiveness of UC treatment, and highlight that drugs licensed for UC may differentially impact the growth and functioning of the colonic microbiota.
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Affiliation(s)
| | - Nidhi Seegobin
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | | | - Frédéric Moens
- ProDigest BV, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium
| | - Hans Duyvejonck
- ProDigest BV, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium
| | - Eline Declerck
- ProDigest BV, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium
| | - Arno Dierick
- ProDigest BV, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium
| | - Massimo Marzorati
- ProDigest BV, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; CMET (University of Ghent), Coupure Links 653, 9000 Ghent, Belgium
| | - Abdul W Basit
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK.
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28
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Culver RN, Spencer SP, Violette A, Lemus Silva EG, Takeuchi T, Nafarzadegan C, Higginbottom SK, Shalon D, Sonnenburg J, Huang KC. Improved mouse models of the small intestine microbiota using region-specific sampling from humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590999. [PMID: 38712253 PMCID: PMC11071525 DOI: 10.1101/2024.04.24.590999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Our understanding of region-specific microbial function within the gut is limited due to reliance on stool. Using a recently developed capsule device, we exploit regional sampling from the human intestines to develop models for interrogating small intestine (SI) microbiota composition and function. In vitro culturing of human intestinal contents produced stable, representative communities that robustly colonize the SI of germ-free mice. During mouse colonization, the combination of SI and stool microbes altered gut microbiota composition, functional capacity, and response to diet, resulting in increased diversity and reproducibility of SI colonization relative to stool microbes alone. Using a diverse strain library representative of the human SI microbiota, we constructed defined communities with taxa that largely exhibited the expected regional preferences. Response to a fiber-deficient diet was region-specific and reflected strain-specific fiber-processing and host mucus-degrading capabilities, suggesting that dietary fiber is critical for maintaining SI microbiota homeostasis. These tools should advance mechanistic modeling of the human SI microbiota and its role in disease and dietary responses.
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Affiliation(s)
- Rebecca N. Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sean Paul Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Arvie Violette
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Evelyn Giselle Lemus Silva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tadashi Takeuchi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ceena Nafarzadegan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dari Shalon
- Envivo Bio, Inc., San Francisco, CA 94107, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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29
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Constantin M, Chifiriuc MC, Mihaescu G, Corcionivoschi N, Burlibasa L, Bleotu C, Tudorache S, Mitache MM, Filip R, Munteanu SG, Gradisteanu Pircalabioru G. Microbiome and cancer: from mechanistic implications in disease progression and treatment to development of novel antitumoral strategies. Front Immunol 2024; 15:1373504. [PMID: 38715617 PMCID: PMC11074409 DOI: 10.3389/fimmu.2024.1373504] [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: 01/19/2024] [Accepted: 04/08/2024] [Indexed: 05/23/2024] Open
Abstract
Cancer is a very aggressive disease and one of mankind's most important health problems, causing numerous deaths each year. Its etiology is complex, including genetic, gender-related, infectious diseases, dysbiosis, immunological imbalances, lifestyle, including dietary factors, pollution etc. Cancer patients also become immunosuppressed, frequently as side effects of chemotherapy and radiotherapy, and prone to infections, which further promote the proliferation of tumor cells. In recent decades, the role and importance of the microbiota in cancer has become a hot spot in human biology research, bringing together oncology and human microbiology. In addition to their roles in the etiology of different cancers, microorganisms interact with tumor cells and may be involved in modulating their response to treatment and in the toxicity of anti-tumor therapies. In this review, we present an update on the roles of microbiota in cancer with a focus on interference with anticancer treatments and anticancer potential.
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Affiliation(s)
- Marian Constantin
- Institute of Biology, Bucharest of Romanian Academy, Bucharest, Romania
- Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest, Bucharest, Romania
- Faculty of Biology, University of Bucharest, Bucharest, Romania
| | | | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
- Faculty of Bioengineering of Animal Resources, Banat University of Agricultural Sciences and Veterinary Medicine-King Michael I of Romania, Timisoara, Romania
- Romanian Academy of Scientists, Bucharest, Romania
| | | | - Coralia Bleotu
- Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest, Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Sorin Tudorache
- Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | | | - Roxana Filip
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, Suceava, Romania
- Suceava Emergency County Hospital, Suceava, Romania
| | | | - Gratiela Gradisteanu Pircalabioru
- Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest, Bucharest, Romania
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Romanian Academy of Scientists, Bucharest, Romania
- eBio-Hub Research Centre, National University of Science and Technology Politehnica Bucharest, Bucharest, Romania
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30
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Huang F, Lyu B, Xie F, Li F, Xing Y, Han Z, Lai J, Ma J, Zou Y, Zeng H, Xu Z, Gao P, Luo Y, Bolund L, Tong G, Fengping X. From gut to liver: unveiling the differences of intestinal microbiota in NAFL and NASH patients. Front Microbiol 2024; 15:1366744. [PMID: 38638907 PMCID: PMC11024258 DOI: 10.3389/fmicb.2024.1366744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is increasingly recognized for its global prevalence and potential progression to more severe liver diseases such as non-alcoholic steatohepatitis (NASH). The gut microbiota plays a pivotal role in the pathogenesis of NAFLD, yet the detailed characteristics and ecological alterations of gut microbial communities during the progression from non-alcoholic fatty liver (NAFL) to NASH remain poorly understood. Methods: In this study, we conducted a comparative analysis of gut microbiota composition in individuals with NAFL and NASH to elucidate differences and characteristics. We utilized 16S rRNA sequencing to compare the intestinal gut microbiota among a healthy control group (65 cases), NAFL group (64 cases), and NASH group (53 cases). Random forest machine learning and database validation methods were employed to analyze the data. Results: Our findings indicate a significant decrease in the diversity of intestinal flora during the progression of NAFLD (p < 0.05). At the phylum level, high abundances of Bacteroidetes and Fusobacteria were observed in both NAFL and NASH patients, whereas Firmicutes were less abundant. At the genus level, a significant decrease in Prevotella expression was seen in the NAFL group (AUC 0.738), whereas an increase in the combination of Megamonas and Fusobacterium was noted in the NASH group (AUC 0.769). Furthermore, KEGG pathway analysis highlighted significant disturbances in various types of glucose metabolism pathways in the NASH group compared to the NAFL group, as well as notably compromised flavonoid and flavonol biosynthesis functions. The study uncovers distinct microbiota characteristics and microecological changes within the gut during the transition from NAFL to NASH, providing insights that could facilitate the discovery of novel biomarkers and therapeutic targets for NAFLD.
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Affiliation(s)
- Furong Huang
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Bo Lyu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Cell, Shenzhen, China
| | - Fanci Xie
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- People's Hospital of Longhua, Shenzhen, China
| | - Fang Li
- BGI, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI Research, Qingdao, China
| | - Yufeng Xing
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Zhiyi Han
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Jianping Lai
- Department of Infectious Diseases, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | | | - Yuanqiang Zou
- BGI, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | - Hua Zeng
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Zhe Xu
- BGI, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI Research, Qingdao, China
| | - Pan Gao
- BGI, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI Research, Qingdao, China
| | - Yonglun Luo
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Cell, Shenzhen, China
- BGI, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI Research, Qingdao, China
| | - Lars Bolund
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- BGI Cell, Shenzhen, China
- BGI, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI Research, Qingdao, China
| | - Guangdong Tong
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xu Fengping
- Department of Sanming Project of Medicine in Shenzhen, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Cell, Shenzhen, China
- BGI, Shenzhen, China
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31
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Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
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32
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Liu J, Malekoltojari A, Asokakumar A, Chow V, Li L, Li H, Grimaldi M, Dang N, Campbell J, Barrett H, Sun J, Navarre W, Wilson D, Wang H, Mani S, Balaguer P, Anakk S, Peng H, Krause HM. Diindoles produced from commensal microbiota metabolites function as endogenous CAR/Nr1i3 ligands. Nat Commun 2024; 15:2563. [PMID: 38519460 PMCID: PMC10960024 DOI: 10.1038/s41467-024-46559-3] [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: 09/09/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
Numerous studies have demonstrated the correlation between human gut bacteria and host physiology, mediated primarily via nuclear receptors (NRs). Despite this body of work, the systematic identification and characterization of microbe-derived ligands that regulate NRs remain a considerable challenge. In this study, we discover a series of diindole molecules produced from commensal bacteria metabolites that act as specific agonists for the orphan constitutive androstane receptor (CAR). Using various biophysical analyses we show that their nanomolar affinities are comparable to those of synthetic CAR agonists, and that they can activate both rodent and human CAR orthologues, which established synthetic agonists cannot. We also find that the diindoles, diindolylmethane (DIM) and diindolylethane (DIE) selectively up-regulate bona fide CAR target genes in primary human hepatocytes and mouse liver without causing significant side effects. These findings provide new insights into the complex interplay between the gut microbiome and host physiology, as well as new tools for disease treatment.
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Affiliation(s)
- Jiabao Liu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ainaz Malekoltojari
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anjana Asokakumar
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Vimanda Chow
- Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
| | - Linhao Li
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD, 21201, USA
| | - Hao Li
- Department of Molecular Pharmacology; Department of Genetics; Department of Medicine; Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Marina Grimaldi
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Université Montpellier, Institut régional du Cancer de Montpellier (ICM), Montpellier, Inserm, U1194, France
| | - Nathanlown Dang
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jhenielle Campbell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Holly Barrett
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- School of the Environment, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - William Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Derek Wilson
- Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD, 21201, USA
| | - Sridhar Mani
- Department of Molecular Pharmacology; Department of Genetics; Department of Medicine; Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Université Montpellier, Institut régional du Cancer de Montpellier (ICM), Montpellier, Inserm, U1194, France
| | - Sayeepriyadarshini Anakk
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hui Peng
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
- School of the Environment, University of Toronto, Toronto, ON, M5S 3H6, Canada.
| | - Henry M Krause
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Kwak MJ, Kang A, Eor J, Ryu S, Choi Y, Heo JM, Song M, Kim JN, Kim HJ, Kim Y. Dietary L-Methionine modulates the gut microbiota and improves the expression of tight junctions in an in vitro model of the chicken gastrointestinal tract. Anim Microbiome 2024; 6:14. [PMID: 38504362 PMCID: PMC10953145 DOI: 10.1186/s42523-024-00303-w] [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: 10/10/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND The poultry industry encounters a number of factors that affect growth performance and productivity; nutrition is essential for sustaining physiological status and protecting against stressors such as heat, density, and disease. The addition of vitamins, minerals, and amino acids to the diet can help restore productivity and support the body's defense mechanisms against stress. Methionine (Met) is indispensable for poultry's energy metabolism, physiology, performance, and feed utilization capacity. Through this study, we aimed to examine the physiological effects of methionine supplementation on poultry as well as alterations of intestinal microbiome. METHODS We utilized the DL- and L- form of methionine on Caenorhabditis elegans and the FIMM (Fermentor for intestine microbiota model) in-vitro digesting system. A genomic-analysis of the transcriptome confirmed that methionine supplementation can modulate growth-related physiological metabolic pathways and immune responses in the host poultry. The C. elegans model was used to assess the general health benefits of a methionine supplement for the host. RESULTS Regardless of the type or concentration of methionine, supplementation with methionine significantly increased the lifespan of C. elegans. Feed grade L-Methionine 95%, exhibited the highest lifespan performance in C. elegans. Methionine supplementation increased the expression of tight junction genes in the primary intestinal cells of both broiler and laying hens, which is directly related to immunity. Feed grade L-Methionine 95% performed similarly or even better than DL-Methionine or L-Methionine treatments with upper doses in terms of enhancing intestinal integrity. In vitro microbial cultures of healthy broilers and laying hens fed methionine revealed changes in intestinal microflora, including increased Clostridium, Bacteroides, and Oscillospira compositions. When laying hens were given feed grade L-Methionine 95% and 100%, pathogenic Campylobacter at the genus level was decreased, while commensal bacteria were increased. CONCLUSIONS Supplementation of feed grade L-Methionine, particularly L-Methionine 95%, was more beneficial to the host poultry than supplementing other source of methionine for maintaining intestinal integrity and healthy microbiome.
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Affiliation(s)
- Min-Jin Kwak
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Korea
| | - Anna Kang
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Korea
| | - JuYoung Eor
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Korea
| | - Sangdon Ryu
- Divisions of Environmental Materials, Honam National Institute of Biological Resources (HNIBR), 58762, Mokpo, Korea
| | - Youbin Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Korea
| | - Jung Min Heo
- Department of Food Science & Nutrition, Dongseo University, Busan, 47011, Korea
| | - Minho Song
- Department of Food Science & Nutrition, Dongseo University, Busan, 47011, Korea
| | - Jong Nam Kim
- CJ Cheiljedang, 330, Dongho-ro, Jung-gu, Seoul, 04560, Korea
| | - Hyeon-Jin Kim
- CJ Cheiljedang, 330, Dongho-ro, Jung-gu, Seoul, 04560, Korea
| | - Younghoon Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Korea.
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34
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Ouyang H, Xu Z, Hong J, Malroy J, Qian L, Ji S, Zhu X. Mining the Metabolic Capacity of Clostridium sporogenes Aided by Machine Learning. Angew Chem Int Ed Engl 2024; 63:e202319925. [PMID: 38286754 PMCID: PMC10986427 DOI: 10.1002/anie.202319925] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 01/31/2024]
Abstract
Anaerobes dominate the microbiota of the gastrointestinal (GI) tract, where a significant portion of small molecules can be degraded or modified. However, the enormous metabolic capacity of gut anaerobes remains largely elusive in contrast to aerobic bacteria, mainly due to the requirement of sophisticated laboratory settings. In this study, we employed an in silico machine learning platform, MoleculeX, to predict the metabolic capacity of a gut anaerobe, Clostridium sporogenes, against small molecules. Experiments revealed that among the top seven candidates predicted as unstable, six indeed exhibited instability in C. sporogenes culture. We further identified several metabolites resulting from the supplementation of everolimus in the bacterial culture for the first time. By utilizing bioinformatics and in vitro biochemical assays, we successfully identified an enzyme encoded in the genome of C. sporogenes responsible for everolimus transformation. Our framework thus can potentially facilitate future understanding of small molecules metabolism in the gut, further improve patient care through personalized medicine, and guide the development of new small molecule drugs and therapeutic approaches.
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Affiliation(s)
- Huanrong Ouyang
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, United States
| | - Zhao Xu
- Department of Computer Science & Engineering, Texas A&M University, College Station, 77843, United States
| | - Joshua Hong
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, United States
| | - Jeshua Malroy
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, United States
| | - Liangyu Qian
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, United States
| | - Shuiwang Ji
- Department of Computer Science & Engineering, Texas A&M University, College Station, 77843, United States
| | - Xuejun Zhu
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, United States; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, 77843, United States
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35
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Wu L, Wang XW, Tao Z, Wang T, Zuo W, Zeng Y, Liu YY, Dai L. Data-driven prediction of colonization outcomes for complex microbial communities. Nat Commun 2024; 15:2406. [PMID: 38493186 PMCID: PMC10944475 DOI: 10.1038/s41467-024-46766-y] [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] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.
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Affiliation(s)
- Lu Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xu-Wen Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zining Tao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shandong Agricultural University, Tai'an, China
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yu Zeng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
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36
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Felchle H, Brunner V, Groll T, Walther CN, Nefzger SM, Zaurito AE, Silva MG, Gissibl J, Topping GJ, Lansink Rotgerink L, Saur D, Steiger K, Combs SE, Tschurtschenthaler M, Fischer JC. Novel Tumor Organoid-Based Mouse Model to Study Image Guided Radiation Therapy of Rectal Cancer After Noninvasive and Precise Endoscopic Implantation. Int J Radiat Oncol Biol Phys 2024; 118:1094-1104. [PMID: 37875245 DOI: 10.1016/j.ijrobp.2023.10.008] [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: 06/23/2023] [Accepted: 10/08/2023] [Indexed: 10/26/2023]
Abstract
PURPOSE Preoperative (neoadjuvant) radiation therapy (RT) is an essential part of multimodal rectal cancer therapy. Recently, total neoadjuvant therapy (TNT), which combines simultaneous radiochemotherapy with additional courses of chemotherapy, has emerged as an effective approach. TNT achieves a pathologic complete remission in approximately 30% of resected patients, opening avenues for treatment strategies that avoid radical organ resection. Furthermore, recent studies have demonstrated that anti-programmed cell death protein 1 immunotherapy can induce clinical complete responses in patients with specific genetic alterations. There is significant potential to enhance outcomes through intensifying, personalizing, and de-escalating treatment approaches. However, the heterogeneous response rates to RT or TNT and strategies to sensitize patients without specific genetic changes to immunotherapy remain poorly understood. METHODS AND MATERIALS We developed a novel orthotopic mouse model of rectal cancer based on precisely defined endoscopic injections of tumor organoids that reflect tumor heterogeneity. Subsequently, we employed endoscopic- and computed tomography-guided RT and validated rectal tumor growth and response rates to therapy using small-animal magnetic resonance imaging and endoscopic follow-up. RESULTS Rectal tumor formation was successfully induced in all mice after 2 organoid injections. Clinically relevant RT regimens with 5 × 5 Gy significantly delayed clinical signs of tumor progression and significantly improved survival. Consistent with human disease, rectal tumor progression correlated with the development of liver and lung metastases. Notably, long-term survivors after RT showed no evidence of tumor recurrence, as demonstrated by in vivo radiologic tumor staging and histopathologic examination. CONCLUSIONS Our novel mouse model combines orthotopic tumor growth via noninvasive and precise rectal organoid injection and small-animal RT. This model holds significant promise for investigating the effect of tumor cell-intrinsic aspects, genetic alterations of the host, and exogenous factors (eg, nutrition or microbiota) on RT outcomes. Furthermore, it allows for the exploration of combination therapies involving chemotherapy, immunotherapy, or novel targeted therapies.
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Affiliation(s)
- Hannah Felchle
- Department of Radiation Oncology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Valentina Brunner
- Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Tanja Groll
- Comparative Experimental Pathology, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Caroline N Walther
- Department of Radiation Oncology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sophie M Nefzger
- Department of Radiation Oncology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Antonio E Zaurito
- Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Miguel G Silva
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany; Institute of Molecular Oncology and Functional Genomics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Gissibl
- Department of Radiation Oncology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Geoffrey J Topping
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Laura Lansink Rotgerink
- Department of Radiation Oncology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dieter Saur
- Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katja Steiger
- Comparative Experimental Pathology, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie E Combs
- Department of Radiation Oncology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany; Helmholtz Zentrum München, Institute of Radiation Medicine, Neuherberg, Germany
| | - Markus Tschurtschenthaler
- Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Julius C Fischer
- Department of Radiation Oncology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
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Jimonet P, Druart C, Blanquet-Diot S, Boucinha L, Kourula S, Le Vacon F, Maubant S, Rabot S, Van de Wiele T, Schuren F, Thomas V, Walther B, Zimmermann M. Gut Microbiome Integration in Drug Discovery and Development of Small Molecules. Drug Metab Dispos 2024; 52:274-287. [PMID: 38307852 DOI: 10.1124/dmd.123.001605] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/04/2024] Open
Abstract
Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.
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Affiliation(s)
- Patrick Jimonet
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Céline Druart
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Stéphanie Blanquet-Diot
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Lilia Boucinha
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Stephanie Kourula
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Françoise Le Vacon
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Sylvie Maubant
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Sylvie Rabot
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Tom Van de Wiele
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Frank Schuren
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Vincent Thomas
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Bernard Walther
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Michael Zimmermann
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
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Müller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, Bork P, Patil KR, Typas A, Garcia-Santamarina S, Maier L. High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities. Nat Protoc 2024; 19:668-699. [PMID: 38092943 DOI: 10.1038/s41596-023-00926-4] [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] [Received: 05/26/2023] [Accepted: 10/05/2023] [Indexed: 03/10/2024]
Abstract
The human gut microbiome is a key contributor to health, and its perturbations are linked to many diseases. Small-molecule xenobiotics such as drugs, chemical pollutants and food additives can alter the microbiota composition and are now recognized as one of the main factors underlying microbiome diversity. Mapping the effects of such compounds on the gut microbiome is challenging because of the complexity of the community, anaerobic growth requirements of individual species and the large number of interactions that need to be quantitatively assessed. High-throughput screening setups offer a promising solution for probing the direct inhibitory effects of hundreds of xenobiotics on tens of anaerobic gut bacteria. When automated, such assays enable the cost-effective investigation of a wide range of compound-microbe combinations. We have developed an experimental setup and protocol that enables testing of up to 5,000 compounds on a target gut species under strict anaerobic conditions within 5 d. In addition, with minor modifications to the protocol, drug effects can be tested on microbial communities either assembled from isolates or obtained from stool samples. Experience in working in an anaerobic chamber, especially in performing delicate work with thick chamber gloves, is required for implementing this protocol. We anticipate that this protocol will accelerate the study of interactions between small molecules and the gut microbiome and provide a deeper understanding of this microbial ecosystem, which is intimately intertwined with human health.
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Affiliation(s)
- Patrick Müller
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Jacobo de la Cuesta-Zuluaga
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Michael Kuhn
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maral Baghai Arassi
- European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Tim Treis
- European Molecular Biology Laboratory, Heidelberg, Germany
- Institute of Computational Biology, Helmholtz Center München, Neuherberg, Germany
| | - Sonja Blasche
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Kiran Raosaheb Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | | | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
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Tan J, Fu B, Zhao X, Ye L. Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism. Eur J Drug Metab Pharmacokinet 2024; 49:131-147. [PMID: 38123834 DOI: 10.1007/s13318-023-00874-0] [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] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. In diverse individuals, variations in the gut microbiota can result in differences in microbe-drug interactions, underscoring the importance of personalized approaches in pharmacotherapy. However, previous studies on drug metabolism in the gut microbiota have been hampered by technical limitations. Nowadays, advances in biotechnological tools, such as microbially derived metabolism screening and microbial gene editing, have provided a deeper insight into the mechanism of drug metabolism by gut microbiota, moving us toward personalized therapeutic interventions. Given this situation, our review summarizes recent advances in the study of gut-microbiota-mediated drug metabolism and showcases techniques and models developed to navigate the challenges posed by the microbial involvement in drug action. Therefore, we not only aim at understanding the complex interaction between the gut microbiota and drugs and outline the development of research techniques and models, but we also summarize the specific applications of new techniques and models in researching gut-microbiota-mediated drug metabolism, with the expectation of providing new insights on how to study drug metabolism by gut microbiota.
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Affiliation(s)
- Jianling Tan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingxuan Fu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaojie Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ling Ye
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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Wang Y, Ma M, Dai W, Shang Q, Yu G. Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota. MICROBIOME 2024; 12:41. [PMID: 38419055 PMCID: PMC10902947 DOI: 10.1186/s40168-024-01768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
Chondroitin sulfate (CS) has widely been used as a symptomatic slow-acting drug or a dietary supplement for the treatment and prevention of osteoarthritis. However, CS could not be absorbed after oral intake due to its polyanionic nature and large molecular weight. Gut microbiota has recently been proposed to play a pivotal role in the metabolism of drugs and nutrients. Nonetheless, how CS is degraded by the human gut microbiota has not been fully characterized. In the present study, we demonstrated that each human gut microbiota was characterized with a unique capability for CS degradation. Degradation and fermentation of CS by the human gut microbiota produced significant amounts of unsaturated CS oligosaccharides (CSOSs) and short-chain fatty acids. To uncover which microbes were responsible for CS degradation, we isolated a total of 586 bacterial strains with a potential CS-degrading capability from 23 human fecal samples. Bacteroides salyersiae was a potent species for CS degradation in the human gut microbiota and produced the highest amount of CSOSs as compared to other well-recognized CS-degraders, including Bacteroides finegoldii, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, and Bacteroides ovatus. Genomic analysis suggested that B. salyersiae was armed with multiple carbohydrate-active enzymes that could potentially degrade CS into CSOSs. By using a spent medium assay, we further demonstrated that the unsaturated tetrasaccharide (udp4) produced by the primary degrader B. salyersiae could serve as a "public goods" molecule for the growth of Bacteroides stercoris, a secondary CS-degrader that was proficient at fermenting CSOSs but not CS. Taken together, our study provides insights into the metabolism of CS by the human gut microbiota, which has promising implications for the development of medical and nutritional therapies for osteoarthritis. Video Abstract.
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Affiliation(s)
- Yamin Wang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Mingfeng Ma
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Wei Dai
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qingsen Shang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China.
- Qingdao Marine Biomedical Research Institute, Qingdao, 266071, China.
| | - Guangli Yu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China.
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Loh JS, Mak WQ, Tan LKS, Ng CX, Chan HH, Yeow SH, Foo JB, Ong YS, How CW, Khaw KY. Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases. Signal Transduct Target Ther 2024; 9:37. [PMID: 38360862 PMCID: PMC10869798 DOI: 10.1038/s41392-024-01743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 01/02/2024] [Accepted: 01/14/2024] [Indexed: 02/17/2024] Open
Abstract
The human gastrointestinal tract is populated with a diverse microbial community. The vast genetic and metabolic potential of the gut microbiome underpins its ubiquity in nearly every aspect of human biology, including health maintenance, development, aging, and disease. The advent of new sequencing technologies and culture-independent methods has allowed researchers to move beyond correlative studies toward mechanistic explorations to shed light on microbiome-host interactions. Evidence has unveiled the bidirectional communication between the gut microbiome and the central nervous system, referred to as the "microbiota-gut-brain axis". The microbiota-gut-brain axis represents an important regulator of glial functions, making it an actionable target to ameliorate the development and progression of neurodegenerative diseases. In this review, we discuss the mechanisms of the microbiota-gut-brain axis in neurodegenerative diseases. As the gut microbiome provides essential cues to microglia, astrocytes, and oligodendrocytes, we examine the communications between gut microbiota and these glial cells during healthy states and neurodegenerative diseases. Subsequently, we discuss the mechanisms of the microbiota-gut-brain axis in neurodegenerative diseases using a metabolite-centric approach, while also examining the role of gut microbiota-related neurotransmitters and gut hormones. Next, we examine the potential of targeting the intestinal barrier, blood-brain barrier, meninges, and peripheral immune system to counteract glial dysfunction in neurodegeneration. Finally, we conclude by assessing the pre-clinical and clinical evidence of probiotics, prebiotics, and fecal microbiota transplantation in neurodegenerative diseases. A thorough comprehension of the microbiota-gut-brain axis will foster the development of effective therapeutic interventions for the management of neurodegenerative diseases.
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Affiliation(s)
- Jian Sheng Loh
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Wen Qi Mak
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Li Kar Stella Tan
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
- Digital Health & Medical Advancements, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Chu Xin Ng
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Hong Hao Chan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Shiau Hueh Yeow
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Jhi Biau Foo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
- Digital Health & Medical Advancements, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Yong Sze Ong
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Chee Wun How
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
| | - Kooi Yeong Khaw
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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42
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Verdegaal AA, Goodman AL. Integrating the gut microbiome and pharmacology. Sci Transl Med 2024; 16:eadg8357. [PMID: 38295186 DOI: 10.1126/scitranslmed.adg8357] [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: 02/13/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024]
Abstract
The gut microbiome harbors trillions of organisms that contribute to human health and disease. These bacteria can also affect the properties of medical drugs used to treat these diseases, and drugs, in turn, can reshape the microbiome. Research addressing interdependent microbiome-host-drug interactions thus has broad impact. In this Review, we discuss these interactions from the perspective of drug bioavailability, absorption, metabolism, excretion, toxicity, and drug-mediated microbiome modulation. We survey approaches that aim to uncover the mechanisms underlying these effects and opportunities to translate this knowledge into new strategies to improve the development, administration, and monitoring of medical drugs.
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Affiliation(s)
- Andrew A Verdegaal
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics. Cell Rep 2024; 43:113519. [PMID: 38142398 DOI: 10.1016/j.celrep.2023.113519] [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: 07/17/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.
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Affiliation(s)
- Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Saria A McKeithen-Mead
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emma R Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Ferenc K, Sokal-Dembowska A, Helma K, Motyka E, Jarmakiewicz-Czaja S, Filip R. Modulation of the Gut Microbiota by Nutrition and Its Relationship to Epigenetics. Int J Mol Sci 2024; 25:1228. [PMID: 38279228 PMCID: PMC10816208 DOI: 10.3390/ijms25021228] [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: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
The intestinal microbiota is a community of microorganisms inhabiting the human intestines, potentially influencing both physiological and pathophysiological processes in the human body. Existing evidence suggests that nutrients can influence the modulation of the gut microbiota. However, there is still limited evidence regarding the effects of vitamin and mineral supplementation on the human gut microbiota through epigenetic modification. It is plausible that maintaining an adequate dietary intake of vitamin D, iron, fibre, zinc and magnesium may have a beneficial effect on alleviating inflammation in the body, reducing oxidative stress, and improving the condition of the intestinal microbiota through various epigenetic mechanisms. Moreover, epigenetics involves alterations in the phenotype of a cell without changing its fundamental DNA sequence. It appears that the modulation of the microbiota by various nutrients may lead to epigenetic regulation. The correlations between microbiota and epigenetics are potentially interdependent. Therefore, the primary objective of this review is to identify the complex relationships between diet, gut microbiota, and epigenetic regulation. These interactions could play a crucial role in systemic health.
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Affiliation(s)
- Katarzyna Ferenc
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Aneta Sokal-Dembowska
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Kacper Helma
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Elżbieta Motyka
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | | | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Gastroenterology with IBD Unit, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
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Wang S, Ju D, Zeng X. Mechanisms and Clinical Implications of Human Gut Microbiota-Drug Interactions in the Precision Medicine Era. Biomedicines 2024; 12:194. [PMID: 38255298 PMCID: PMC10813426 DOI: 10.3390/biomedicines12010194] [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: 11/05/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
The human gut microbiota, comprising trillions of microorganisms residing in the gastrointestinal tract, has emerged as a pivotal player in modulating various aspects of human health and disease. Recent research has shed light on the intricate relationship between the gut microbiota and pharmaceuticals, uncovering profound implications for drug metabolism, efficacy, and safety. This review depicted the landscape of molecular mechanisms and clinical implications of dynamic human gut Microbiota-Drug Interactions (MDI), with an emphasis on the impact of MDI on drug responses and individual variations. This review also discussed the therapeutic potential of modulating the gut microbiota or harnessing its metabolic capabilities to optimize clinical treatments and advance personalized medicine, as well as the challenges and future directions in this emerging field.
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Affiliation(s)
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China;
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China;
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He X, Gao X, Hong Y, Zhong J, Li Y, Zhu W, Ma J, Huang W, Li Y, Li Y, Wang H, Liu Z, Bao Y, Pan L, Zheng N, Sheng L, Li H. High Fat Diet and High Sucrose Intake Divergently Induce Dysregulation of Glucose Homeostasis through Distinct Gut Microbiota-Derived Bile Acid Metabolism in Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:230-244. [PMID: 38079533 DOI: 10.1021/acs.jafc.3c02909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
A high calorie diet such as excessive fat and sucrose intake is always accompanied by impaired glucose homeostasis such as T2DM (type 2 diabetes mellitus). However, it remains unclear how fat and sucrose individually affect host glucose metabolism. In this study, mice were fed with high fat diet (HFD) or 30% sucrose in drinking water (HSD) for 24 weeks, and glucose metabolism, gut microbiota composition, as well as bile acid (BA) profile were investigated. In addition, the functional changes of HFD or HSD-induced gut microbiota were further verified by fecal microbiota transplantation (FMT) and ex vivo culture of gut bacteria with BAs. Our results showed that both HFD and HSD caused dysregulated lipid metabolism, while HFD feeding had a more severe effect on impaired glucose homeostasis, accompanied by reduced hyocholic acid (HCA) levels in all studied tissues. Meanwhile, HFD had a more dramatic influence on composition and function of gut microbiota based on α diversity indices, β diversity analysis, as well as the abundance of secondary BA producers than HSD. In addition, the phenotypes of impaired glucose homeostasis and less formation of HCA caused by HFD can be transferred to recipient mice by FMT. Ex vivo culture with gut bacteria and BAs revealed HFD-altered gut bacteria produced less HCA than HSD, which might closely associate with reduced relative abundance of C7 epimerase-coding bacteria g_norank/unclassified_f_Eggerthellaceae and bile salt hydrolase-producing bacteria Lactobacillus and Bifidobacterium in HFD group. Our findings revealed that the divergent effects of different high-calorie diets on glucose metabolism may be due to the gut microbiota-mediated generation and metabolism of BAs, highlighting the importance of dietary management in T2DM.
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Affiliation(s)
- Xiaofang He
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xinxin Gao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ying Hong
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jing Zhong
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou 313000, China
| | - Yue Li
- Department of Endocrinology, Shanghai Fifth People's Hospital, Shanghai Medical School, Fudan University, Shanghai 200032, China
| | - Weize Zhu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Junli Ma
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wenjin Huang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yifan Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yan Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hao Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zekun Liu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yiyang Bao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lingyun Pan
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ningning Zheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Sheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Houkai Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Raslan MA, Raslan SA, Shehata EM, Mahmoud AS, Viana MVC, Aburjaile F, Barh D, Sabri NA, Azevedo V. Mass Spectrometry Applications to Study Human Microbiome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:87-101. [PMID: 38409417 DOI: 10.1007/978-3-031-50624-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbiotas are an adaptable component of ecosystems, including human ecology. Microorganisms influence the chemistry of their specialized niche, such as the human gut, as well as the chemistry of distant surroundings, such as other areas of the body. Metabolomics based on mass spectrometry (MS) is one of the primary methods for detecting and identifying small compounds generated by the human microbiota, as well as understanding the functional significance of these microbial metabolites. This book chapter gives basic knowledge on the kinds of untargeted mass spectrometry as well as the data types that may be generated in the context of microbiome study. While data analysis remains a barrier, the emphasis is on data analysis methodologies and integrative analysis, particularly the integration of microbiome sequencing data. Mass spectrometry (MS)-based techniques have resurrected culture methods for studying the human gut microbiota, filling in the gaps left by high-throughput sequencing methods in terms of culturing minor populations.
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Affiliation(s)
| | | | | | - Amr S Mahmoud
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marcus Vinicius Canário Viana
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávia Aburjaile
- Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Nagwa A Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Wan L, Shi X, Yan H, Liang Y, Liu X, Zhu G, Zhang J, Wang J, Wang M, Yang G. Abnormalities in Clostridioides and related metabolites before ACTH treatment may be associated with its efficacy in patients with infantile epileptic spasm syndrome. CNS Neurosci Ther 2024; 30:e14398. [PMID: 37553527 PMCID: PMC10805391 DOI: 10.1111/cns.14398] [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: 05/08/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023] Open
Abstract
OBJECTIVE Adrenocorticotropic hormone (ACTH) is the first-line treatment of infantile epileptic spasm syndrome (IESS). Its reported effectiveness varies, and our current understanding regarding the role of gut microbiota composition in IESS treatment response is limited. This study assessed the microbiome-metabolome association to understand the role and mechanism of gut microbiota composition in IESS treatment outcomes. METHODS Children with IESS undergoing ACTH treatment were enrolled. Pre-treatment stool and serum samples were collected for 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry, respectively. The children were divided into "responsive" and "non-responsive" groups, and gut microbiota and serum metabolome differences were analyzed. RESULTS Of the 30 patients with IESS, 14 responded to ACTH and 16 did not. The "non-responsive" group had larger maleficent Clostridioides and Peptoclostridium_phage_p630P populations (linear discriminant analysis >2; false discovery rate q < 0.05). Ten metabolites were upregulated (e.g., xanthurenic acid) and 15 were downregulated (e.g., vanillylmandelic acid) (p < 0.05). Association analysis of the gut microbiome and serum metabolome revealed that Clostridioides and Peptoclostridium_phage_p630P2 were positively correlated with linoleic and xanthurenic acids, while Clostridioides was negatively correlated with vanillylmandelic acid (p < 0.05). A classifier using differential gut bacteria and metabolites achieved an area under the receiver operating characteristic curve of 0.906 to distinguish responders from non-responders. CONCLUSION This study found significant differences in pre-treatment gut microbiota and serum metabolome between children with IESS who responded to ACTH and those who did not. Additional exploration may provide valuable information for treatment selection and potential interventions. Our results suggest that varying ACTH responses in patients with IESS may be associated with increased gut Clostridioides bacteria and kynurenine pathway alteration, but additional experiments are needed to verify this association.
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Affiliation(s)
- Lin Wan
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
| | - Xiuyu Shi
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
- The Second School of Clinical MedicineSouthern Medical UniversityGuangzhouChina
| | - Huimin Yan
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
| | - Yan Liang
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
| | - Xinting Liu
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
| | - Gang Zhu
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
| | - Jing Zhang
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
| | - Jing Wang
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
| | - Mingbang Wang
- Microbiome Therapy Center, South China Hospital, Medical School, Shenzhen UniversityShenzhenChina
- Shanghai Key Laboratory of Birth Defects, Division of NeonatologyChildren's Hospital of Fudan University, National Center for Children's HealthShanghaiChina
- Marshall Laboratory of Biomedical EngineeringMedical School, Shenzhen UniversityShenzhenChina
| | - Guang Yang
- Senior Department of PediatricsThe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of PediatricsThe First Medical Centre, Chinese PLA General HospitalBeijingChina
- Medical School of Chinese People's Liberation ArmyBeijingChina
- The Second School of Clinical MedicineSouthern Medical UniversityGuangzhouChina
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Zhou L, Lu G, Nie Y, Ren Y, Shi JS, Xue Y, Xu ZH, Geng Y. Restricted intake of sulfur-containing amino acids reversed the hepatic injury induced by excess Desulfovibrio through gut-liver axis. Gut Microbes 2024; 16:2370634. [PMID: 38935546 PMCID: PMC11212577 DOI: 10.1080/19490976.2024.2370634] [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: 02/01/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
Diet is a key player in gut-liver axis. However, the effect of different dietary patterns on gut microbiota and liver functions remains unclear. Here, we used rodent standard chow and purified diet to mimic two common human dietary patterns: grain and plant-based diet and refined-food-based diet, respectively and explored their impacts on gut microbiota and liver. Gut microbiota experienced a great shift with notable increase in Desulfovibrio, gut bile acid (BA) levels elevated significantly, and liver inflammation was observed in mice fed with the purified diet. Liver inflammation and elevated gut BA levels also occurred in mice fed with the chow diet after receiving Desulfovibrio desulfuricans ATCC 29,577 (DSV). Restriction of sulfur-containing amino acids (SAAs) prevented liver injury mainly through higher hepatic antioxidant and detoxifying ability and reversed the elevated BA levels due to excess Desulfovibrio. Ex vivo fermentation of human fecal microbiota with primary BAs demonstrated that DSV enhanced production of secondary BAs. Higher concentration of both primary and secondary BAs were found in the gut of germ-free mice after receiving DSV. In conclusion, Restriction of SAAs in diet may become an effective dietary intervention to prevent liver injury associated with excess Desulfovibrio in the gut.
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Affiliation(s)
- Lingxi Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Gexue Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Yawen Nie
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Yilin Ren
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Yuzheng Xue
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Zheng-Hong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Yan Geng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
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50
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Martinelli F, Thiele I. Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities. Gut Microbes 2024; 16:2387400. [PMID: 39150897 PMCID: PMC11332652 DOI: 10.1080/19490976.2024.2387400] [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: 01/31/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/18/2024] Open
Abstract
This comprehensive review elucidates the pivotal role of microbes in drug metabolism, synthesizing insights from an exhaustive analysis of over two hundred papers. Employing a structural classification system grounded in drug atom involvement, the review categorizes the microbiome-mediated drug-metabolizing capabilities of over 80 drugs. Additionally, it compiles pharmacodynamic and enzymatic details related to these reactions, striving to include information on encoding genes and specific involved microorganisms. Bridging biochemistry, pharmacology, genetics, and microbiology, this review not only serves to consolidate diverse research fields but also highlights the potential impact of microbial drug metabolism on future drug design and in silico studies. With a visionary outlook, it also lays the groundwork for personalized medicine interventions, emphasizing the importance of interdisciplinary collaboration for advancing drug development and enhancing therapeutic strategies.
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Affiliation(s)
- Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Digital Metabolic Twin Centre, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland
- Digital Metabolic Twin Centre, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
- School of Microbiology, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
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