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Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R. The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases. Gastroenterology 2023; 164:1069-1085. [PMID: 36841488 PMCID: PMC10205675 DOI: 10.1053/j.gastro.2023.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 02/27/2023]
Abstract
The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the expense of untargeted metabolomics and lack of ability to process the data. In this review, we focused on the rapidly expanding information about the bile acid repertoire produced by the gut microbiome, including the impacts of bile acids on a wide range of host physiological processes and diseases, and discussed the role of short-chain fatty acids and other important gut microbiome-derived metabolites. Of particular note is the action of gut microbiome-derived metabolites throughout the body, which impact processes ranging from obesity to aging to disorders traditionally thought of as diseases of the nervous system, but that are now recognized as being strongly influenced by the gut microbiome and the metabolites it produces. We also highlighted the emerging role for modifying the gut microbiome to improve health or to treat disease, including the "engineered native bacteria'' approach that takes bacterial strains from a patient, modifies them to alter metabolism, and reintroduces them. Taken together, study of the metabolites derived from the gut microbiome provided insights into a wide range of physiological and pathophysiological processes, and has substantial potential for new approaches to diagnostics and therapeutics of disease of, or involving, the gastrointestinal tract.
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Affiliation(s)
- Kelly A Fogelson
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California; Department of Pediatrics, University of California San Diego, San Diego, California; Center for Microbiome Innovation, University of California San Diego, San Diego, California.
| | - Amir Zarrinpar
- Center for Microbiome Innovation, University of California San Diego, San Diego, California; Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, San Diego, California; Division of Gastroenterology, University of California San Diego, San Diego, California; Institute of Diabetes and Metabolic Health, University of California San Diego, San Diego, California.
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California; Center for Microbiome Innovation, University of California San Diego, San Diego, California; Department of Bioengineering, University of California San Diego, San Diego, California; Department of Computer Science and Engineering, University of California San Diego, San Diego, California.
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Kuchibhotla KV, Hindmarsh Sten T, Papadoyannis ES, Elnozahy S, Fogelson KA, Kumar R, Boubenec Y, Holland PC, Ostojic S, Froemke RC. Dissociating task acquisition from expression during learning reveals latent knowledge. Nat Commun 2019; 10:2151. [PMID: 31089133 PMCID: PMC6517418 DOI: 10.1038/s41467-019-10089-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/07/2019] [Indexed: 11/30/2022] Open
Abstract
Performance on cognitive tasks during learning is used to measure knowledge, yet it remains controversial since such testing is susceptible to contextual factors. To what extent does performance during learning depend on the testing context, rather than underlying knowledge? We trained mice, rats and ferrets on a range of tasks to examine how testing context impacts the acquisition of knowledge versus its expression. We interleaved reinforced trials with probe trials in which we omitted reinforcement. Across tasks, each animal species performed remarkably better in probe trials during learning and inter-animal variability was strikingly reduced. Reinforcement feedback is thus critical for learning-related behavioral improvements but, paradoxically masks the expression of underlying knowledge. We capture these results with a network model in which learning occurs during reinforced trials while context modulates only the read-out parameters. Probing learning by omitting reinforcement thus uncovers latent knowledge and identifies context- not “smartness”- as the major source of individual variability. Performance is generally used as a metric to assay whether an animal has learnt a particular perceptual task. Here the authors demonstrate that in the context of probe trials without the possibility of reward, animals perform the correct instrumental response suggesting a latent knowledge of the task much before it is manifest in their performance.
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Affiliation(s)
- Kishore V Kuchibhotla
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Neuroscience, Johns Hopkins Medical School, Baltimore, MD, 21218, USA.
| | - Tom Hindmarsh Sten
- Departments of Otolaryngology, Neuroscience and Physiology, Skirball Institute, Neuroscience Institute, New York University School of Medicine, New York, NY, 10016, USA.,Center for Neural Science, New York University, New York, NY, 10003, USA.,Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, 10065, USA
| | - Eleni S Papadoyannis
- Departments of Otolaryngology, Neuroscience and Physiology, Skirball Institute, Neuroscience Institute, New York University School of Medicine, New York, NY, 10016, USA.,Center for Neural Science, New York University, New York, NY, 10003, USA
| | - Sarah Elnozahy
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kelly A Fogelson
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rupesh Kumar
- Laboratoire des Systèmes Perceptifs, UMR8248, École Normale Supérieure-PSL Research University, 75006, Paris, France
| | - Yves Boubenec
- Laboratoire des Systèmes Perceptifs, UMR8248, École Normale Supérieure-PSL Research University, 75006, Paris, France
| | - Peter C Holland
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, 21218, USA.,Department of Neuroscience, Johns Hopkins Medical School, Baltimore, MD, 21218, USA
| | - Srdjan Ostojic
- Laboratoire de Neurosciences Cognitives, INSERM U960, École Normale Supérieure-PSL Research University, 75006, Paris, France
| | - Robert C Froemke
- Departments of Otolaryngology, Neuroscience and Physiology, Skirball Institute, Neuroscience Institute, New York University School of Medicine, New York, NY, 10016, USA.,Center for Neural Science, New York University, New York, NY, 10003, USA.,Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MA, 20815, USA
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