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Mathieu E, Léjard V, Ezzine C, Govindin P, Morat A, Giat M, Lapaque N, Doré J, Blottière HM. An Insight into Functional Metagenomics: A High-Throughput Approach to Decipher Food-Microbiota-Host Interactions in the Human Gut. Int J Mol Sci 2023; 24:17630. [PMID: 38139456 PMCID: PMC10744307 DOI: 10.3390/ijms242417630] [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: 11/15/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Our understanding of the symbiotic relationship between the microbiota and its host has constantly evolved since our understanding that the "self" was not only defined by our genetic patrimony but also by the genomes of bugs living in us. The first culture-based methods highlighted the important functions of the microbiota. However, these methods had strong limitations and did not allow for a full understanding of the complex relationships that occur at the interface between the microbiota and the host. The recent development of metagenomic approaches has been a groundbreaking step towards this understanding. Its use has provided new insights and perspectives. In the present chapter, we will describe the advances of functional metagenomics to decipher food-microbiota and host-microbiota interactions. This powerful high-throughput approach allows for the assessment of the microbiota as a whole (including non-cultured bacteria) and enabled the discovery of new signaling pathways and functions involved in the crosstalk between food, the gut microbiota and its host. We will present the pipeline and highlight the most important studies that helped to develop the field. To conclude, we will emphasize the most recent developments and hot topics in functional metagenomics.
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Affiliation(s)
- Elliot Mathieu
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Véronique Léjard
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Chaima Ezzine
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Pauline Govindin
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Aurélien Morat
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Margot Giat
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Nicolas Lapaque
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France;
| | - Joël Doré
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France;
| | - Hervé M. Blottière
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
- Nantes Université, INRAE, UMR 1280, PhAN, 44000 Nantes, France
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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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4
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Apjok G, Számel M, Christodoulou C, Seregi V, Vásárhelyi BM, Stirling T, Eszenyi B, Sári T, Vidovics F, Nagrand E, Kovács D, Szili P, Lantos II, Méhi O, Jangir PK, Herczeg R, Gálik B, Urbán P, Gyenesei A, Draskovits G, Nyerges Á, Fekete G, Bodai L, Zsindely N, Dénes B, Yosef I, Qimron U, Papp B, Pál C, Kintses B. Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains. Nat Microbiol 2023; 8:410-423. [PMID: 36759752 PMCID: PMC9981461 DOI: 10.1038/s41564-023-01320-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.
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Affiliation(s)
- Gábor Apjok
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Mónika Számel
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Chryso Christodoulou
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Viktória Seregi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary
| | - Bálint Márk Vásárhelyi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Tamás Stirling
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary ,grid.481814.00000 0004 0479 9817Institute of Biochemistry, Biological Research Centre, National Laboratory for Health Security, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Bálint Eszenyi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Tóbiás Sári
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Fanni Vidovics
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erika Nagrand
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Dorina Kovács
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Petra Szili
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Ildikó Ilona Lantos
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Orsolya Méhi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Pramod K. Jangir
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary ,grid.4991.50000 0004 1936 8948Present Address: Department of Zoology, University of Oxford, Oxford, UK
| | - Róbert Herczeg
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Bence Gálik
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary ,grid.48324.390000000122482838Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Péter Urbán
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Attila Gyenesei
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary ,grid.48324.390000000122482838Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Gábor Draskovits
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ákos Nyerges
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gergely Fekete
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - László Bodai
- grid.9008.10000 0001 1016 9625Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Nóra Zsindely
- grid.9008.10000 0001 1016 9625Department of Genetics, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Béla Dénes
- grid.432859.10000 0004 4647 7293Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Ido Yosef
- grid.12136.370000 0004 1937 0546Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Udi Qimron
- grid.12136.370000 0004 1937 0546Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Balázs Papp
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.481814.00000 0004 0479 9817Institute of Biochemistry, Biological Research Centre, National Laboratory for Health Security, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Csaba Pál
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
| | - Bálint Kintses
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary. .,HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary. .,Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
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5
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Lai Y, Hayashi N, Lu TK. Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology. Curr Opin Chem Biol 2022; 70:102178. [PMID: 35759819 DOI: 10.1016/j.cbpa.2022.102178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/28/2022] [Indexed: 11/29/2022]
Abstract
The role of the microbiome in health and disease is attracting the attention of researchers seeking to engineer microorganisms for diagnostic and therapeutic applications. Recent progress in synthetic biology may enable the dissection of host-microbiota interactions. Sophisticated genetic circuits that can sense, compute, memorize, and respond to signals have been developed for the stable commensal bacterium Bacteroides thetaiotaomicron, dominant in the human gut. In this review, we highlight recent advances in expanding the genetic toolkit for B. thetaiotaomicron and foresee several applications of this species for microbiome engineering. We provide our perspective on the challenges and future opportunities for the engineering of human gut-associated bacteria as living therapeutic agents.
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Affiliation(s)
- Yong Lai
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Naoki Hayashi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., 35 Shinanomachi, Shinjuku, Tokyo 160-8582, Japan
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Senti Biosciences, 2 Corporate Drive South San Francisco, CA 94080, USA.
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Abdelsalam NA, Ramadan AT, ElRakaiby MT, Aziz RK. Toxicomicrobiomics: The Human Microbiome vs. Pharmaceutical, Dietary, and Environmental Xenobiotics. Front Pharmacol 2020; 11:390. [PMID: 32372951 PMCID: PMC7179069 DOI: 10.3389/fphar.2020.00390] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/16/2020] [Indexed: 12/13/2022] Open
Abstract
The harmful impact of xenobiotics on the environment and human health is being more widely recognized; yet, inter- and intraindividual genetic variations among humans modulate the extent of harm, mostly through modulating the outcome of xenobiotic metabolism and detoxification. As the Human Genome Project revealed that host genetic, epigenetic, and regulatory variations could not sufficiently explain the complexity of interindividual variability in xenobiotics metabolism, its sequel, the Human Microbiome Project, is investigating how this variability may be influenced by human-associated microbial communities. Xenobiotic-microbiome relationships are mutual and dynamic. Not only does the human microbiome have a direct metabolizing potential on xenobiotics, but it can also influence the expression of the host metabolizing genes and the activity of host enzymes. On the other hand, xenobiotics may alter the microbiome composition, leading to a state of dysbiosis, which is linked to multiple diseases and adverse health outcomes, including increased toxicity of some xenobiotics. Toxicomicrobiomics studies these mutual influences between the ever-changing microbiome cloud and xenobiotics of various origins, with emphasis on their fate and toxicity, as well the various classes of microbial xenobiotic-modifying enzymes. This review article discusses classic and recent findings in toxicomicrobiomics, with examples of interactions between gut, skin, urogenital, and oral microbiomes with pharmaceutical, food-derived, and environmental xenobiotics. The current state and future prospects of toxicomicrobiomic research are discussed, and the tools and strategies for performing such studies are thoroughly and critically compared.
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Affiliation(s)
| | - Ahmed Tarek Ramadan
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Marwa Tarek ElRakaiby
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy Karam Aziz
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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8
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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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