1
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Metabolism of organic carcinogens by gut bacteria induces bladder tumours. Nature 2024:10.1038/d41586-024-02740-8. [PMID: 39198604 DOI: 10.1038/d41586-024-02740-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2024]
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2
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Lariviere PJ, Ashraf AHMZ, Navarro-Escalante L, Leonard SP, Miller LG, Moran NA, Barrick JE. One-step genome engineering in bee gut bacterial symbionts. mBio 2024:e0139224. [PMID: 39105596 DOI: 10.1128/mbio.01392-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 08/07/2024] Open
Abstract
Mechanistic understanding of interactions in many host-microbe systems, including the honey bee microbiome, is limited by a lack of easy-to-use genome engineering approaches. To this end, we demonstrate a one-step genome engineering approach for making gene deletions and insertions in the chromosomes of honey bee gut bacterial symbionts. Electroporation of linear or non-replicating plasmid DNA containing an antibiotic resistance cassette flanked by regions with homology to a symbiont genome reliably results in chromosomal integration. This lightweight approach does not require expressing any exogenous recombination machinery. The high concentrations of large DNAs with long homology regions needed to make the process efficient can be readily produced using modern DNA synthesis and assembly methods. We use this approach to knock out genes, including genes involved in biofilm formation, and insert fluorescent protein genes into the chromosome of the betaproteobacterial bee gut symbiont Snodgrassella alvi. We are also able to engineer the genomes of multiple strains of S. alvi and another species, Snodgrassella communis, which is found in the bumble bee gut microbiome. Finally, we use the same method to engineer the chromosome of another bee symbiont, Bartonella apis, which is an alphaproteobacterium. As expected, gene knockout in S. alvi using this approach is recA-dependent, suggesting that this straightforward procedure can be applied to other microbes that lack convenient genome engineering methods. IMPORTANCE Honey bees are ecologically and economically important crop pollinators with bacterial gut symbionts that influence their health. Microbiome-based strategies for studying or improving bee health have utilized wild-type or plasmid-engineered bacteria. We demonstrate that a straightforward, single-step method can be used to insert cassettes and replace genes in the chromosomes of multiple bee gut bacteria. This method can be used for investigating the mechanisms of host-microbe interactions in the bee gut community and stably engineering symbionts that benefit pollinator health.
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Affiliation(s)
- Patrick J Lariviere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - A H M Zuberi Ashraf
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | | | - Sean P Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Laurel G Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Nancy A Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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3
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Zhang S, Hou R, Sun C, Huang Q, Lin L, Li H, Liu S, Cheng Y, Xu X. Metabolic activity of gut microbial enrichment cultures from different marine species and their transformation abilities to plastic additives. ENVIRONMENT INTERNATIONAL 2024; 190:108882. [PMID: 38996798 DOI: 10.1016/j.envint.2024.108882] [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: 04/15/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024]
Abstract
The role of the gut microbiota in host physiology has been previously elucidated for some marine organisms, but little information is available on their metabolic activity involved in transformation of environmental pollutants. This study assessed the metabolic profiles of the gut microbial cultures from grouper (Epinephelus coioides), green mussel (Perna viridis) and giant tiger prawn (Penaeus monodon) and investigated their transformation mechanisms to typical plastic additives. Community-level physiological profiling analysis confirmed the utilization profiles of the microbial cultures including carbon sources of carbohydrates, amines, carboxylic acids, phenolic compounds, polymers and amino acids, and the plastic additives of organophosphate flame retardants, tetrabromobisphenol A derivates and bisphenols. Using in vitro incubation, triphenyl phosphate (TPHP) was found to be rapidly metabolized into diphenyl phosphate by the gut microbiota as a representative ester-containing plastic additive, whereas the transformation of BPA (a representative phenol) was relatively slower. Interestingly, all three kinds of microbial cultures efficiently transformed the hepatic metabolite of BPA (BPA-G) back to BPA, thereby increasing its bioavailability in the body. The specific enzyme analysis confirmed the ability of the gut microbiota to perform the metabolic reactions. The results of 16S rRNA sequencing and network analysis revealed that the genera Escherichia-Shigella, Citrobacter, and Anaerospora were functional microbes, and their collaboration with fermentative microbes played pivotal roles in the transformation of the plastic additives. The structure-specific transformations by the gut microbiota and their distinct bioavailability deserve more attention in the future.
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Affiliation(s)
- Siqi Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Hou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Chuansheng Sun
- Marine College, Shandong University, Weihai 264209, China
| | - Qianyi Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lang Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hengxiang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Shan Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yuanyue Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xiangrong Xu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China.
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4
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Caldarelli M, Rio P, Marrone A, Giambra V, Gasbarrini A, Gambassi G, Cianci R. Inflammaging: The Next Challenge-Exploring the Role of Gut Microbiota, Environmental Factors, and Sex Differences. Biomedicines 2024; 12:1716. [PMID: 39200181 PMCID: PMC11351301 DOI: 10.3390/biomedicines12081716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 09/02/2024] Open
Abstract
The term 'inflammaging' has been coined to describe the chronic state of inflammation derived from ongoing cycles of tissue damage and the subsequent immune responses. This inflammatory status contributes to the decline of organs and physiological functions, accelerates the aging process, and increases the risk of age-related illnesses and death. During aging, the gut microbiota (GM) undergoes significant changes, including a decreased diversity of species, a decline in beneficial bacteria, and a rise in proinflammatory ones, resulting in persistent low-grade inflammation. Moreover, environmental factors, such as diet and medications, contribute to age-related changes in GM and immune function, preventing or promoting inflammaging. This narrative review aims to clarify the underlying mechanisms of inflammaging and to specifically investigate the influence of GM and several environmental factors on these mechanisms, while also exploring potential differences related to sex. Moreover, lifestyle and pharmacological interventions will be suggested to promote healthy aging.
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Affiliation(s)
- Mario Caldarelli
- Department of Translational Medicine and Surgery, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.C.); (P.R.); (A.M.); (A.G.); (G.G.)
- Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
| | - Pierluigi Rio
- Department of Translational Medicine and Surgery, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.C.); (P.R.); (A.M.); (A.G.); (G.G.)
- Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
| | - Andrea Marrone
- Department of Translational Medicine and Surgery, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.C.); (P.R.); (A.M.); (A.G.); (G.G.)
- Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
| | - Vincenzo Giambra
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy;
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.C.); (P.R.); (A.M.); (A.G.); (G.G.)
- Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
| | - Giovanni Gambassi
- Department of Translational Medicine and Surgery, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.C.); (P.R.); (A.M.); (A.G.); (G.G.)
- Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
| | - Rossella Cianci
- Department of Translational Medicine and Surgery, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.C.); (P.R.); (A.M.); (A.G.); (G.G.)
- Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
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Roje B, Zhang B, Mastrorilli E, Kovačić A, Sušak L, Ljubenkov I, Ćosić E, Vilović K, Meštrović A, Vukovac EL, Bučević-Popović V, Puljiz Ž, Karaman I, Terzić J, Zimmermann M. Gut microbiota carcinogen metabolism causes distal tissue tumours. Nature 2024; 632:1137-1144. [PMID: 39085612 PMCID: PMC11358042 DOI: 10.1038/s41586-024-07754-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Exposure to environmental pollutants and human microbiome composition are important predisposition factors for tumour development1,2. Similar to drug molecules, pollutants are typically metabolized in the body, which can change their carcinogenic potential and affect tissue distribution through altered toxicokinetics3. Although recent studies demonstrated that human-associated microorganisms can chemically convert a wide range of xenobiotics and influence the profile and tissue exposure of resulting metabolites4,5, the effect of microbial biotransformation on chemical-induced tumour development remains unclear. Here we show that the depletion of the gut microbiota affects the toxicokinetics of nitrosamines, which markedly reduces the development and severity of nitrosamine-induced urinary bladder cancer in mice6,7. We causally linked this carcinogen biotransformation to specific gut bacterial isolates in vitro and in vivo using individualized bacterial culture collections and gnotobiotic mouse models, respectively. We tested gut communities from different human donors to demonstrate that microbial carcinogen metabolism varies between individuals and we showed that this metabolic activity applies to structurally related nitrosamine carcinogens. Altogether, these results indicate that gut microbiota carcinogen metabolism may be a contributing factor for chemical-induced carcinogenesis, which could open avenues to target the microbiome for improved predisposition risk assessment and prevention of cancer.
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Affiliation(s)
- Blanka Roje
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Boyao Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eleonora Mastrorilli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ana Kovačić
- Public Health Institute of Split and Dalmatia County, Split, Croatia
| | - Lana Sušak
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Ivica Ljubenkov
- Department of Chemistry, University of Split Faculty of Science, Split, Croatia
| | - Elena Ćosić
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Katarina Vilović
- Department of Pathology, University Hospital of Split, Split, Croatia
| | - Antonio Meštrović
- Department of Gastroenterology, University Hospital of Split, Split, Croatia
| | | | | | - Željko Puljiz
- Department of Gastroenterology, University Hospital of Split, Split, Croatia
| | - Ivana Karaman
- Department of Pathology, University Hospital of Split, Split, Croatia
| | - Janoš Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia.
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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6
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Xie Y, Zhu H, Yuan Y, Guan X, Xie Q, Dong Z. Baseline gut microbiota profiles affect treatment response in patients with depression. Front Microbiol 2024; 15:1429116. [PMID: 39021622 PMCID: PMC11251908 DOI: 10.3389/fmicb.2024.1429116] [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: 05/07/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
The role of the gut microbiota in the pathophysiology of depression has been explored in numerous studies, which have confirmed that the baseline gut microbial profiles of patients with depression differ from those of healthy individuals. The gut microbiome affects metabolic activity in the immune and central nervous systems and regulates intestinal ecology through the neuroendocrine system. Additionally, baseline changes in the gut microbiota differed among patients with depression who demonstrated varying treatment response. Currently, probiotics are an emerging treatment for depression; however, the efficacy of modulating the gut microbiota in the treatment of depression remains uncertain. Additionally, the mechanisms by which changes in the gut microbiota affect treatment response in patients with depression remain unclear. In this review, we aimed to summarize the differences in the baseline gut microbiota between the remission and non-remission groups after antidepressant therapy. Additionally, we summarized the possible mechanisms that may contribute to antidepressant resistance through the effects of the gut microbiome on the immune and nervous systems, various enzymes, bioaccumulation, and blood-brain barrier, and provide a basis for treating depression by targeting the gut microbiota.
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Affiliation(s)
- Yingjing Xie
- West China Hospital, Sichuan University, Chengdu, China
| | - Hanwen Zhu
- West China Hospital, Sichuan University, Chengdu, China
| | - Yanling Yuan
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Xuan Guan
- Chengdu Medical College, Chengdu, China
| | - Qinglian Xie
- Department of Outpatient, West China Hospital, Sichuan University, Chengdu, China
| | - Zaiquan Dong
- Department of Psychiatry and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, China
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7
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Shin YC, Than N, Park SJ, Kim HJ. Bioengineered human gut-on-a-chip for advancing non-clinical pharmaco-toxicology. Expert Opin Drug Metab Toxicol 2024; 20:593-606. [PMID: 38849312 DOI: 10.1080/17425255.2024.2365254] [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: 02/09/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
INTRODUCTION There is a growing need for alternative models to advance current non-clinical experimental models because they often fail to accurately predict drug responses in human clinical trials. Human organ-on-a-chip models have emerged as promising approaches for advancing the predictability of drug behaviors and responses. AREAS COVERED We summarize up-to-date human gut-on-a-chip models designed to demonstrate intricate interactions involving the host, microbiome, and pharmaceutical compounds since these models have been reported a decade ago. This overview covers recent advances in gut-on-a-chip models as a bridge technology between non-clinical and clinical assessments of drug toxicity and metabolism. We highlight the promising potential of gut-on-a-chip platforms, offering a reliable and valid framework for investigating reciprocal crosstalk between the host, gut microbiome, and drug compounds. EXPERT OPINION Gut-on-a-chip platforms can attract multiple end users as predictive, human-relevant, and non-clinical model. Notably, gut-on-a-chip platforms provide a unique opportunity to recreate a human intestinal microenvironment, including dynamic bowel movement, luminal flow, oxygen gradient, host-microbiome interactions, and disease-specific manipulations restricted in animal and in vitro cell culture models. Additionally, given the profound impact of the gut microbiome on pharmacological bioprocess, it is critical to leverage breakthroughs of gut-on-a-chip technology to address knowledge gaps and drive innovations in predictive drug toxicology and metabolism.
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Affiliation(s)
- Yong Cheol Shin
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nam Than
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Soo Jin Park
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hyun Jung Kim
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Inflammation and Immunity, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
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8
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Enright AL, Heelan WJ, Ward RD, Peters JM. CRISPRi functional genomics in bacteria and its application to medical and industrial research. Microbiol Mol Biol Rev 2024; 88:e0017022. [PMID: 38809084 PMCID: PMC11332340 DOI: 10.1128/mmbr.00170-22] [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: 05/30/2024] Open
Abstract
SUMMARYFunctional genomics is the use of systematic gene perturbation approaches to determine the contributions of genes under conditions of interest. Although functional genomic strategies have been used in bacteria for decades, recent studies have taken advantage of CRISPR (clustered regularly interspaced short palindromic repeats) technologies, such as CRISPRi (CRISPR interference), that are capable of precisely modulating expression of all genes in the genome. Here, we discuss and review the use of CRISPRi and related technologies for bacterial functional genomics. We discuss the strengths and weaknesses of CRISPRi as well as design considerations for CRISPRi genetic screens. We also review examples of how CRISPRi screens have defined relevant genetic targets for medical and industrial applications. Finally, we outline a few of the many possible directions that could be pursued using CRISPR-based functional genomics in bacteria. Our view is that the most exciting screens and discoveries are yet to come.
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Affiliation(s)
- Amy L. Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - William J. Heelan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Duan Y, Nan Y, Xiao M, Yang Y. Toxicity of three microcystin variants on the histology, physiological and metabolism of hepatopancreas and intestinal microbiota of Litopenaeus vannamei. Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109904. [PMID: 38508355 DOI: 10.1016/j.cbpc.2024.109904] [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: 02/15/2024] [Revised: 03/10/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Microcystins (MCs) are prevalent harmful contaminants within shrimp aquaculture systems, exhibiting a diverse array of variants. Gut microbiota can engage in mutual interactions with the host through the gut-liver axis. In this study, the shrimp Litopenaeus vannamei were subjected to three different variants of MCs (LR, YR, RR) at a concentration of 1 μg/L each, and elucidated the alterations in both intestinal microbiota and hepatopancreas physiological homeostasis. The results showed that all three variants of MCs prompted histological alterations in the hepatopancreas, induced elevated levels of oxidative stress biomarkers (H2O2, T-SOD, and CAT), disturbed the transcription levels of immune-related genes (Crus, ALF, and Lys), along with an increase in apoptotic genes (Casp-3 and P53). Furthermore, the metabolic profiles of the hepatopancreas were perturbed, particularly in amino acid metabolism such as "lysine degradation" and "β-alanine metabolism"; the mTOR and FoxO signaling were also influenced, encompassing alterations in the transcription levels of related genes. Additionally, the alterations were observed in the intestinal microbiota's diversity and composition, particularly potential beneficial bacteria (Alloprevotella, Bacteroides, Collinsella, Faecalibacterium, and Prevotellaceae UCG-001), which exhibited a positive correlation with the metabolite berberine. These findings reveal that the three MCs variants can impact the health of the shrimp by interfering with the homeostasis of intestinal microbial and hepatopancreas physiology.
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Affiliation(s)
- Yafei Duan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, PR China.
| | - Yuxiu Nan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Meng Xiao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Yukai Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518121, PR China
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Balleza-Alejandri LR, Peña-Durán E, Beltrán-Ramírez A, Reynoso-Roa AS, Sánchez-Abundis LD, García-Galindo JJ, Suárez-Rico DO. Decoding the Gut Microbiota-Gestational Diabetes Link: Insights from the Last Seven Years. Microorganisms 2024; 12:1070. [PMID: 38930451 PMCID: PMC11205738 DOI: 10.3390/microorganisms12061070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/04/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
The human microbiome, a complex ecosystem of bacteria, viruses, and protozoans living in symbiosis with the host, plays a crucial role in human health, influencing everything from metabolism to immune function. Dysbiosis, or an imbalance in this ecosystem, has been linked to various health issues, including diabetes and gestational diabetes (GD). In diabetes, dysbiosis affects the function of adipose tissue, leading to the release of adipokines and cytokines, which increase inflammation and insulin resistance. During pregnancy, changes to the microbiome can exacerbate glucose intolerance, a common feature of GD. Over the past years, burgeoning insights into the gut microbiota have unveiled its pivotal role in human health. This article comprehensively reviews literature from the last seven years, highlighting the association between gut microbiota dysbiosis and GD, as well as the metabolism of antidiabetic drugs and the potential influences of diet and probiotics. The underlying pathophysiological mechanisms discussed include the impact of dysbiosis on systemic inflammation and the interplay with genetic and environmental factors. By focusing on recent studies, the importance of considering microbial health in the prevention and treatment of GD is emphasized, providing insights into future research directions and clinical applications to improve maternal-infant health outcomes.
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Affiliation(s)
- Luis Ricardo Balleza-Alejandri
- Doctorado en Farmacología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (L.R.B.-A.); (A.S.R.-R.)
| | - Emiliano Peña-Durán
- Licenciatura en Médico Cirujano y Partero, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Alberto Beltrán-Ramírez
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Calle Sierra Mojada 950, Independencia Oriente, Guadalajara 44340, Mexico; (A.B.-R.); (J.J.G.-G.)
| | - Africa Samantha Reynoso-Roa
- Doctorado en Farmacología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (L.R.B.-A.); (A.S.R.-R.)
| | - Luis Daniel Sánchez-Abundis
- Hospital Civil de Guadalajara, Fray Antonio Alcalde, Instituto de Patología Infecciosa y Experimental, Guadalajara 44200, Mexico;
| | - Jesús Jonathan García-Galindo
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Calle Sierra Mojada 950, Independencia Oriente, Guadalajara 44340, Mexico; (A.B.-R.); (J.J.G.-G.)
| | - Daniel Osmar Suárez-Rico
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Calle Sierra Mojada 950, Independencia Oriente, Guadalajara 44340, Mexico; (A.B.-R.); (J.J.G.-G.)
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11
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Vazquez-Uribe R, Hedin KA, Licht TR, Nieuwdorp M, Sommer MOA. Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases. Trends Endocrinol Metab 2024:S1043-2760(24)00115-2. [PMID: 38782649 DOI: 10.1016/j.tem.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The rising prevalence of metabolic diseases calls for innovative treatments. Peptide-based drugs have transformed the management of conditions such as obesity and type 2 diabetes. Yet, challenges persist in oral delivery of these peptides. This review explores the potential of 'advanced microbiome therapeutics' (AMTs), which involve engineered microbes for delivery of peptides in situ, thereby enhancing their bioavailability. Preclinical work on AMTs has shown promise in treating animal models of metabolic diseases, including obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease. Outstanding challenges toward realizing the potential of AMTs involve improving peptide expression, ensuring predictable colonization control, enhancing stability, and managing safety and biocontainment concerns. Still, AMTs have potential for revolutionizing the treatment of metabolic diseases, potentially offering dynamic and personalized novel therapeutic approaches.
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Affiliation(s)
- Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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12
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Stevanoska M, Folz J, Beekmann K, Aichinger G. Physiologically based kinetic (PBK) modeling as a new approach methodology (NAM) for predicting systemic levels of gut microbial metabolites. Toxicol Lett 2024; 396:94-102. [PMID: 38685289 DOI: 10.1016/j.toxlet.2024.04.013] [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: 01/17/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
There is a clear need to develop new approach methodologies (NAMs) that combine in vitro and in silico testing to reduce and replace animal use in chemical risk assessment. Physiologically based kinetic (PBK) models are gaining popularity as NAMs in toxico/pharmacokinetics, but their coverage of complex metabolic pathways occurring in the gut are incomplete. Chemical modification of xenobiotics by the gut microbiome plays a critical role in the host response, for example, by prolonging exposure to harmful metabolites, but there is not a comprehensive approach to quantify this impact on human health. There are examples of PBK models that have implemented gut microbial biotransformation of xenobiotics with the gut as a dedicated metabolic compartment. However, the integration of microbial metabolism and parameterization of PBK models is not standardized and has only been applied to a few chemical transformations. A challenge in this area is the measurement of microbial metabolic kinetics, for which different fermentation approaches are used. Without a standardized method to measure gut microbial metabolism ex vivo/in vitro, the kinetic constants obtained will lead to conflicting conclusions drawn from model predictions. Nevertheless, there are specific cases where PBK models accurately predict systemic concentrations of gut microbial metabolites, offering potential solutions to the challenges outlined above. This review focuses on models that integrate gut microbial bioconversions and use ex vivo/in vitro methods to quantify metabolic constants that accurately represent in vivo conditions.
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Affiliation(s)
- Maja Stevanoska
- Laboratory of Toxicology, Institute of Food, Nutrition and Health (IFNH), Department of Health Sciences and Technology, ETH Zürich, Switzerland
| | - Jacob Folz
- Laboratory of Toxicology, Institute of Food, Nutrition and Health (IFNH), Department of Health Sciences and Technology, ETH Zürich, Switzerland
| | - Karsten Beekmann
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, the Netherlands
| | - Georg Aichinger
- Laboratory of Toxicology, Institute of Food, Nutrition and Health (IFNH), Department of Health Sciences and Technology, ETH Zürich, Switzerland.
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13
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Li G, Hou Y, Zhang C, Zhou X, Bao F, Yang Y, Chen L, Yu D. Interplay Between Drug-Induced Liver Injury and Gut Microbiota: A Comprehensive Overview. Cell Mol Gastroenterol Hepatol 2024; 18:101355. [PMID: 38729523 PMCID: PMC11260867 DOI: 10.1016/j.jcmgh.2024.05.003] [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: 02/21/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Drug-induced liver injury is a prevalent severe adverse event in clinical settings, leading to increased medical burdens for patients and presenting challenges for the development and commercialization of novel pharmaceuticals. Research has revealed a close association between gut microbiota and drug-induced liver injury in recent years. However, there has yet to be a consensus on the specific mechanism by which gut microbiota is involved in drug-induced liver injury. Gut microbiota may contribute to drug-induced liver injury by increasing intestinal permeability, disrupting intestinal metabolite homeostasis, and promoting inflammation and oxidative stress. Alterations in gut microbiota were found in drug-induced liver injury caused by antibiotics, psychotropic drugs, acetaminophen, antituberculosis drugs, and antithyroid drugs. Specific gut microbiota and their abundance are associated closely with the severity of drug-induced liver injury. Therefore, gut microbiota is expected to be a new target for the treatment of drug-induced liver injury. This review focuses on the association of gut microbiota with common hepatotoxic drugs and the potential mechanisms by which gut microbiota may contribute to the pathogenesis of drug-induced liver injury, providing a more comprehensive reference for the interaction between drug-induced liver injury and gut microbiota.
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Affiliation(s)
- Guolin Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China; Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yifu Hou
- Department of Organ Transplantation, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China; Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province and Organ Transplantation Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Changji Zhang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China; Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoshi Zhou
- Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Furong Bao
- Department of Nursing, Guanghan People's Hospital, Guanghan, China
| | - Yong Yang
- Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
| | - Lu Chen
- Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China; Department of Organ Transplantation, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
| | - Dongke Yu
- Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
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14
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Argaw-Denboba A, Schmidt TSB, Di Giacomo M, Ranjan B, Devendran S, Mastrorilli E, Lloyd CT, Pugliese D, Paribeni V, Dabin J, Pisaniello A, Espinola S, Crevenna A, Ghosh S, Humphreys N, Boruc O, Sarkies P, Zimmermann M, Bork P, Hackett JA. Paternal microbiome perturbations impact offspring fitness. Nature 2024; 629:652-659. [PMID: 38693261 PMCID: PMC11096121 DOI: 10.1038/s41586-024-07336-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
The gut microbiota operates at the interface of host-environment interactions to influence human homoeostasis and metabolic networks1-4. Environmental factors that unbalance gut microbial ecosystems can therefore shape physiological and disease-associated responses across somatic tissues5-9. However, the systemic impact of the gut microbiome on the germline-and consequently on the F1 offspring it gives rise to-is unexplored10. Here we show that the gut microbiota act as a key interface between paternal preconception environment and intergenerational health in mice. Perturbations to the gut microbiota of prospective fathers increase the probability of their offspring presenting with low birth weight, severe growth restriction and premature mortality. Transmission of disease risk occurs via the germline and is provoked by pervasive gut microbiome perturbations, including non-absorbable antibiotics or osmotic laxatives, but is rescued by restoring the paternal microbiota before conception. This effect is linked with a dynamic response to induced dysbiosis in the male reproductive system, including impaired leptin signalling, altered testicular metabolite profiles and remapped small RNA payloads in sperm. As a result, dysbiotic fathers trigger an elevated risk of in utero placental insufficiency, revealing a placental origin of mammalian intergenerational effects. Our study defines a regulatory 'gut-germline axis' in males, which is sensitive to environmental exposures and programmes offspring fitness through impacting placenta function.
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Affiliation(s)
- Ayele Argaw-Denboba
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Monica Di Giacomo
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Bobby Ranjan
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Saravanan Devendran
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Eleonora Mastrorilli
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Catrin T Lloyd
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Danilo Pugliese
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Violetta Paribeni
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Juliette Dabin
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Alessandra Pisaniello
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Sergio Espinola
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Alvaro Crevenna
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Subhanita Ghosh
- MRC London Institute for Medical Science (LMS), London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Neil Humphreys
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Olga Boruc
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Peter Sarkies
- MRC London Institute for Medical Science (LMS), London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Michael Zimmermann
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
- Department of Bioinformatics, Biozentrum, University of Würzburg, Würzburg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
| | - Jamie A Hackett
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy.
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15
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Lee DY, Kim J, Lee GS, Park S, Song J, Lee BS, Lee SR, Kim KH, Kim CS. Characterization of Chemical Interactions between Clinical Drugs and the Oral Bacterium, Corynebacterium matruchotii, via Bioactivity-HiTES. ACS Chem Biol 2024; 19:973-980. [PMID: 38514380 DOI: 10.1021/acschembio.3c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
In the field of natural product research, the rediscovery of already-known compounds is one of the significant issues hindering new drug development. Recently, an innovative approach called bioactivity-HiTES has been developed to overcome this limitation, and several new bioactive metabolites have been successfully characterized by this method. In this study, we applied bioactivity-HiTES to Corynebacterium matruchotii, the human oral bacterium, with 3120 clinical drugs as potential elicitors. As a result, we identified two cryptic metabolites, methylindole-3-acetate (MIAA) and indole-3-acetic acid (IAA), elicited by imidafenacin, a urinary antispasmodic drug approved by the Japanese Pharmaceuticals and Medical Devices Agency (PMDA). MIAA showed weak antibacterial activity against a pulmonary disease-causing Mycobacterium conceptionense with an IC50 value of 185.7 μM. Unexpectedly, we also found that C. matruchotii metabolized fludarabine phosphate, a USFDA-approved anticancer drug, to 2-fluoroadenine which displayed moderate antibacterial activity against both Bacillus subtilis and Escherichia coli, with IC50 values of 8.9 and 20.1 μM, respectively. Finally, acelarin, a prodrug of the anticancer drug gemcitabine, was found to exhibit unreported antibacterial activity against B. subtilis with an IC50 value of 33.6 μM through the bioactivity-HiTES method as well. These results indicate that bioactivity-HiTES can also be applied to discover biotransformed products in addition to finding cryptic metabolites in microbes.
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Affiliation(s)
- Da Yeong Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jonghwan Kim
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gyu Sung Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sehwan Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeongwon Song
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Bum Soo Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seoung Rak Lee
- College of Pharmacy and Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Chung Sub Kim
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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16
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Zhang HJ, Yu H, Fu J, Keranmu A, Zhang ZW, Xu H, Hu JC, Lu JY, Yang XY, Bu MM, Zhai Z, Wang JY, Jiang JD, Wang Y. Biotransformation of antioxidant eriocitrin into characteristic metabolites by the gut microbiota. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:510-518. [PMID: 37705345 DOI: 10.1080/10286020.2023.2251123] [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: 03/15/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023]
Abstract
Eriocitrin is a flavonoid glycoside with strong antioxidant capacity that has a variety of pharmacological activities, such as hypolipidemic, anticancer and anti-inflammatory effects. We found that the gut microbiota could rapidly metabolize eriocitrin. By using LC/MSn-IT-TOF, we identified three metabolites of eriocitrin metabolized in the intestinal microbiota: eriodictyol-7-O-glucoside, eriodictyol, and dihydrocaffeic acid. By comparing these two metabolic pathways of eriocitrin (the gut microbiota and liver microsomes), the intestinal microbiota may be the primary metabolic site of eriocitrin metabolism. These findings provide a theoretical foundation for the study of pharmacologically active substances.
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Affiliation(s)
- Hao-Jian Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Hang Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Jie Fu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Adili Keranmu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Zheng-Wei Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Hui Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Jia-Chun Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Jin-Yue Lu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Xin-Yu Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Meng-Meng Bu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Zhao Zhai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Jing-Yue Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Jian-Dong Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
| | - Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100050, China
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17
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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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18
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Xie P, Zhou X, Li Y, Wu J, Zhang H, Huang Y, Tan X, Wen L, Olasunkanmi OI, Zhou J, Sun Z, Liu M, Zhang G, Wang Y, Xie P, Yang J, Zheng P. Gut microbial CAZymes markers for depression. Transl Psychiatry 2024; 14:135. [PMID: 38443364 PMCID: PMC10914822 DOI: 10.1038/s41398-024-02850-x] [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: 08/01/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/07/2024] Open
Abstract
Major depressive disorder (MDD) is a serious mental illness, characterized by disturbances of gut microbiome, it is required to further explore how the carbohydrate-active enzymes (CAZymes) were changed in MDD. Here, using the metagenomic data from patients with MDD (n = 118) and heath controls (HC, n = 118), we found that the whole CAZymes signatures of MDD were significantly discriminated from that in HC. α-diversity indexes of the two groups were also significantly different. The patients with MDD were characterized by enriched Glycoside Hydrolases (GHs) and Polysaccharide Lyases (PLs) relative to HC. A panel of makers composed of 9 CAZymes mainly belonging to GHs enabled to discriminate the patients with MDD and HC with AUC of 0.824. In addition, this marker panel could classify blinded test samples from the two groups with an AUC of 0.736. Moreover, we found that baseline 4 CAZymes levels also could predict the antidepressant efficacy after adjusted confounding factors and times of depressive episode. Our findings showed that MDD was associated with disturbances of gut CAZymes, which may help to develop diagnostic and predictive tools for depression.
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Affiliation(s)
- Peijun Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xingyu Zhou
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yifan Li
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hanping Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Huang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xunmin Tan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lu Wen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | | | - Jingjing Zhou
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Zuoli Sun
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Min Liu
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Guofu Zhang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Ying Wang
- Department of Rehabilitation, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian Yang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing, China.
- Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing Medical University, Chongqing, China.
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19
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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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20
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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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21
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Wlaź P, Wiater A, Majewska M, Wyska E, Grąz M, Śliwa-Dominiak J, Gapińska N, Socała K. Effect of dietary supplementation with Lactobacillus helveticus R0052 on seizure thresholds and antiseizure potency of sodium valproate in mice. Psychopharmacology (Berl) 2024; 241:327-340. [PMID: 37966492 PMCID: PMC10805985 DOI: 10.1007/s00213-023-06489-2] [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: 06/13/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
OBJECTIVE Both animal and human studies, though limited, showed that multi-strain probiotic supplementation may reduce the number of seizures and/or seizure severity. Here, we evaluated the effect of a single strain probiotic supplementation on seizure susceptibility, antiseizure efficacy of sodium valproate, and several behavioral parameters in mice. METHODS Lactobacillus helveticus R0052 was given orally for 28 days. Its influence on seizure thresholds was evaluated in the ivPTZ- and electrically-induced seizure tests. The effect on the antiseizure potency of valproate was assessed in the scPTZ test. We also investigated the effects of probiotic supplementation on anxiety-related behavior (in the elevated plus maze and light/dark box tests), motor coordination (in the accelerating rotarod test), neuromuscular strength (in the grip-strength test), and spontaneous locomotor activity. Serum and brain concentrations of valproate as well as cecal contents of SCFAs and lactate were determined using HPLC method. RESULTS L. helveticus R0052 significantly increased the threshold for the 6 Hz-induced psychomotor seizure. There was also a slight increase in the threshold for myoclonic and clonic seizure in the ivPTZ test. L. helveticus R0052 did not affect the threshold for tonic seizures both in the maximal electroshock- and ivPTZ-induced seizure tests. No changes in the antiseizure potency of valproate against the PTZ-induced seizures were reported. Interestingly, L. helveticus R0052 increased valproate concentration in serum, but not in the brain. Moreover, L. helveticus R0052 did not produce any significant effects on anxiety-related behavior, motor coordination, neuromuscular strength, and locomotor activity. L. helveticus R0052 supplementation resulted in increased concentrations of total SCFAs, acetate, and butyrate. CONCLUSIONS Altogether, this study shows that a single-strain probiotic - L. helveticus R0052 may decrease seizure susceptibility and this effect can be mediated, at least in part, by increased production of SCFAs. In addition, L. helveticus R0052 may affect bioavailability of valproate, which warrants further investigations.
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Affiliation(s)
- Piotr Wlaź
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, PL 20-033, Lublin, Poland
| | - Adrian Wiater
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, PL 20-033, Lublin, Poland
| | - Małgorzata Majewska
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, PL 20-033, Lublin, Poland
| | - Elżbieta Wyska
- Department of Pharmacokinetics and Physical Pharmacy, Jagiellonian University Medical College, Medyczna 9, PL 30-688, Kraków, Poland
| | - Marcin Grąz
- Department of Biochemistry and Biotechnology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, PL 20-033, Lublin, Poland
| | - Joanna Śliwa-Dominiak
- R&D and Scientific Department, Sanprobi Sp. z o.o Sp.k., Quality Control and Microbiology Laboratory, Kurza Stopka 5/C, PL 70-535, Szczecin, Poland
| | - Nikola Gapińska
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, PL 20-033, Lublin, Poland
| | - Katarzyna Socała
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, PL 20-033, Lublin, Poland.
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22
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Liu S, Gao A, Ma Y, Ding Z, Wang S, Seif M, Xu X. Nonspecific immune, histology and accumulation of marine worm, Urechis unicinctus in response to bisphenol A (BPA). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 271:115993. [PMID: 38271890 DOI: 10.1016/j.ecoenv.2024.115993] [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: 09/11/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
Bisphenol A (BPA) is one of the environmental endocrine disruptors, due to its chemical stability it exists in abundant concentrations in water and soil consequently accumulating in the food chain and causing many endocrine-related health problems. So far, studies on the effects of BPA on marine invertebrates have focused on acute toxicity, endocrine regulation, reproduction, and development. However, fewer studies have been conducted on marine benthos. The current study aimed to detect the accumulation of BPA and its impact on tissue structure, antioxidant capacity, and immune indexes in marine worm, Urechis unicinctus. U. unicinctus, as a common marine benthic animal, were exposed to different concentrations of BPA. Blood cells and intestinal tract were taken for tissue structure inspection, and supernatant of the coelomic fluid was collected for oxidative and antioxidant biomarkers. Results showed that the accumulation of BPA in muscles of U. unicinctus tended to increase with exposure time. BPA induced a rise in H2O2 and MDA content, and altered the activities of CAT, T-SOD, GST, LSZ and ACP, weaken the immune system functions. Moreover, pathological observation showed that BPA caused severe histopathology in the respiratory intestine, stomach, and midgut. These results will be helpful to understand the response mechanism of U. unicinctus under BPA exposure and provide a reference for controlling the aquaculture conditions and marine water quality of U. unicinctus.
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Affiliation(s)
- Shun Liu
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu 222005 China
| | - Ang Gao
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu 222005 China
| | - Yuyang Ma
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu 222005 China
| | - Ziyuan Ding
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu 222005 China
| | - Sijie Wang
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu 222005 China
| | - Mohamed Seif
- Department of Toxicology and Food Contaminants, Institute of Food Industries and Nutrition, Research, National Research Centre, P.O. 12622, Dokki, Giza, Egypt
| | - Xinghong Xu
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu 222005 China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, Jiangsu 222005 China.
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23
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Okada K, Yokota J, Yamashita T, Inui T, Kishimoto W, Nakase H, Mizuguchi H. Establishment of human intestinal organoids derived from commercially available cryopreserved intestinal epithelium and evaluation for pharmacokinetic study. Drug Metab Pharmacokinet 2024; 54:100532. [PMID: 38064926 DOI: 10.1016/j.dmpk.2023.100532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 02/06/2024]
Abstract
Human intestinal organoids (HIOs) have been reported to exert their functions in a way that mimics living organs, and HIOs-derived monolayers are expected to be applied to in vitro intestinal pharmacokinetic studies. However, HIOs are established from human tissue, which raises issues of availability and ethics. In the present study, to solve these problems, we have established intestinal organoids using commercially available cryopreserved human intestinal epithelial cells (C-IOs), and compared their functions with biopsy-derived human intestinal organoids (B-IOs) from a pharmacokinetic point of view. Both C-IOs and B-IOs reproduced the morphological features of the intestinal tract and were shown to be composed of epithelial cells. Monolayers generated from C-IOs and B-IOs (C-IO-2D, B-IO-2D, respectively) structurally mimic the small intestine. The C-IOs showed gene expression levels comparable to those of the B-IOs, which were close to those of adult human small intestine. Importantly, the C-IOs-2D showed levels of pharmacokinetics-related protein expression and activity-including cytochrome P450 3A4 (CYP3A4) and carboxylesterase 2 (CES2) enzymatic activities and P-glycoprotein (P-gp) transporter activities -similar to those of B-IOs-2D. This study addresses the difficulties associated with B-IOs and provides fundamental characteristics for the application of C-IOs in pharmacokinetic studies.
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Affiliation(s)
- Kentaro Okada
- Laboratory of Biochemistry and Molecular Biology, School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Laboratory of Functional Organoid for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Jumpei Yokota
- Laboratory of Functional Organoid for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan; Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Tomoki Yamashita
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Tatsuya Inui
- Laboratory of Functional Organoid for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan; Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Wataru Kishimoto
- Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Kobe, Hyogo, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido, Japan
| | - Hiroyuki Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Laboratory of Functional Organoid for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan; Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
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24
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Roach J, Mital R, Haffner JJ, Colwell N, Coats R, Palacios HM, Liu Z, Godinho JLP, Ness M, Peramuna T, McCall LI. Microbiome metabolite quantification methods enabling insights into human health and disease. Methods 2024; 222:81-99. [PMID: 38185226 DOI: 10.1016/j.ymeth.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.
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Affiliation(s)
- Jarrod Roach
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Rohit Mital
- Department of Biology, University of Oklahoma
| | - Jacob J Haffner
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Nathan Colwell
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Randy Coats
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Horvey M Palacios
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Zongyuan Liu
- Department of Chemistry and Biochemistry, University of Oklahoma
| | | | - Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma; Department of Chemistry and Biochemistry, San Diego State University.
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25
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Ricaurte D, Huang Y, Sheth RU, Gelsinger DR, Kaufman A, Wang HH. High-throughput transcriptomics of 409 bacteria-drug pairs reveals drivers of gut microbiota perturbation. Nat Microbiol 2024; 9:561-575. [PMID: 38233648 PMCID: PMC11287798 DOI: 10.1038/s41564-023-01581-x] [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: 03/06/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Many drugs can perturb the gut microbiome, potentially leading to negative health consequences. However, mechanisms of most microorganism-drug responses have not been elucidated at the genetic level. Using high-throughput bacterial transcriptomics, we systematically characterized the gene expression profiles of prevalent human gut bacteria exposed to the most frequently prescribed orally administered pharmaceuticals. Across >400 drug-microorganism pairs, significant and reproducible transcriptional responses were observed, including pathways involved in multidrug resistance, metabolite transport, tartrate metabolism and riboflavin biosynthesis. Importantly, we discovered that statin-mediated upregulation of the AcrAB-TolC efflux pump in Bacteroidales species enhances microbial sensitivity to vitamin A and secondary bile acids. Moreover, gut bacteria carrying acrAB-tolC genes are depleted in patients taking simvastatin, suggesting that drug-efflux interactions generate collateral toxicity that depletes pump-containing microorganisms from patient microbiomes. This study provides a resource to further understand the drivers of drug-mediated microbiota shifts for better informed clinical interventions.
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Affiliation(s)
- Deirdre Ricaurte
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | | | - Andrew Kaufman
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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26
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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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27
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Zhu H, Wang W, Li Y. The interplay between microbiota and brain-gut axis in epilepsy treatment. Front Pharmacol 2024; 15:1276551. [PMID: 38344171 PMCID: PMC10853364 DOI: 10.3389/fphar.2024.1276551] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/12/2024] [Indexed: 08/12/2024] Open
Abstract
The brain-gut axis plays a vital role in connecting the cognitive and emotional centers of the brain with the intricate workings of the intestines. An imbalance in the microbiota-mediated brain-gut axis extends far beyond conditions like Irritable Bowel Syndrome (IBS) and obesity, playing a critical role in the development and progression of various neurological disorders, including epilepsy, depression, Alzheimer's disease (AD), and Parkinson's disease (PD). Epilepsy, a brain disorder characterized by unprovoked seizures, affects approximately 50 million people worldwide. Accumulating evidence suggests that rebuilding the gut microbiota through interventions such as fecal microbiota transplantation, probiotics, and ketogenic diets (KD) can benefit drug-resistant epilepsy. The disturbances in the gut microbiota could contribute to the toxic side effects of antiepileptic drugs and the development of drug resistance in epilepsy patients. These findings imply the potential impact of the gut microbiota on epilepsy and suggest that interventions targeting the microbiota, such as the KD, hold promise for managing and treating epilepsy. However, the full extent of the importance of microbiota in epilepsy treatment is not yet fully understood, and many aspects of this field remain unclear. Therefore, this article aims to provide an overview of the clinical and animal evidence supporting the regulatory role of gut microbiota in epilepsy, and of potential pathways within the brain-gut axis that may be influenced by the gut microbiota in epilepsy. Furthermore, we will discuss the recent advancements in epilepsy treatment, including the KD, fecal microbiota transplantation, and antiseizure drugs, all from the perspective of the gut microbiota.
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Affiliation(s)
- Hanxiao Zhu
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
- Clinical Medical School, Dali University, Dali, China
| | - Wei Wang
- Neurobiology Laboratory, China Agricultural University, Beijing, China
| | - Yun Li
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
- Clinical Medical School, Dali University, Dali, China
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28
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Zhao L, Chen J, Bai B, Song G, Zhang J, Yu H, Huang S, Wang Z, Lu G. Topical drug delivery strategies for enhancing drug effectiveness by skin barriers, drug delivery systems and individualized dosing. Front Pharmacol 2024; 14:1333986. [PMID: 38293666 PMCID: PMC10825035 DOI: 10.3389/fphar.2023.1333986] [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: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Topical drug delivery is widely used in various diseases because of the advantages of not passing through the gastrointestinal tract, avoiding gastrointestinal irritation and hepatic first-pass effect, and reaching the lesion directly to reduce unnecessary adverse reactions. The skin helps the organism to defend itself against a huge majority of external aggressions and is one of the most important lines of defense of the body. However, the skin's strong barrier ability is also a huge obstacle to the effectiveness of topical medications. Allowing the bioactive, composition in a drug to pass through the stratum corneum barrier as needed to reach the target site is the most essential need for the bioactive, composition to exert its therapeutic effect. The state of the skin barrier, the choice of delivery system for the bioactive, composition, and individualized disease detection and dosing planning influence the effectiveness of topical medications. Nowadays, enhancing transdermal absorption of topically applied drugs is the hottest research area. However, enhancing transdermal absorption of drugs is not the first choice to improve the effectiveness of all drugs. Excessive transdermal absorption enhances topical drug accumulation at non-target sites and the occurrence of adverse reactions. This paper introduces topical drug delivery strategies to improve drug effectiveness from three perspectives: skin barrier, drug delivery system and individualized drug delivery, describes the current status and shortcomings of topical drug research, and provides new directions and ideas for topical drug research.
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Affiliation(s)
- Lin Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiamei Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Bai Bai
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guili Song
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jingwen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Han Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shiwei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhang Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guanghua Lu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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29
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Joyce SA, Clarke DJ. Microbial metabolites as modulators of host physiology. Adv Microb Physiol 2024; 84:83-133. [PMID: 38821635 DOI: 10.1016/bs.ampbs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.
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Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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30
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Gonçalves CL, Doifode T, Rezende VL, Costa MA, Rhoads JM, Soutullo CA. The many faces of microbiota-gut-brain axis in autism spectrum disorder. Life Sci 2024; 337:122357. [PMID: 38123016 DOI: 10.1016/j.lfs.2023.122357] [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: 09/20/2023] [Revised: 12/02/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
The gut-brain axis is gaining more attention in neurodevelopmental disorders, especially autism spectrum disorder (ASD). Many factors can influence microbiota in early life, including host genetics and perinatal events (infections, mode of birth/delivery, medications, nutritional supply, and environmental stressors). The gut microbiome can influence blood-brain barrier (BBB) permeability, drug bioavailability, and social behaviors. Developing microbiota-based interventions such as probiotics, gastrointestinal (GI) microbiota transplantation, or metabolite supplementation may offer an exciting approach to treating ASD. This review highlights that RNA sequencing, metabolomics, and transcriptomics data are needed to understand how microbial modulators can influence ASD pathophysiology. Due to the substantial clinical heterogeneity of ASD, medical caretakers may be unlikely to develop a broad and effective general gut microbiota modulator. However, dietary modulation followed by administration of microbiota modulators is a promising option for treating ASD-related behavioral and gastrointestinal symptoms. Future work should focus on the accuracy of biomarker tests and developing specific psychobiotic agents tailored towards the gut microbiota seen in ASD patients, which may include developing individualized treatment options.
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Affiliation(s)
- Cinara L Gonçalves
- Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil.
| | - Tejaswini Doifode
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health (UTHealth), Houston, TX, USA
| | - Victoria L Rezende
- Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Maiara A Costa
- Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - J Marc Rhoads
- Department of Pediatrics, Division of Pediatric Gastroenterology, McGovern Medical School, The University of Texas Health (UTHealth), Houston, TX, USA
| | - Cesar A Soutullo
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health (UTHealth), Houston, TX, USA
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31
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Kraimi N, Ross T, Pujo J, De Palma G. The gut microbiome in disorders of gut-brain interaction. Gut Microbes 2024; 16:2360233. [PMID: 38949979 PMCID: PMC11218806 DOI: 10.1080/19490976.2024.2360233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/21/2024] [Indexed: 07/03/2024] Open
Abstract
Functional gastrointestinal disorders (FGIDs), chronic disorders characterized by either abdominal pain, altered intestinal motility, or their combination, have a worldwide prevalence of more than 40% and impose a high socioeconomic burden with a significant decline in quality of life. Recently, FGIDs have been reclassified as disorders of gut-brain interaction (DGBI), reflecting the key role of the gut-brain bidirectional communication in these disorders and their impact on psychological comorbidities. Although, during the past decades, the field of DGBIs has advanced significantly, the molecular mechanisms underlying DGBIs pathogenesis and pathophysiology, and the role of the gut microbiome in these processes are not fully understood. This review aims to discuss the latest body of literature on the complex microbiota-gut-brain interactions and their implications in the pathogenesis of DGBIs. A better understanding of the existing communication pathways between the gut microbiome and the brain holds promise in developing effective therapeutic interventions for DGBIs.
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Affiliation(s)
- Narjis Kraimi
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
| | - Taylor Ross
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
| | - Julien Pujo
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
| | - Giada De Palma
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
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32
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Gao K, Wang PX, Mei X, Yang T, Yu K. Untapped potential of gut microbiome for hypertension management. Gut Microbes 2024; 16:2356278. [PMID: 38825779 PMCID: PMC11152106 DOI: 10.1080/19490976.2024.2356278] [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: 12/08/2023] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
The gut microbiota has been shown to be associated with a range of illnesses and disorders, including hypertension, which is recognized as the primary factor contributing to the development of serious cardiovascular diseases. In this review, we conducted a comprehensive analysis of the progression of the research domain pertaining to gut microbiota and hypertension. Our primary emphasis was on the interplay between gut microbiota and blood pressure that are mediated by host and gut microbiota-derived metabolites. Additionally, we elaborate the reciprocal communication between gut microbiota and antihypertensive drugs, and its influence on the blood pressure of the host. The field of computer science has seen rapid progress with its great potential in the application in biomedical sciences, we prompt an exploration of the use of microbiome databases and artificial intelligence in the realm of high blood pressure prediction and prevention. We propose the use of gut microbiota as potential biomarkers in the context of hypertension prevention and therapy.
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Affiliation(s)
- Kan Gao
- Department of Pharmacy, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Pu Xiu Wang
- Department of Pharmacy, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xue Mei
- School of Pharmacy, Institute of Materia Medica, North Sichuan Medical College, Nanchang, Sichuan, China
| | - Tao Yang
- Department of Physiology and Pharmacology, Center for Hypertension and Precision Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Kai Yu
- Department of General Practice, The First Hospital of China Medical University, Shenyang, Liaoning, China
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33
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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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34
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Speckmann B, Ehring E, Hu J, Rodriguez Mateos A. Exploring substrate-microbe interactions: a metabiotic approach toward developing targeted synbiotic compositions. Gut Microbes 2024; 16:2305716. [PMID: 38300741 PMCID: PMC10841028 DOI: 10.1080/19490976.2024.2305716] [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: 09/14/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Gut microbiota is an important modulator of human health and contributes to high inter-individual variation in response to food and pharmaceutical ingredients. The clinical outcomes of interventions with prebiotics, probiotics, and synbiotics have been mixed and often unpredictable, arguing for novel approaches for developing microbiome-targeted therapeutics. Here, we review how the gut microbiota determines the fate of and individual responses to dietary and xenobiotic compounds via its immense metabolic potential. We highlight that microbial metabolites play a crucial role as targetable mediators in the microbiota-host health relationship. With this in mind, we expand the concept of synbiotics beyond prebiotics' role in facilitating growth and engraftment of probiotics, by focusing on microbial metabolism as a vital mode of action thereof. Consequently, we discuss synbiotic compositions that enable the guided metabolism of dietary or co-formulated ingredients by specific microbes leading to target molecules with beneficial functions. A workflow to develop novel synbiotics is presented, including the selection of promising target metabolites (e.g. equol, urolithin A, spermidine, indole-3 derivatives), identification of suitable substrates and producer strains applying bioinformatic tools, gut models, and eventually human trials.In conclusion, we propose that discovering and enabling specific substrate-microbe interactions is a valuable strategy to rationally design synbiotics that could establish a new category of hybrid nutra-/pharmaceuticals.
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Affiliation(s)
| | | | - Jiaying Hu
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Ana Rodriguez Mateos
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
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35
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de Castilhos J, Tillmanns K, Blessing J, Laraño A, Borisov V, Stein-Thoeringer CK. Microbiome and pancreatic cancer: time to think about chemotherapy. Gut Microbes 2024; 16:2374596. [PMID: 39024520 PMCID: PMC11259062 DOI: 10.1080/19490976.2024.2374596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer characterized by late diagnosis, rapid progression, and a high mortality rate. Its complex biology, characterized by a dense, stromal tumor environment with an immunosuppressive milieu, contributes to resistance against standard treatments like chemotherapy and radiation. This comprehensive review explores the dynamic role of the microbiome in modulating chemotherapy efficacy and outcomes in PDAC. It delves into the microbiome's impact on drug metabolism and resistance, and the interaction between microbial elements, drugs, and human biology. We also highlight the significance of specific bacterial species and microbial enzymes in influencing drug action and the immune response in the tumor microenvironment. Cutting-edge methodologies, including artificial intelligence, low-biomass microbiome analysis and patient-derived organoid models, are discussed, offering insights into the nuanced interactions between microbes and cancer cells. The potential of microbiome-based interventions as adjuncts to conventional PDAC treatments are discussed, paving the way for personalized therapy approaches. This review synthesizes recent research to provide an in-depth understanding of how the microbiome affects chemotherapy efficacy. It focuses on elucidating key mechanisms and identifying existing knowledge gaps. Addressing these gaps is crucial for enhancing personalized medicine and refining cancer treatment strategies, ultimately improving patient outcomes.
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Affiliation(s)
- Juliana de Castilhos
- Translational Microbiome Research, Internal Medicine I and M3 Research Center, University Hospital Tuebingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Tübingen, Germany
| | - Katharina Tillmanns
- Translational Microbiome Research, Internal Medicine I and M3 Research Center, University Hospital Tuebingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Tübingen, Germany
| | - Jana Blessing
- Translational Microbiome Research, Internal Medicine I and M3 Research Center, University Hospital Tuebingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Tübingen, Germany
| | - Arnelyn Laraño
- Translational Microbiome Research, Internal Medicine I and M3 Research Center, University Hospital Tuebingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Tübingen, Germany
| | - Vadim Borisov
- Translational Microbiome Research, Internal Medicine I and M3 Research Center, University Hospital Tuebingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Tübingen, Germany
| | - Christoph K. Stein-Thoeringer
- Translational Microbiome Research, Internal Medicine I and M3 Research Center, University Hospital Tuebingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Tübingen, Germany
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36
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Anbalagan S. "Blind men and an elephant": The need for animals in research, drug safety studies, and understanding civilizational diseases. Animal Model Exp Med 2023; 6:627-633. [PMID: 38062666 PMCID: PMC10757217 DOI: 10.1002/ame2.12364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/26/2023] [Indexed: 12/31/2023] Open
Abstract
Animal-based research and drug safety studies are essential to understanding the mysteries of nature and the long-term survival of humans. Due to the rapid increase in the global human population, conflict- and economically driven human migration, tourism-related activities, densely populated metropolitan areas, and local policies, humans will be affected by a multitude of novel disease-causing microorganisms and civilizational diseases. Despite disparities among countries, recent and planned changes in regulations concerning animal research and drug safety studies could have detrimental effects on both the animal research community and nations lacking sufficient social support systems. Based on existing scientific literature, I argue that we need animal research encompassing aspects such as animal development, behavior, drug safety studies, and for the understanding of future civilizational diseases. Depending on the nature of the research questions and local challenges, a suitable animal model organism should be made mandatory.
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Affiliation(s)
- Savani Anbalagan
- Faculty of Biology, Institute of Molecular Biology and BiotechnologyAdam Mickiewicz University in PoznańPoznańPoland
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Tan Y, Liang J, Lai M, Wan S, Luo X, Li F. Advances in synthetic biology toolboxes paving the way for mechanistic understanding and strain engineering of gut commensal Bacteroides spp. and Clostridium spp. Biotechnol Adv 2023; 69:108272. [PMID: 37844770 DOI: 10.1016/j.biotechadv.2023.108272] [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: 08/13/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.
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Affiliation(s)
- Yang Tan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
| | - Jing Liang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingchi Lai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Sai Wan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuli Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
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38
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Hatzios SK. Moonlighting in the membrane. Nat Chem Biol 2023; 19:1436-1437. [PMID: 37349584 DOI: 10.1038/s41589-023-01369-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Affiliation(s)
- Stavroula K Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
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Singh S, Sarma DK, Verma V, Nagpal R, Kumar M. Unveiling the future of metabolic medicine: omics technologies driving personalized solutions for precision treatment of metabolic disorders. Biochem Biophys Res Commun 2023; 682:1-20. [PMID: 37788525 DOI: 10.1016/j.bbrc.2023.09.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Metabolic disorders are increasingly prevalent worldwide, leading to high rates of morbidity and mortality. The variety of metabolic illnesses can be addressed through personalized medicine. The goal of personalized medicine is to give doctors the ability to anticipate the best course of treatment for patients with metabolic problems. By analyzing a patient's metabolomic, proteomic, genetic profile, and clinical data, physicians can identify relevant diagnostic, and predictive biomarkers and develop treatment plans and therapy for acute and chronic metabolic diseases. To achieve this goal, real-time modeling of clinical data and multiple omics is essential to pinpoint underlying biological mechanisms, risk factors, and possibly useful data to promote early diagnosis and prevention of complex diseases. Incorporating cutting-edge technologies like artificial intelligence and machine learning is crucial for consolidating diverse forms of data, examining multiple variables, establishing databases of clinical indicators to aid decision-making, and formulating ethical protocols to address concerns. This review article aims to explore the potential of personalized medicine utilizing omics approaches for the treatment of metabolic disorders. It focuses on the recent advancements in genomics, epigenomics, proteomics, metabolomics, and nutrigenomics, emphasizing their role in revolutionizing personalized medicine.
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Affiliation(s)
- Samradhi Singh
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Ravinder Nagpal
- Department of Nutrition and Integrative Physiology, College of Health and Human Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Manoj Kumar
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India.
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Lou YC, Rubin BE, Schoelmerich MC, DiMarco KS, Borges AL, Rovinsky R, Song L, Doudna JA, Banfield JF. Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species. Nat Commun 2023; 14:7417. [PMID: 37973815 PMCID: PMC10654741 DOI: 10.1038/s41467-023-43279-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2'-fucosyllactose (2'FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2'FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2'FL breakdown, thus critical for B. breve's growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2'FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual's microbiome.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland
| | - Kaden S DiMarco
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Leo Song
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
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Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Boettcher T, Cheng JX, Wagner M. The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.12.566429. [PMID: 38014294 PMCID: PMC10680583 DOI: 10.1101/2023.11.12.566429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.
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Zhu R, Gao Y, Dong J, Li Z, Ren Z. The changes of gut microbiota and metabolites in different drug-induced liver injuries. J Med Microbiol 2023; 72. [PMID: 38015063 DOI: 10.1099/jmm.0.001778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
The increasing incidence of drug-induced liver injury (DILI) has become a major concern. Gut microbiota, as another organ of the human body, has been studied in various tumors, cardiovascular metabolic diseases, inflammatory bowel disease and human immunity. The studies mentioned above have confirmed its important impact on the occurrence and development of DILI. The gut-liver axis explains the close relationship between the gut and the liver, and it may be a pathway by which gut microbes contribute to DILI. In addition, the interaction between drugs and gut microbes affects both separately, which in turn may have positive or negative effects on the body, including DILI. There are both common and specific changes in liver injury caused by different drugs. The alteration of metabolites in DILI is also a new direction of therapeutic exploration. The application of microbiomics, metabolomics and other multi-omics to DILI has also explored new ideas for DILI. In this review, we conclude the alterations of gut microbes and metabolites under different DILI, and the significance of applying gut microbiome-metabolomics to DILI, so as to explore the metabolic characteristics of DILI and possible novel metabolic biomarkers.
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Affiliation(s)
- Ruirui Zhu
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250000, PR China
- Gene Hospital of Henan Province; Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Yinghui Gao
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
- Gene Hospital of Henan Province; Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Jianxia Dong
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
- Gene Hospital of Henan Province; Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Zhiqin Li
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
- Gene Hospital of Henan Province; Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Zhigang Ren
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250000, PR China
- Gene Hospital of Henan Province; Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
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Cai J, Auster A, Cho S, Lai Z. Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage. J Adv Res 2023; 52:171-201. [PMID: 37419381 PMCID: PMC10555929 DOI: 10.1016/j.jare.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND The gut microbiome is a diverse system within the gastrointestinal tract composed of trillions of microorganisms (gut microbiota), along with their genomes. Accumulated evidence has revealed the significance of the gut microbiome in human health and disease. Due to its ability to alter drug/xenobiotic pharmacokinetics and therapeutic outcomes, this once-forgotten "metabolic organ" is receiving increasing attention. In parallel with the growing microbiome-driven studies, traditional analytical techniques and technologies have also evolved, allowing researchers to gain a deeper understanding of the functional and mechanistic effects of gut microbiome. AIM OF REVIEW From a drug development perspective, microbial drug metabolism is becoming increasingly critical as new modalities (e.g., degradation peptides) with potential microbial metabolism implications emerge. The pharmaceutical industry thus has a pressing need to stay up-to-date with, and continue pursuing, research efforts investigating clinical impact of the gut microbiome on drug actions whilst integrating advances in analytical technology and gut microbiome models. Our review aims to practically address this need by comprehensively introducing the latest innovations in microbial drug metabolism research- including strengths and limitations, to aid in mechanistically dissecting the impact of the gut microbiome on drug metabolism and therapeutic impact, and to develop informed strategies to address microbiome-related drug liability and minimize clinical risk. KEY SCIENTIFIC CONCEPTS OF REVIEW We present comprehensive mechanisms and co-contributing factors by which the gut microbiome influences drug therapeutic outcomes. We highlight in vitro, in vivo, and in silico models for elucidating the mechanistic role and clinical impact of the gut microbiome on drugs in combination with high-throughput, functionally oriented, and physiologically relevant techniques. Integrating pharmaceutical knowledge and insight, we provide practical suggestions to pharmaceutical scientists for when, why, how, and what is next in microbial studies for improved drug efficacy and safety, and ultimately, support precision medicine formulation for personalized and efficacious therapies.
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Affiliation(s)
- Jingwei Cai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA.
| | - Alexis Auster
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Sungjoon Cho
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Zijuan Lai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
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Wuyts S, Alves R, Zimmermann‐Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P. Consistency across multi-omics layers in a drug-perturbed gut microbial community. Mol Syst Biol 2023; 19:e11525. [PMID: 37485738 PMCID: PMC10495815 DOI: 10.15252/msb.202311525] [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: 01/09/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.
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Affiliation(s)
- Sander Wuyts
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Renato Alves
- European Molecular Biology LaboratoryHeidelbergGermany
| | | | | | - Sonja Blasche
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | | | - Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Rajna Hercog
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Ece Kartal
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Johannes B Müller
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Sarela Garcia Santamarina
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
MOSTMICRO Unit, Instituto de Tecnologia Quimica e BiologicaUniversidade Nova de LisboaOeirasPortugal
| | | | | | - Anja Telzerow
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peter V Treit
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tobias Wenzel
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Catolica de ChileSantiagoChile
| | | | - Kiran R Patil
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Proteomics Program, NNF Center for Protein Research, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Michael Kuhn
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peer Bork
- European Molecular Biology LaboratoryHeidelbergGermany
- Max Delbrück Centre for Molecular MedicineBerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei UniversitySeoulSouth Korea
- Department of Bioinformatics, BiocenterUniversity of WürzburgWürzburgGermany
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Han H, Xing L, Chen BT, Liu Y, Zhou TJ, Wang Y, Zhang LF, Li L, Cho CS, Jiang HL. Progress on the pathological tissue microenvironment barrier-modulated nanomedicine. Adv Drug Deliv Rev 2023; 200:115051. [PMID: 37549848 DOI: 10.1016/j.addr.2023.115051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Imbalance in the tissue microenvironment is the main obstacle to drug delivery and distribution in the human body. Before penetrating the pathological tissue microenvironment to the target site, therapeutic agents are usually accompanied by three consumption steps: the first step is tissue physical barriers for prevention of their penetration, the second step is inactivation of them by biological molecules, and the third step is a cytoprotective mechanism for preventing them from functioning on specific subcellular organelles. However, recent studies in drug-hindering mainly focus on normal physiological rather than pathological microenvironment, and the repair of damaged physiological barriers is also rarely discussed. Actually, both the modulation of pathological barriers and the repair of damaged physiological barriers are essential in the disease treatment and the homeostasis maintenance. In this review, we present an overview describing the latest advances in the generality of these pathological barriers and barrier-modulated nanomedicine. Overall, this review holds considerable significance for guiding the design of nanomedicine to increase drug efficacy in the future.
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Affiliation(s)
- Han Han
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Lei Xing
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Bi-Te Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Yang Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Tian-Jiao Zhou
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Ling-Feng Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Ling Li
- Department of Endocrinology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China.
| | - Chong-Su Cho
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Hu-Lin Jiang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; College of Pharmacy, Yanbian University, Yanji 133002, China.
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Han ZY, Chen QW, Zheng DW, Chen KW, Huang QX, Zhuang ZN, Zhang XZ. Inhalable Capsular Polysaccharide-Camouflaged Gallium-Polyphenol Nanoparticles Enhance Lung Cancer Chemotherapy by Depleting Local Lung Microbiota. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302551. [PMID: 37310059 DOI: 10.1002/adma.202302551] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/29/2023] [Indexed: 06/14/2023]
Abstract
Local lung microbiota is closely associated with lung tumorigenesis and therapeutic response. It is found that lung commensal microbes induce chemoresistance in lung cancer by directly inactivating therapeutic drugs via biotransformation. Accordingly, an inhalable microbial capsular polysaccharide (CP)-camouflaged gallium-polyphenol metal-organic network (MON) is designed to eliminate lung microbiota and thereby abrogate microbe-induced chemoresistance. As a substitute for iron uptake, Ga3+ released from MON acts as a "Trojan horse" to disrupt bacterial iron respiration, effectively inactivating multiple microbes. Moreover, CP cloaks endow MON with reduced immune clearance by masquerading as normal host-tissue molecules, significantly increasing residence time in lung tissue for enhanced antimicrobial efficacy. In multiple lung cancer mice models, microbe-induced drug degradation is remarkably inhibited when drugs are delivered by antimicrobial MON. Tumor growth is sufficiently suppressed and mouse survival is prolonged. The work develops a novel microbiota-depleted nanostrategy to overcome chemoresistance in lung cancer by inhibiting local microbial inactivation of therapeutic drugs.
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Affiliation(s)
- Zi-Yi Han
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Qi-Wen Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Di-Wei Zheng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Ke-Wei Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Qian-Xiao Huang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Ze-Nan Zhuang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
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Zhao DK, Liang J, Huang XY, Shen S, Wang J. Organoids technology for advancing the clinical translation of cancer nanomedicine. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2023; 15:e1892. [PMID: 37088100 DOI: 10.1002/wnan.1892] [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: 12/14/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 04/25/2023]
Abstract
The past decades have witnessed the rapid development and widespread application of nanomedicines in cancer treatment; however, the clinical translation of experimental findings has been low, as evidenced by the low percentage of commercialized nanomedicines. Incomplete understanding of nanomedicine-tumor interactions and inappropriate evaluation models are two important challenges limiting the clinical translation of cancer nanomedicines. Currently, nanomedicine-tumor interaction and therapeutic effects are mainly investigated using cell lines or mouse models, which do not recapitulate the complex tumor microenvironment in human patients. Thus, information obtained from cell lines and mouse models cannot provide adequate guidance for the rational redesign of nanomedicine. Compared with other preclinical models, tumor organoids constructed from patient-derived tumor tissues are superior in retaining the key histopathological, genetic, and phenotypic features of the parent tumor. We speculate that organoid technology would help elucidate nanomedicine-tumor interaction in the tumor microenvironment and guide the design of nanomedicine, making it a reliable tool to accurately predict drug responses in patients with cancer. This review highlighted the advantages of drug delivery systems in cancer treatment, challenges limiting the clinical translation of antitumor nanomedicines, and potential application of patient-derived organoids (PDO) in nanomedicine. We propose that combining organoids and nanotechnology would facilitate the development of safe and effective cancer nanomedicines and accelerate their clinical application. This review discussed the potential translational value of integrative research using organoids and cancer nanomedicine. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Dong-Kun Zhao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
| | - Jie Liang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Xiao-Yi Huang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Song Shen
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Jun Wang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
- Key Laboratory of Biomedical Engineering of Guangdong Province, and Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, China
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48
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Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnúsdóttir S, Martinelli F, Nap B, Preciat G, Edirisinghe JN, Henry CS, Fleming RMT, Thiele I. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nat Biotechnol 2023; 41:1320-1331. [PMID: 36658342 PMCID: PMC10497413 DOI: 10.1038/s41587-022-01628-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/30/2022] [Indexed: 01/21/2023]
Abstract
The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host-microbiome metabolic interactions.
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Affiliation(s)
- Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- INSERM UMRS 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), University of Lorraine, Nancy, France
| | - Johannes Hertel
- School of Medicine, University of Galway, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Geeta Acharya
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Dmitry A Ravcheev
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | | | | | - Marcus Hogan
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Stefanía Magnúsdóttir
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Bram Nap
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - German Preciat
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Janaka N Edirisinghe
- Computation Institute, University of Chicago, Chicago, IL, USA
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Ronan M T Fleming
- School of Medicine, University of Galway, Galway, Ireland
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland.
- Ryan Institute, University of Galway, Galway, Ireland.
- Division of Microbiology, University of Galway, Galway, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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49
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Mengoli M, Conti G, Fabbrini M, Candela M, Brigidi P, Turroni S, Barone M. Microbiota-gut-brain axis and ketogenic diet: how close are we to tackling epilepsy? MICROBIOME RESEARCH REPORTS 2023; 2:32. [PMID: 38045924 PMCID: PMC10688818 DOI: 10.20517/mrr.2023.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 12/05/2023]
Abstract
The microbiota-gut-brain axis refers to the intricate bidirectional communication between commensal microorganisms residing in the digestive tract and the central nervous system, along neuroendocrine, metabolic, immune, and inflammatory pathways. This axis has been suggested to play a role in several neurological disorders, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, and epilepsy, paving the way for microbiome-based intervention strategies for the mitigation and treatment of symptoms. Epilepsy is a multifaceted neurological condition affecting more than 50 million individuals worldwide, 30% of whom do not respond to conventional pharmacological therapies. Among the first-hand microbiota modulation strategies, nutritional interventions represent an easily applicable option in both clinical and home settings. In this narrative review, we summarize the mechanisms underlying the microbiota-gut-brain axis involvement in epilepsy, discuss the impact of antiepileptic drugs on the gut microbiome, and then the impact of a particular dietary pattern, the ketogenic diet, on the microbiota-gut-brain axis in epileptic patients. The investigation of the microbiota response to non-pharmacological therapies is an ever-expanding field with the potential to allow the design of increasingly accessible and successful intervention strategies.
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Affiliation(s)
- Mariachiara Mengoli
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
| | - Gabriele Conti
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
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50
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Yan Y, Wang Z, Zhou YL, Gao Z, Ning L, Zhao Y, Xuan B, Ma Y, Tong T, Huang X, Hu M, Fang JY, Cui Z, Chen H, Hong J. Commensal bacteria promote azathioprine therapy failure in inflammatory bowel disease via decreasing 6-mercaptopurine bioavailability. Cell Rep Med 2023; 4:101153. [PMID: 37586320 PMCID: PMC10439275 DOI: 10.1016/j.xcrm.2023.101153] [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: 11/28/2022] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Azathioprine (AZA) therapy failure, though not the primary cause, contributes to disease relapse and progression in inflammatory bowel disease (IBD). However, the role of gut microbiota in AZA therapy failure remains poorly understood. We found a high prevalence of Blautia wexlerae in patients with IBD with AZA therapy failure, associated with shorter disease flare survival time. Colonization of B. wexlerae increased inflammatory macrophages and compromised AZA's therapeutic efficacy in mice with intestinal colitis. B. wexlerae colonization reduced 6-mercaptopurine (6-MP) bioavailability by enhancing selenium-dependent xanthine dehydrogenase (sd-XDH) activity. The enzyme sd-XDH converts 6-MP into its inactive metabolite, 6-thioxanthine (6-TX), thereby impairing its ability to inhibit inflammation in mice. Supplementation with Bacillus (B.) subtilis enriched in hypoxanthine phosphoribosyltransferase (HPRT) effectively mitigated B. wexlerae-induced AZA treatment failure in mice with intestinal colitis. These findings emphasize the need for tailored management strategies based on B. wexlerae levels in patients with IBD.
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Affiliation(s)
- Yuqing Yan
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhenhua Wang
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yi-Lu Zhou
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Ziyun Gao
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Lijun Ning
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Ying Zhao
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Baoqin Xuan
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yanru Ma
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Tianying Tong
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiaowen Huang
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Muni Hu
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhe Cui
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Middle Shandong Road, Shanghai 200001, China.
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
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