51
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Guo Y, Lee H, Jeong H. Gut microbiota in reductive drug metabolism. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:61-93. [PMID: 32475528 DOI: 10.1016/bs.pmbts.2020.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gut bacteria are predominant microorganisms in the gut microbiota and have been recognized to mediate a variety of biotransformations of xenobiotic compounds in the gut. This review is focused on one of the gut bacterial xenobiotic metabolisms, reduction. Xenobiotics undergo different types of reductive metabolisms depending on chemically distinct groups: azo (-NN-), nitro (-NO2), alkene (-CC-), ketone (-CO), N-oxide (-NO), and sulfoxide (-SO). In this review, we have provided select examples of drugs in six chemically distinct groups that are known or suspected to be subjected to the reduction by gut bacteria. For some drugs, responsible enzymes in specific gut bacteria have been identified and characterized, but for many drugs, only circumstantial evidence is available that indicates gut bacteria-mediated reductive metabolism. The physiological roles of even known gut bacterial enzymes have not been well defined.
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Affiliation(s)
- Yukuang Guo
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Hyunwoo Lee
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States.
| | - Hyunyoung Jeong
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States.
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52
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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53
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Dempsey JL, Wang D, Siginir G, Fei Q, Raftery D, Gu H, Yue Cui J. Pharmacological Activation of PXR and CAR Downregulates Distinct Bile Acid-Metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis. Toxicol Sci 2020; 168:40-60. [PMID: 30407581 DOI: 10.1093/toxsci/kfy271] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gut microbiome regulates important host metabolic pathways including xenobiotic metabolism and intermediary metabolism, such as the conversion of primary bile acids (BAs) into secondary BAs. The nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are well-known regulators for xenobiotic biotransformation in liver. However, little is known regarding the potential effects of PXR and CAR on the composition and function of the gut microbiome. To test our hypothesis that activation of PXR and CAR regulates gut microbiota and secondary BA synthesis, 9-week-old male conventional and germ-free mice were orally gavaged with corn oil, PXR agonist PCN (75 mg/kg), or CAR agonist TCPOBOP (3 mg/kg) once daily for 4 days. PCN and TCPOBOP decreased two taxa in the Bifidobacterium genus, which corresponded with decreased gene abundance of the BA-deconjugating enzyme bile salt hydrolase. In liver and small intestinal content of germ-free mice, there was a TCPOBOP-mediated increase in total, primary, and conjugated BAs corresponding with increased Cyp7a1 mRNA. Bifidobacterium, Dorea, Peptociccaceae, Anaeroplasma, and Ruminococcus positively correlated with T-UDCA in LIC, but negatively correlated with T-CDCA in serum. In conclusion, PXR and CAR activation downregulates BA-metabolizing bacteria in the intestine and modulates BA homeostasis in a gut microbiota-dependent manner.
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Affiliation(s)
- Joseph L Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Dongfang Wang
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109.,Chongqing Blood Center, Chongqing 400015, P.R. China
| | - Gunseli Siginir
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Qiang Fei
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109.,Department of Chemistry, Jilin University, Changchun, Jilin Province 130061, P.R. China
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, Center for Metabolic and Vascular Biology, School of Nutrition and Health Promotion, College of Health Solutions, Arizona State University, Phoenix, Arizona 85004
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
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54
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Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB. Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response. Nat Rev Rheumatol 2020; 16:282-292. [PMID: 32157196 DOI: 10.1038/s41584-020-0395-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
In the past three decades, extraordinary advances have been made in the understanding of the pathogenesis of, and treatment options for, inflammatory arthritides, including rheumatoid arthritis and spondyloarthritis. The use of methotrexate and subsequently biologic therapies (such as TNF inhibitors, among others) and oral small molecules have substantially improved clinical outcomes for many patients with inflammatory arthritis; for others, however, these agents do not substantially improve their symptoms. The emerging field of pharmacomicrobiomics, which investigates the effect of variations within the human gut microbiome on drugs, has already provided important insights into these therapeutics. Pharmacomicrobiomic studies have demonstrated that human gut microorganisms and their enzymatic products can affect the bioavailability, clinical efficacy and toxicity of a wide array of drugs through direct and indirect mechanisms. This discipline promises to facilitate the advent of microbiome-based precision medicine approaches in inflammatory arthritis, including strategies for predicting response to treatment and for modulating the microbiome to improve response to therapy or reduce drug toxicity.
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Affiliation(s)
- Jose U Scher
- Department of Medicine, Division of Rheumatology, New York University Langone Health, New York, NY, USA.
| | - Renuka R Nayak
- Rheumatology Division, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Carles Ubeda
- Centro Superior de Investigacion en Salud Publica - FISABIO, Valencia, Spain.,CIBER en Epidemiologia y Salud Publica, Madrid, Spain
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Steven B Abramson
- Department of Medicine, Division of Rheumatology, New York University Langone Health, New York, NY, USA
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55
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Chae S, Kim DJ, Cho JY. Complex influences of gut microbiome metabolism on various drug responses. Transl Clin Pharmacol 2020; 28:7-16. [PMID: 32274377 PMCID: PMC7136083 DOI: 10.12793/tcp.2020.28.e3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 01/04/2023] Open
Abstract
The gut microbiome closely interacts with the host, and it has a major influence on drug response. Many studies have reported the possible microbial influences on drugs and the possible influences of drugs on the microbiome. This knowledge has led to a better understanding of intra- and inter-individual variabilities in clinical pharmacology. For a more precise understanding of the complex correlation between the microbiome and drugs, in this review, we summarized the current knowledge on the interactions between the gut microbiome and drug response. Moreover, we suggest gut microbiome-derived metabolites as possible modulators of drug response and recommend metabolomics as a powerful tool to achieve such understanding.
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Affiliation(s)
- Sihyun Chae
- Department of Clinical Pharmacology and Therapeutics, Seoul National University, College of Medicine and Hospital, Seoul 03080, Korea
| | - Da Jung Kim
- Department of Clinical Pharmacology and Therapeutics, Seoul National University, College of Medicine and Hospital, Seoul 03080, Korea
| | - Joo-Youn Cho
- Department of Clinical Pharmacology and Therapeutics, Seoul National University, College of Medicine and Hospital, Seoul 03080, Korea
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56
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Tan W, Liao TH, Wang J, Ye Y, Wei YC, Zhou HK, Xiao Y, Zhi XY, Shao ZH, Lyu LD, Zhao GP. A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation. J Biol Chem 2020; 295:5051-5066. [PMID: 32111737 DOI: 10.1074/jbc.ra120.012859] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN-FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.
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Affiliation(s)
- Wei Tan
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Tian-Hua Liao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yu Ye
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Yu-Chen Wei
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Hao-Kui Zhou
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Hui Shao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Ping Zhao
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China .,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China
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57
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Draft Genome Sequences of 13 Isolates of Adlercreutzia equolifaciens, Eggerthella lenta, and Gordonibacter urolithinfaciens, Isolated from Human Fecal Samples in Karlsruhe, Germany. Microbiol Resour Announc 2020; 9:9/8/e00017-20. [PMID: 32079628 PMCID: PMC7033265 DOI: 10.1128/mra.00017-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the annotated draft genome sequences of 13 Eggerthellaceae strains isolated from fecal samples from two healthy human volunteers in Karlsruhe, Germany, i.e., Adlercreutzia equolifaciens ResAG-91, Eggerthella lenta MRI-F 36, MRI-F 37, MRI-F 40, ResAG-49, ResAG-88, ResAG-121, and ResAG-145, and Gordonibacter urolithinfaciens ResAG-5, ResAG-26, ResAG-43, ResAG-50, and ResAG-59.
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58
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Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP. A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. eLife 2020; 9:e50845. [PMID: 32067637 PMCID: PMC7028382 DOI: 10.7554/elife.50845] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Catechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the human gut bacterium Eggerthella lenta that dehydroxylates catecholamine neurotransmitters. Our findings suggest that this activity enables E. lenta to use dopamine as an electron acceptor. We also identify candidate dehydroxylases that metabolize additional host- and plant-derived catechols. These dehydroxylases belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, confirming the presence of this chemistry in habitats beyond the human gut. These results suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Paola Nol Bernadino
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Michael U Luescher
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Sina Kiamehr
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Chip Le
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Jordan E Bisanz
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Peter J Turnbaugh
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Elizabeth N Bess
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
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59
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Jariwala PB, Pellock SJ, Goldfarb D, Cloer EW, Artola M, Simpson JB, Bhatt AP, Walton WG, Roberts LR, Major MB, Davies GJ, Overkleeft HS, Redinbo MR. Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling. ACS Chem Biol 2020; 15:217-225. [PMID: 31774274 PMCID: PMC7321802 DOI: 10.1021/acschembio.9b00788] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is increasingly clear that interindividual variability in human gut microbial composition contributes to differential drug responses. For example, gastrointestinal (GI) toxicity is not observed in all patients treated with the anticancer drug irinotecan, and it has been suggested that this variability is a result of differences in the types and levels of gut bacterial β-glucuronidases (GUSs). GUS enzymes promote drug toxicity by hydrolyzing the inactive drug-glucuronide conjugate back to the active drug, which damages the GI epithelium. Proteomics-based identification of the exact GUS enzymes responsible for drug reactivation from the complexity of the human microbiota has not been accomplished, however. Here, we discover the specific bacterial GUS enzymes that generate SN-38, the active and toxic metabolite of irinotecan, from human fecal samples using a unique activity-based protein profiling (ABPP) platform. We identify and quantify gut bacterial GUS enzymes from human feces with an ABPP-enabled proteomics pipeline and then integrate this information with ex vivo kinetics to pinpoint the specific GUS enzymes responsible for SN-38 reactivation. Furthermore, the same approach also reveals the molecular basis for differential gut bacterial GUS inhibition observed between human fecal samples. Taken together, this work provides an unprecedented technical and bioinformatics pipeline to discover the microbial enzymes responsible for specific reactions from the complexity of human feces. Identifying such microbial enzymes may lead to precision biomarkers and novel drug targets to advance the promise of personalized medicine.
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Affiliation(s)
- Parth B. Jariwala
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samuel J. Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dennis Goldfarb
- Institute for Informatics, Washington University, St. Louis, Missouri 63130, United States
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63130, United States
| | - Erica W. Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Marta Artola
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2311, The Netherlands
| | - Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aadra P. Bhatt
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G. Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lee R. Roberts
- Exploratory Science Center, Merck & Company Inc., Cambridge, Massachusetts 02141, United States
| | - Michael B. Major
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63130, United States
- Department of Otolaryngology, Washington University, St. Louis, Missouri 63130, United States
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Herman S. Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2311, The Netherlands
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Integrated Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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60
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Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP. Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism. Science 2019; 364:364/6445/eaau6323. [PMID: 31196984 PMCID: PMC7745125 DOI: 10.1126/science.aau6323] [Citation(s) in RCA: 352] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 04/18/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022]
Abstract
The human gut microbiota metabolizes the Parkinson’s disease medication Levodopa (L-dopa), potentially reducing drug availability and causing side effects. However, the organisms, genes, and enzymes responsible for this activity in patients and their susceptibility to inhibition by host-targeted drugs are unknown. Here, we describe an interspecies pathway for gut bacterial L-dopa metabolism. Conversion of L-dopa to dopamine by a pyridoxal phosphate-dependent tyrosine decarboxylase from Enterococcus faecalis is followed by transformation of dopamine to m-tyramine by a molybdenum-dependent dehydroxylase from Eggerthella lenta. These enzymes predict drug metabolism in complex human gut microbiotas. Although a drug that targets host aromatic amino acid decarboxylase does not prevent gut microbial L-dopa decarboxylation, we identified a compound that inhibits this activity in Parkinson’s patient microbiotas and increases L-dopa bioavailability in mice.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Elizabeth N Bess
- Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92617, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92617, USA
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA. .,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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61
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Sharma A, Das P, Buschmann M, Gilbert JA. The Future of Microbiome-Based Therapeutics in Clinical Applications. Clin Pharmacol Ther 2019; 107:123-128. [PMID: 31617205 DOI: 10.1002/cpt.1677] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/02/2019] [Indexed: 12/24/2022]
Abstract
The microbiome, a collection of microorganisms, their genomes, and the surrounding environmental conditions, is akin to a human organ, and knowledge is emerging on its role in human health and diseases. The influence of the microbiome in drug response has only been investigated in detail for the last 10 years. The human microbiome is a complex and highly dynamic system, which varies dramatically between individuals, yet there exists a common core microbiome that is heritable and can be transmitted to progeny. Here, we review the role of the human microbiome, which is now widely accepted as a major factor that drives the interpersonal variation in therapeutic response. We describe examples in which the microbiome modifies drug action. Despite its complexity, the microbiome can be readily altered, with the potential to increase the benefits and reduce the toxicity and side effects associated with pharmaceutical drugs. The potential of new microbiome-based strategies, such as fecal microbiota transplant, probiotics, and phage therapy, as promising medical therapeutics are outlined. We also suggest a combination reductionist and system-level approaches that could be applied to further investigate the role of microbiota in drug metabolism modulation of drug response. Finally, we emphasize the importance of combining microbiome and pharmacology studies as a novel means to treat disease and reduce side effects.
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Affiliation(s)
- Anukriti Sharma
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
| | - Mary Buschmann
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
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62
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Circulating Metabolites Originating from Gut Microbiota Control Endothelial Cell Function. Molecules 2019; 24:molecules24213992. [PMID: 31694161 PMCID: PMC6864778 DOI: 10.3390/molecules24213992] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 11/03/2019] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular functionality strictly depends on endothelial cell trophism and proper biochemical function. Any condition (environmental, pharmacological/toxicological, physical, or neuro-humoral) that changes the vascular endothelium has great consequences for the organism’s wellness and on the outcome and evolution of severe cardiovascular pathologies. Thus, knowledge of the mechanisms, both endogenous and external, that affect endothelial dysfunction is pivotal to preventing and treating these disorders. In recent decades, significant attention has been focused on gut microbiota and how these symbiotic microorganisms can influence host health and disease development. Indeed, dysbiosis has been reported to be at the base of a range of different pathologies, including pathologies of the cardiovascular system. The study of the mechanism underlying this relationship has led to the identification of a series of metabolites (released by gut bacteria) that exert different effects on all the components of the vascular system, and in particular on endothelial cells. The imbalance of factors promoting or blunting endothelial cell viability and function and angiogenesis seems to be a potential target for the development of new therapeutic interventions. This review highlights the circulating factors identified to date, either directly produced by gut microbes or resulting from the metabolism of diet derivatives as polyphenols.
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63
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Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria. Nat Microbiol 2019; 5:56-66. [PMID: 31686027 PMCID: PMC6941677 DOI: 10.1038/s41564-019-0596-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 09/18/2019] [Indexed: 12/14/2022]
Abstract
Plant-derived lignans, consumed daily by most individuals, are thought to protect against cancer and other diseases1; however, their bioactivity requires gut bacterial conversion to enterolignans2. Here, we dissect a four-species bacterial consortium sufficient for all five reactions in this pathway. A single enzyme (benzyl ether reductase; ber), was sufficient for the first two biotransformations, variable between strains of Eggerthella lenta, critical for enterolignan production in gnotobiotic mice, and unique to Coriobacteriia. Transcriptional profiling (RNAseq) independently identified ber and genomic loci upregulated by each of the remaining substrates. Despite their low abundance in gut microbiomes and restricted phylogenetic range, all of the identified genes were detectable in the distal gut microbiomes of most individuals living in Northern California. Together, these results emphasize the importance of considering strain-level variations and bacterial co-occurrence to gain a mechanistic understanding of the bioactivation of plant secondary metabolites by the human gut microbiome.
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64
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Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM, Aldrovandi GM. Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis. Open Forum Infect Dis 2019; 6:ofz463. [PMID: 32258202 PMCID: PMC7105055 DOI: 10.1093/ofid/ofz463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Oral daily tenofovir (TFV) disoproxil fumarate/emtricitabine (TDF/FTC) for human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is highly effective for HIVprevention, yet long-term effects are not fully understood. We investigated the effects of PrEP on the rectal microbiome in a cohort of men who have sex with men (MSM). METHODS This cross-sectional analysis included HIV-negative MSM either on PrEP (n = 37) or not (n = 37) selected from an ongoing cohort using propensity score matching. Rectal swabs were used to examine microbiome composition using 16S ribosomal ribonucleic acid gene sequencing, and associations between PrEP use and microbiota abundance were examined. Hair specimens were used to quantify TFV and FTC exposure over the past 6 weeks on a subset of participants (n = 15). RESULTS Pre-exposure prophylaxis use was associated with a significant increase in Streptococcus abundance (adjusted P = .015). Similar associations were identified using least absolute shrinkage and selection operator (LASSO) regression, confirming the increase in Streptococcus and also showing increased Mitsuokella, Fusobacterium, and decreased Escherichia/Shigella. Increased Fusobacterium was significantly associated with increasing TFV exposure. CONCLUSIONS Oral TDF/FTC for PrEP is associated with rectal microbiome changes compared to well matched controls, specifically increased Streptococcus and Fusobacterium abundance. This study highlights the need for future investigations of the role of microbiome changes on HIV susceptibility and effectiveness of PrEP.
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Affiliation(s)
- Jennifer A Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Fan Li
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Ryan R Cook
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Sara Zabih
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Alexander Louie
- Division of HIV, Infectious Diseases, and Global Medicine (Hair Analytical Laboratory), Department of Medicine, University of California, San Francisco, California, USA
| | - Hideaki Okochi
- Division of HIV, Infectious Diseases, and Global Medicine (Hair Analytical Laboratory), Department of Medicine, University of California, San Francisco, California, USA
| | - Nicole H Tobin
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine (Hair Analytical Laboratory), Department of Medicine, University of California, San Francisco, California, USA
| | - Steven Shoptaw
- Department of Family Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Pamina M Gorbach
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Grace M Aldrovandi
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. Cell Host Microbe 2019; 26:325-335.e5. [PMID: 31492655 DOI: 10.1016/j.chom.2019.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/20/2019] [Accepted: 08/13/2019] [Indexed: 12/26/2022]
Abstract
Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered "hyper-targeted" phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.
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Affiliation(s)
- Paola Soto-Perez
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jordan E Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joel D Berry
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kathy N Lam
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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66
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Chagwedera DN, Ang QY, Bisanz JE, Leong YA, Ganeshan K, Cai J, Patterson AD, Turnbaugh PJ, Chawla A. Nutrient Sensing in CD11c Cells Alters the Gut Microbiota to Regulate Food Intake and Body Mass. Cell Metab 2019; 30:364-373.e7. [PMID: 31130466 PMCID: PMC6687538 DOI: 10.1016/j.cmet.2019.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/08/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022]
Abstract
Microbial dysbiosis and inflammation are implicated in diet-induced obesity and insulin resistance. However, it is not known whether crosstalk between immunity and microbiota also regulates metabolic homeostasis in healthy animals. Here, we report that genetic deletion of tuberous sclerosis 1 (Tsc1) in CD11c+ myeloid cells (Tsc1f/fCD11cCre mice) reduced food intake and body mass in the absence of metabolic disease. Co-housing and fecal transplant experiments revealed a dominant role for the healthy gut microbiota in regulation of body weight. 16S rRNA sequencing, selective culture, and reconstitution experiments further confirmed that selective deficiency of Lactobacillus johnsonii Q1-7 contributed to decreased food intake and body mass in Tsc1f/fCD11cCre mice. Mechanistically, activation of mTORC1 signaling in CD11c cells regulated production of L. johnsonii Q1-7-specific IgA, allowing for its stable colonization in the gut. Together, our findings reveal an unexpected transkingdom immune-microbiota feedback loop for homeostatic regulation of food intake and body mass in mammals.
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Affiliation(s)
- D Nyasha Chagwedera
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA
| | - Qi Yan Ang
- Department of Microbiology & Immunology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Jordan E Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Yew Ann Leong
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA; Centre for Inflammatory Diseases, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Kirthana Ganeshan
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA
| | - Jingwei Cai
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Ajay Chawla
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA; Departments of Physiology and Medicine, University of California, San Francisco, San Francisco, CA 94143-0795, USA.
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67
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Abstract
Levodopa (L-dopa) is the primary treatment for Parkinson's disease. The gut microbiome can metabolize levodopa, potentially leading to decreased efficacy and side effects, but responsible bacteria were unknown. Maini Rekdal et al. (2019) characterize enzymes in two gut bacteria that sequentially metabolize L-dopa and identify a novel inhibitor that may improve outcomes.
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Affiliation(s)
- Reese Hitchings
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., The Bronx, NY 10461, USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., The Bronx, NY 10461, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave., The Bronx, NY 10461, USA.
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68
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Kelly L. Harnessing the Microbiome to Improve Drug Therapy. Clin Pharmacol Ther 2019; 106:287-289. [DOI: 10.1002/cpt.1510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/16/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Libusha Kelly
- Department of Systems and Computational BiologyAlbert Einstein College of Medicine Bronx New York USA
- Department of Microbiology and ImmunologyAlbert Einstein College of Medicine Bronx New York USA
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69
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Lam KN, Alexander M, Turnbaugh PJ. Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes. Cell Host Microbe 2019; 26:22-34. [PMID: 31295421 PMCID: PMC6709864 DOI: 10.1016/j.chom.2019.06.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Despite the recognition, nearly a century ago, that the human microbiome plays a clinically relevant role in drug disposition, mechanistic insights, and translational applications are still limited. Here, we highlight the recent re-emergence of "pharmacomicrobiomics," which seeks to understand how inter-individual variations in the microbiome shape drug efficacy and side effect profiles. Multiple bacterial species, genes, and enzymes have already been implicated in the direct biotransformation of drugs, both from targeted case studies and from systematic computational and experimental analyses. Indirect mechanisms are also at play; for example, microbial interactions with the host immune system can have broad effects on immunomodulatory drugs. Finally, we discuss multiple emerging strategies for the precise manipulation of complex microbial communities to improve treatment outcomes. In the coming years, we anticipate a shift toward a more comprehensive view of precision medicine that encompasses our human and microbial genomes and their combined metabolic activities.
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Affiliation(s)
- Kathy N Lam
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Margaret Alexander
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94143, USA.
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70
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Guthrie L, Wolfson S, Kelly L. The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs. eLife 2019; 8:42866. [PMID: 31184303 PMCID: PMC6559788 DOI: 10.7554/elife.42866] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
Microbes are nature's chemists, capable of producing and metabolizing a diverse array of compounds. In the human gut, microbial biochemistry can be beneficial, for example vitamin production and complex carbohydrate breakdown; or detrimental, such as the reactivation of an inactive drug metabolite leading to patient toxicity. Identifying clinically relevant microbiome metabolism requires linking microbial biochemistry and ecology with patient outcomes. Here we present MicrobeFDT, a resource which clusters chemically similar drug and food compounds and links these compounds to microbial enzymes and known toxicities. We demonstrate that compound structural similarity can serve as a proxy for toxicity, enzyme sharing, and coarse-grained functional similarity. MicrobeFDT allows users to flexibly interrogate microbial metabolism, compounds of interest, and toxicity profiles to generate novel hypotheses of microbe-diet-drug-phenotype interactions that influence patient outcomes. We validate one such hypothesis experimentally, using MicrobeFDT to reveal unrecognized gut microbiome metabolism of the ovarian cancer drug altretamine.
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Affiliation(s)
- Leah Guthrie
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, United States
| | - Sarah Wolfson
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, United States
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, United States.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, United States
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71
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Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
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72
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Draft Genome Sequences of Type Strains of Gordonibacter faecihominis, Paraeggerthella hongkongensis , Parvibacter caecicola,Slackia equolifaciens, Slackia faecicanis, and Slackia isoflavoniconvertens. Microbiol Resour Announc 2019; 8:MRA01532-18. [PMID: 30643901 PMCID: PMC6328674 DOI: 10.1128/mra.01532-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/03/2018] [Indexed: 12/01/2022] Open
Abstract
Here, we report the annotated draft genome sequences of six type strains of the family Eggerthellaceae, Gordonibacter faecihominis JCM 16058, Paraeggerthella hongkongensis DSM 16106, Parvibacter caecicola DSM 22242, Slackia equolifaciens DSM 24851, Slackia faecicanis DSM 17537, and Slackia isoflavoniconvertens DSM 22006. Here, we report the annotated draft genome sequences of six type strains of the family Eggerthellaceae, Gordonibacter faecihominis JCM 16058, Paraeggerthella hongkongensis DSM 16106, Parvibacter caecicola DSM 22242, Slackia equolifaciens DSM 24851, Slackia faecicanis DSM 17537, and Slackia isoflavoniconvertens DSM 22006.
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73
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Aziz RK, Hegazy SM, Yasser R, Rizkallah MR, ElRakaiby MT. Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug-microbiome interactions. Expert Opin Drug Metab Toxicol 2018; 14:1043-1055. [PMID: 30269615 DOI: 10.1080/17425255.2018.1530216] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Pharmacomicrobiomics and toxicomicrobiomics study how variations within the human microbiome (the combination of human-associated microbial communities and their genomes) affect drug disposition, action, and toxicity. These emerging fields, interconnecting microbiology, bioinformatics, systems pharmacology, and toxicology, complement pharmacogenomics and toxicogenomics, expanding the scope of precision medicine. Areas covered: This article reviews some of the most recently reported pharmacomicrobiomic and toxicomicrobiomic interactions. Examples include the impact of the human gut microbiota on cardiovascular drugs, natural products, and chemotherapeutic agents, including immune checkpoint inhibitors. Although the gut microbiota has been the most extensively studied, some key drug-microbiome interactions involve vaginal, intratumoral, and environmental bacteria, and are briefly discussed here. Additionally, computational resources, moving the field from cataloging to predicting interactions, are introduced. Expert opinion: The rapid pace of discovery triggered by the Human Microbiome Project is moving pharmacomicrobiomic research from scattered observations to systematic studies focusing on screening microbiome variants against different drug classes. Better representation of all human populations will improve such studies by avoiding sampling bias, and the integration of multiomic studies with designed experiments will allow establishing causation. In the near future, pharmacomicrobiomic testing is expected to be a key step in screening novel drugs and designing precision therapeutics.
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Affiliation(s)
- Ramy K Aziz
- a Department of Microbiology and Immunology, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Shaimaa M Hegazy
- b Undergraduate program, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Reem Yasser
- b Undergraduate program, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Mariam R Rizkallah
- c Department of Biometry and Data Management , Leibniz Institute for Prevention Research and Epidemiology - BIPS , Bremen , Germany
| | - Marwa T ElRakaiby
- a Department of Microbiology and Immunology, Faculty of Pharmacy , Cairo University , Cairo , Egypt
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74
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Bisanz JE, Spanogiannopoulos P, Pieper LM, Bustion AE, Turnbaugh PJ. How to Determine the Role of the Microbiome in Drug Disposition. Drug Metab Dispos 2018; 46:1588-1595. [PMID: 30111623 DOI: 10.1124/dmd.118.083402] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
With a paradigm shift occurring in health care toward personalized and precision medicine, understanding the numerous environmental factors that impact drug disposition is of paramount importance. The highly diverse and variant nature of the human microbiome is now recognized as a factor driving interindividual variation in therapeutic outcomes. The purpose of this review is to provide a practical guide on methodology that can be applied to study the effects of microbes on the absorption, distribution, metabolism, and excretion of drugs. We also highlight recent examples of how these methods have been successfully applied to help build the basis for researching the intersection of the microbiome and pharmacology. Although in vitro and in vivo preclinical models are highlighted, these methods are also relevant in late-phase drug development or even as a part of routine after-market surveillance. These approaches will aid in filling major knowledge gaps for both current and upcoming therapeutics with the long-term goal of achieving a new type of knowledge-based medicine that integrates data on the host and the microbiome.
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Affiliation(s)
- Jordan E Bisanz
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California (J.E.B., P.S., L.M.P., A.E.B., P.J.T.) and Chan Zuckerberg Biohub, San Francisco, California (P.J.T.)
| | - Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California (J.E.B., P.S., L.M.P., A.E.B., P.J.T.) and Chan Zuckerberg Biohub, San Francisco, California (P.J.T.)
| | - Lindsey M Pieper
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California (J.E.B., P.S., L.M.P., A.E.B., P.J.T.) and Chan Zuckerberg Biohub, San Francisco, California (P.J.T.)
| | - Annamarie E Bustion
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California (J.E.B., P.S., L.M.P., A.E.B., P.J.T.) and Chan Zuckerberg Biohub, San Francisco, California (P.J.T.)
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California (J.E.B., P.S., L.M.P., A.E.B., P.J.T.) and Chan Zuckerberg Biohub, San Francisco, California (P.J.T.)
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75
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Davey SG. Deciphering digoxin deactivation. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0017-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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