1
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Lee H, Yang X, Jin PR, Won KJ, Kim CH, Jeong H. The Discovery of Gut Microbial Metabolites as Modulators of Host Susceptibility to Acetaminophen-Induced Hepatotoxicity. Drug Metab Dispos 2024; 52:754-764. [PMID: 38302428 DOI: 10.1124/dmd.123.001541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
The mammalian gut microbiota plays diverse and essential roles in modulating host physiology. Key mediators determining the outcome of the microbiota-host interactions are the small molecule metabolites produced by the gut microbiota. The liver is a major organ exposed to gut microbial metabolites, and it serves as the nexus for maintaining healthy interactions between the gut microbiota and the host. At the same time, the liver is the primary target of potentially harmful gut microbial metabolites. In this review, we provide an up-to-date list of gut microbial metabolites that have been identified to either increase or decrease host susceptibility to acetaminophen (APAP)-induced liver injury. The signaling pathways and molecular factors involved in the progression of APAP-induced hepatotoxicity are well-established, and we propose that the mouse model of APAP-induced hepatotoxicity serves as a model system for uncovering gut microbial metabolites with previously unknown functions. Furthermore, we envision that gut microbial metabolites identified to alter APAP-induced hepatotoxicity likely have broader implications in other liver diseases. SIGNIFICANCE STATEMENT: This review provides an overview of the role of the gut microbiota in modulating the host susceptibility to acetaminophen (APAP)-induced liver injury. It focuses on the roles of gut bacterial small molecule metabolites as mediators of the interaction between the gut microbiota and the liver. It also illustrates the utility of APAP-induced liver injury as a model to identify gut microbial metabolites with biological function.
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Affiliation(s)
- Hyunwoo Lee
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Xiaotong Yang
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Pei-Ru Jin
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Kyoung-Jae Won
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Chang H Kim
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Hyunyoung Jeong
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
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2
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Shin YC, Than N, Park SJ, Kim HJ. Bioengineered human gut-on-a-chip for advancing non-clinical pharmaco-toxicology. Expert Opin Drug Metab Toxicol 2024:1-14. [PMID: 38849312 DOI: 10.1080/17425255.2024.2365254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
INTRODUCTION There is a growing need for alternative models to advance current non-clinical experimental models because they often fail to accurately predict drug responses in human clinical trials. Human organ-on-a-chip models have emerged as promising approaches for advancing the predictability of drug behaviors and responses. AREAS COVERED We summarize up-to-date human gut-on-a-chip models designed to demonstrate intricate interactions involving the host, microbiome, and pharmaceutical compounds since these models have been reported a decade ago. This overview covers recent advances in gut-on-a-chip models as a bridge technology between non-clinical and clinical assessments of drug toxicity and metabolism. We highlight the promising potential of gut-on-a-chip platforms, offering a reliable and valid framework for investigating reciprocal crosstalk between the host, gut microbiome, and drug compounds. EXPERT OPINION Gut-on-a-chip platforms can attract multiple end users as predictive, human-relevant, and non-clinical model. Notably, gut-on-a-chip platforms provide a unique opportunity to recreate a human intestinal microenvironment, including dynamic bowel movement, luminal flow, oxygen gradient, host-microbiome interactions, and disease-specific manipulations restricted in animal and in vitro cell culture models. Additionally, given the profound impact of the gut microbiome on pharmacological bioprocess, it is critical to leverage breakthroughs of gut-on-a-chip technology to address knowledge gaps and drive innovations in predictive drug toxicology and metabolism.
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Affiliation(s)
- Yong Cheol Shin
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nam Than
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Soo Jin Park
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hyun Jung Kim
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Inflammation and Immunity, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
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3
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Huang Y, Zhang Y, Wu K, Tan X, Lan T, Wang G. Role of Gut Microecology in the Pathogenesis of Drug-Induced Liver Injury and Emerging Therapeutic Strategies. Molecules 2024; 29:2663. [PMID: 38893536 PMCID: PMC11173750 DOI: 10.3390/molecules29112663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Drug-induced liver injury (DILI) is a common clinical pharmacogenic disease. In the United States and Europe, DILI is the most common cause of acute liver failure. Drugs can cause hepatic damage either directly through inherent hepatotoxic properties or indirectly by inducing oxidative stress, immune responses, and inflammatory processes. These pathways can culminate in hepatocyte necrosis. The role of the gut microecology in human health and diseases is well recognized. Recent studies have revealed that the imbalance in the gut microecology is closely related to the occurrence and development of DILI. The gut microecology plays an important role in liver injury caused by different drugs. Recent research has revealed significant changes in the composition, relative abundance, and distribution of gut microbiota in both patients and animal models with DILI. Imbalance in the gut microecology causes intestinal barrier destruction and microorganism translocation; the alteration in microbial metabolites may initiate or aggravate DILI, and regulation and control of intestinal microbiota can effectively mitigate drug-induced liver injury. In this paper, we provide an overview on the present knowledge of the mechanisms by which DILI occurs, the common drugs that cause DILI, the gut microbiota and gut barrier composition, and the effects of the gut microbiota and gut barrier on DILI, emphasizing the contribution of the gut microecology to DILI.
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Affiliation(s)
- Yuqiao Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yu Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Kaireng Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xinxin Tan
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Tian Lan
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Guixiang Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
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4
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Safdar M, Ullah M, Hamayun S, Wahab A, Khan SU, Abdikakhorovich SA, Haq ZU, Mehreen A, Naeem M, Mustopa AZ, Hasan N. Microbiome miracles and their pioneering advances and future frontiers in cardiovascular disease. Curr Probl Cardiol 2024; 49:102686. [PMID: 38830479 DOI: 10.1016/j.cpcardiol.2024.102686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Cardiovascular diseases (CVDs) represent a significant global health challenge, underscoring the need for innovative approaches to prevention and treatment. Recent years have seen a surge in interest in unraveling the complex relationship between the gut microbiome and cardiovascular health. This article delves into current research on the composition, diversity, and impact of the gut microbiome on CVD development. Recent advancements have elucidated the profound influence of the gut microbiome on disease progression, particularly through key mediators like Trimethylamine-N-oxide (TMAO) and other microbial metabolites. Understanding these mechanisms reveals promising therapeutic targets, including interventions aimed at modulating the gut microbiome's interaction with the immune system and its contribution to endothelial dysfunction. Harnessing this understanding, personalized medicine strategies tailored to individuals' gut microbiome profiles offer innovative avenues for reducing cardiovascular risk. As research in this field continues to evolve, there is vast potential for transformative advancements in cardiovascular medicine, paving the way for precision prevention and treatment strategies to address this global health challenge.
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Affiliation(s)
- Mishal Safdar
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Muneeb Ullah
- College of Pharmacy, Pusan National University, Busandaehak-ro 63 beon-gil 2, Geumjeong-gu, Busan 46241, Republic of Korea; Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485 Punjab, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shahid Ullah Khan
- Department of Biochemistry, Women Medical and Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | | | - Zia Ul Haq
- Department of Public Health, Institute of Public Health Sciences, Khyber Medical University, Peshawar 25120, Pakistan
| | - Aqsa Mehreen
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, National Research, and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar 90245, Republic of Indonesia.
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5
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Liu T, Zhang C, Zhang H, Jin J, Li X, Liang S, Xue Y, Yuan F, Zhou Y, Bian X, Wei H. A new evaluation system for drug-microbiota interactions. IMETA 2024; 3:e199. [PMID: 38898986 PMCID: PMC11183188 DOI: 10.1002/imt2.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 06/21/2024]
Abstract
The drug response phenotype is determined by a combination of genetic and environmental factors. The high clinical conversion failure rate of gene-targeted drugs might be attributed to the lack of emphasis on environmental factors and the inherent individual variability in drug response (IVDR). Current evidence suggests that environmental variables, rather than the disease itself, are the primary determinants of both gut microbiota composition and drug metabolism. Additionally, individual differences in gut microbiota create a unique metabolic environment that influences the in vivo processes underlying drug absorption, distribution, metabolism, and excretion (ADME). Here, we discuss how gut microbiota, shaped by both genetic and environmental factors, affects the host's ADME microenvironment within a new evaluation system for drug-microbiota interactions. Furthermore, we propose a new top-down research approach to investigate the intricate nature of drug-microbiota interactions in vivo. This approach utilizes germ-free animal models, providing foundation for the development of a new evaluation system for drug-microbiota interactions.
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Affiliation(s)
- Tian‐Hao Liu
- Yu‐Yue Pathology Scientific Research CenterChongqingChina
- Department of PathologyArmy Medical UniversityChongqingChina
- Department of GastroenterologyAffiliated Hospital of Jiangnan UniversityWuxiJiangsuChina
| | - Chen‐Yang Zhang
- Department of GastroenterologyAffiliated Hospital of Jiangnan UniversityWuxiJiangsuChina
- Institute of Integrated traditional Chinese and Western MedicineAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Hang Zhang
- College of Animal Science and Technology, College of Animal MedicineHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jing Jin
- Department of PathologyArmy Medical UniversityChongqingChina
| | - Xue Li
- Wuxi Hospital Affiliated to Nanjing University of Chinese MedicineWuxiJiangsuChina
| | - Shi‐Qiang Liang
- College of Animal Science and Technology, College of Animal MedicineHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yu‐Zheng Xue
- Department of GastroenterologyAffiliated Hospital of Jiangnan UniversityWuxiJiangsuChina
| | - Feng‐Lai Yuan
- Institute of Integrated traditional Chinese and Western MedicineAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Ya‐Hong Zhou
- Wuxi Hospital Affiliated to Nanjing University of Chinese MedicineWuxiJiangsuChina
| | - Xiu‐Wu Bian
- Yu‐Yue Pathology Scientific Research CenterChongqingChina
- Department of PathologyArmy Medical UniversityChongqingChina
| | - Hong Wei
- Yu‐Yue Pathology Scientific Research CenterChongqingChina
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6
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Sivaprasadan S, Anila KN, Nair K, Mallick S, Biswas L, Valsan A, Praseedom RK, Nair BKG, Sudhindran S. Microbiota and Gut-Liver Axis: An Unbreakable Bond? Curr Microbiol 2024; 81:193. [PMID: 38805045 DOI: 10.1007/s00284-024-03694-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/08/2024] [Indexed: 05/29/2024]
Abstract
The gut microbiota, amounting to approximately 100 trillion (1014) microbes represents a genetic repertoire that is bigger than the human genome itself. Evidence on bidirectional interplay between human and microbial genes is mounting. Microbiota probably play vital roles in diverse aspects of normal human metabolism, such as digestion, immune modulation, and gut endocrine function, as well as in the genesis and progression of many human diseases. Indeed, the gut microbiota has been most closely linked to various chronic ailments affecting the liver, although concrete scientific data are sparse. In this narrative review, we initially discuss the basic epidemiology of gut microbiota and the factors influencing their initial formation in the gut. Subsequently, we delve into the gut-liver axis and the evidence regarding the link between gut microbiota and the genesis or progression of various liver diseases. Finally, we summarise the recent research on plausible ways to modulate the gut microbiota to alter the natural history of liver disease.
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Affiliation(s)
- Saraswathy Sivaprasadan
- Department of Gastrointestinal Surgery and Solid Organ Transplantation, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, India
| | - K N Anila
- Department of Gastrointestinal Surgery and Solid Organ Transplantation, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Krishnanunni Nair
- Department of Gastrointestinal Surgery and Solid Organ Transplantation, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Shweta Mallick
- Department of Gastrointestinal Surgery and Solid Organ Transplantation, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Lalitha Biswas
- Amrita School of Nanosciences and Molecular Medicine, Kochi, India
| | - Arun Valsan
- Department of Hepatology & Gastroenterology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, India
| | | | | | - Surendran Sudhindran
- Department of Gastrointestinal Surgery and Solid Organ Transplantation, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, India.
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7
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Kok CR, Rose DJ, Cui J, Whisenhunt L, Hutkins R. Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses. BMC Microbiol 2024; 24:183. [PMID: 38796418 PMCID: PMC11127362 DOI: 10.1186/s12866-024-03344-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. RESULTS Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. CONCLUSIONS Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.
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Affiliation(s)
- Car Reen Kok
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Devin J Rose
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Lisa Whisenhunt
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Robert Hutkins
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 258 Food Innovation Center, Lincoln, NE, 68588-6205, USA.
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8
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Chen P. Targeting gut microbiota to counteract acetaminophen-induced acute liver injury. Trends Microbiol 2024; 32:419-421. [PMID: 38472076 DOI: 10.1016/j.tim.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Acetaminophen (N-acetyl-p-aminophenol; APAP) overdose-induced acute liver injury (AILI) is a huge threat to public health worldwide. Recent research clearly shows that the intestinal microbiota (IM) is a key modulator in AILI. Herein, I discuss the latest findings on how the IM regulates AILI and the potential interventions to combat AILI by targeting the IM.
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Affiliation(s)
- Peng Chen
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, China; Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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9
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Lodge S, Litton E, Gray N, Ryan M, Millet O, Fear M, Raby E, Currie A, Wood F, Holmes E, Wist J, Nicholson JK. Stratification of Sepsis Patients on Admission into the Intensive Care Unit According to Differential Plasma Metabolic Phenotypes. J Proteome Res 2024; 23:1328-1340. [PMID: 38513133 PMCID: PMC11002934 DOI: 10.1021/acs.jproteome.3c00803] [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: 11/20/2023] [Revised: 02/15/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
Delayed diagnosis of patients with sepsis or septic shock is associated with increased mortality and morbidity. UPLC-MS and NMR spectroscopy were used to measure panels of lipoproteins, lipids, biogenic amines, amino acids, and tryptophan pathway metabolites in blood plasma samples collected from 152 patients within 48 h of admission into the Intensive Care Unit (ICU) where 62 patients had no sepsis, 71 patients had sepsis, and 19 patients had septic shock. Patients with sepsis or septic shock had higher concentrations of neopterin and lower levels of HDL cholesterol and phospholipid particles in comparison to nonsepsis patients. Septic shock could be differentiated from sepsis patients based on different concentrations of 10 lipids, including significantly lower concentrations of five phosphatidylcholine species, three cholesterol esters, one dihydroceramide, and one phosphatidylethanolamine. The Supramolecular Phospholipid Composite (SPC) was reduced in all ICU patients, while the composite markers of acute phase glycoproteins were increased in the sepsis and septic shock patients within 48 h admission into ICU. We show that the plasma metabolic phenotype obtained within 48 h of ICU admission is diagnostic for the presence of sepsis and that septic shock can be differentiated from sepsis based on the lipid profile.
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Affiliation(s)
- Samantha Lodge
- Australian
National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Edward Litton
- Intensive
Care Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
- Intensive
Care Unit, St John of God Hospital, Subiaco, WA 6009, Australia
- School
of Medicine, University of Western Australia, Crawley, WA 6009, Australia
| | - Nicola Gray
- Australian
National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Monique Ryan
- Australian
National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Oscar Millet
- Precision
Medicine and Metabolism Laboratory, CIC
bioGUNE, Parque Tecnológico
de Bizkaia, Bld. 800, Derio 48160, Spain
| | - Mark Fear
- Burn
Injury Research Unit, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
- Fiona
Wood Foundation, Perth, WA 6150, Australia
| | - Edward Raby
- Department
of Infectious Diseases, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
| | - Andrew Currie
- School
of Medical, Molecular & Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- Centre
for Molecular Medicine & Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
- Wesfarmers
Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Fiona Wood
- Burn
Injury Research Unit, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
- Fiona
Wood Foundation, Perth, WA 6150, Australia
- Burns
service of Western Australia, WA Department
of Health, Murdoch, WA 6150, Australia
| | - Elaine Holmes
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Institute
of Global Health Innovation, Faculty of Medicine, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, U.K.
| | - Julien Wist
- Australian
National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
- Department of Metabolism, Digestion and
Reproduction, Faculty of Medicine, Imperial
College London, Sir Alexander
Fleming Building, South Kensington, London SW7 2AZ, U.K.
| | - Jeremy K. Nicholson
- Australian
National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA6150, Australia
- Department of Metabolism, Digestion and
Reproduction, Faculty of Medicine, Imperial
College London, Sir Alexander
Fleming Building, South Kensington, London SW7 2AZ, U.K.
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10
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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11
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Abooshahab R, Razavi F, Ghorbani F, Hooshmand K, Zarkesh M, Hedayati M. Thyroid cancer cell metabolism: A glance into cell culture system-based metabolomics approaches. Exp Cell Res 2024; 435:113936. [PMID: 38278284 DOI: 10.1016/j.yexcr.2024.113936] [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: 10/31/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Thyroid cancer is the most common malignancy of the endocrine system and the seventh most prevalent cancer in women worldwide. It is a complex and diverse disease characterized by heterogeneity, underscoring the importance of understanding the underlying metabolic alterations within tumor cells. Metabolomics technologies offer a powerful toolset to explore and identify endogenous and exogenous biochemical reaction products, providing crucial insights into the intricate metabolic pathways and processes within living cells. Metabolism plays a central role in cell function, making metabolomics a valuable reflection of a cell's phenotype. In the OMICs era, metabolomics analysis of cells brings numerous advantages over existing methods, propelling cell metabolomics as an emerging field with vast potential for investigating metabolic pathways and their perturbation in pathophysiological conditions. This review article aims to look into recent developments in applying metabolomics for characterizing and interpreting the cellular metabolome in thyroid cancer cell lines, exploring their unique metabolic characteristics. Understanding the metabolic alterations in tumor cells can lead to the identification of critical nodes in the metabolic network that could be targeted for therapeutic intervention.
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Affiliation(s)
- Raziyeh Abooshahab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Curtin Medical School, Curtin University, Bentley 6102, Australia
| | - Fatemeh Razavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Ghorbani
- Department of Molecular Immunology, Ruhr University Bochum, Bochum, Germany
| | | | - Maryam Zarkesh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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12
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Rodrigues SG, van der Merwe S, Krag A, Wiest R. Gut-liver axis: Pathophysiological concepts and medical perspective in chronic liver diseases. Semin Immunol 2024; 71:101859. [PMID: 38219459 DOI: 10.1016/j.smim.2023.101859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/11/2023] [Accepted: 12/04/2023] [Indexed: 01/16/2024]
Affiliation(s)
- Susana G Rodrigues
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Schalk van der Merwe
- Department of Gastroenterology and Hepatology, University hospital Gasthuisberg, University of Leuven, Belgium
| | - Aleksander Krag
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Centre for Liver Research, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark, University of Southern Denmark, Odense, Denmark
| | - Reiner Wiest
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland.
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13
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Verdegaal AA, Goodman AL. Integrating the gut microbiome and pharmacology. Sci Transl Med 2024; 16:eadg8357. [PMID: 38295186 DOI: 10.1126/scitranslmed.adg8357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024]
Abstract
The gut microbiome harbors trillions of organisms that contribute to human health and disease. These bacteria can also affect the properties of medical drugs used to treat these diseases, and drugs, in turn, can reshape the microbiome. Research addressing interdependent microbiome-host-drug interactions thus has broad impact. In this Review, we discuss these interactions from the perspective of drug bioavailability, absorption, metabolism, excretion, toxicity, and drug-mediated microbiome modulation. We survey approaches that aim to uncover the mechanisms underlying these effects and opportunities to translate this knowledge into new strategies to improve the development, administration, and monitoring of medical drugs.
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Affiliation(s)
- Andrew A Verdegaal
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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14
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Wang S, Ju D, Zeng X. Mechanisms and Clinical Implications of Human Gut Microbiota-Drug Interactions in the Precision Medicine Era. Biomedicines 2024; 12:194. [PMID: 38255298 PMCID: PMC10813426 DOI: 10.3390/biomedicines12010194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
The human gut microbiota, comprising trillions of microorganisms residing in the gastrointestinal tract, has emerged as a pivotal player in modulating various aspects of human health and disease. Recent research has shed light on the intricate relationship between the gut microbiota and pharmaceuticals, uncovering profound implications for drug metabolism, efficacy, and safety. This review depicted the landscape of molecular mechanisms and clinical implications of dynamic human gut Microbiota-Drug Interactions (MDI), with an emphasis on the impact of MDI on drug responses and individual variations. This review also discussed the therapeutic potential of modulating the gut microbiota or harnessing its metabolic capabilities to optimize clinical treatments and advance personalized medicine, as well as the challenges and future directions in this emerging field.
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Affiliation(s)
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China;
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China;
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15
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Adhikary S, Esmeeta A, Dey A, Banerjee A, Saha B, Gopan P, Duttaroy AK, Pathak S. Impacts of gut microbiota alteration on age-related chronic liver diseases. Dig Liver Dis 2024; 56:112-122. [PMID: 37407321 DOI: 10.1016/j.dld.2023.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
The gut microbiome and its metabolites are involved in developing and progressing liver disease. Various liver illnesses, such as non-alcoholic fatty liver disease, alcoholic liver disease, hepatitis C, and hepatocellular carcinoma, are made worse and have worse prognoses with aging. Dysbiosis, which occurs when the symbiosis between the microbiota and the host is disrupted, can significantly negatively impact health. Liver disease is linked to qualitative changes, such as an increase in hazardous bacteria and a decrease in good bacteria, as well as quantitative changes in the overall amount of bacteria (overgrowth). Intestinal gut microbiota and their metabolites may lead to chronic liver disease development through various mechanisms, such as increasing gut permeability, persistent systemic inflammation, production of SCFA, bile acids, and alteration in metabolism. Age-related gut dysbiosis can disrupt the communication between gut microbiota and the host, impacting the host's health and lifespan. With aging, a gradual loss of the ability to maintain homeostasis because of structural alteration and gut dysbiosis leads to the disease progression in end-stage liver disease. Recently chronic liver disease has been identified as a global problem. A large number of patients are receiving liver transplants yearly. Thereby gut microbiome ecology is changing in the patients of the gut due to the changes in pathophysiology during the preoperative stage. The present review summarises the age-associated dysbiosis of gut microbial composition and its contribution to chronic liver disease. This review also provides information about the impact of liver transplant on the gut microbiome and possible disadvantageous effects of alteration in gut microbiota.
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Affiliation(s)
- Subhamay Adhikary
- Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education(CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Kelambakkam 603103, India
| | - Akanksha Esmeeta
- Amity Institute of Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh 201301, India
| | - Amit Dey
- Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education(CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Kelambakkam 603103, India
| | - Antara Banerjee
- Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education(CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Kelambakkam 603103, India
| | - Biki Saha
- Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education(CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Kelambakkam 603103, India
| | - Pournami Gopan
- Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education(CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Kelambakkam 603103, India
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Norway.
| | - Surajit Pathak
- Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education(CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Kelambakkam 603103, India.
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16
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Cerdó T, Ruiz-Rodríguez A, Acuña I, Torres-Espínola FJ, Menchén-Márquez S, Gámiz F, Gallo M, Jehmlich N, Haange SB, von Bergen M, Campoy C, Suárez A. Infant gut microbiota contributes to cognitive performance in mice. Cell Host Microbe 2023; 31:1974-1988.e4. [PMID: 38052208 DOI: 10.1016/j.chom.2023.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
Gut microbiota has been linked to infant neurodevelopment. Here, an association between infant composite cognition and gut microbiota composition is established as soon as 6 months. Higher diversity and evenness characterize microbial communities of infants with composite cognition above (Inf-aboveCC) versus below (Inf-belowCC) median values. Metaproteomic and metabolomic analyses establish an association between microbial histidine ammonia lyase and infant histidine metabolome with cognition. Fecal transplantation from Inf-aboveCC versus Inf-belowCC donors into germ-free mice shows that memory, assessed by a novel object recognition test, is a transmissible trait. Furthermore, Inf-aboveCC mice are enriched in species belonging to Phocaeicola, as well as Bacteroides and Bifidobacterium, previously linked to cognition. Finally, Inf-aboveCC mice show lower fecal histidine and urocanate:histidine and urocanate:glutamate ratios in the perirhinal cortex compared to Inf-belowCC mice. Overall, these findings reveal a causative role of gut microbiota on infant cognition, pointing at the modulation of histidine metabolite levels as a potential underlying mechanism.
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Affiliation(s)
- Tomás Cerdó
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; Centre for Rheumatology Research, Division of Medicine, University College London, London WC1E 6JF, UK
| | - Alicia Ruiz-Rodríguez
- Department of Biochemistry and Molecular Biology 2, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain; Department of Microbiology, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain.
| | - Inmaculada Acuña
- Department of Biochemistry and Molecular Biology 2, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Francisco José Torres-Espínola
- EURISTIKOS Excellence Centre for Pediatric Research, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Sergio Menchén-Márquez
- Department of Psychobiology, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Fernando Gámiz
- Department of Psychobiology, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Milagros Gallo
- Department of Psychobiology, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain; Instituto de Investigación Biosanitaria (IBS), 18014 Granada, Spain
| | - Nico Jehmlich
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Cristina Campoy
- EURISTIKOS Excellence Centre for Pediatric Research, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain; Instituto de Investigación Biosanitaria (IBS), 18014 Granada, Spain; Department of Pediatrics, School of Medicine, University of Granada, 18016 Granada, Spain
| | - Antonio Suárez
- Department of Biochemistry and Molecular Biology 2, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
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17
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Jian J, He D, Gao S, Tao X, Dong X. Pharmacokinetics in Pharmacometabolomics: Towards Personalized Medication. Pharmaceuticals (Basel) 2023; 16:1568. [PMID: 38004434 PMCID: PMC10675232 DOI: 10.3390/ph16111568] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Indiscriminate drug administration may lead to drug therapy results with varying effects on patients, and the proposal of personalized medication can help patients to receive effective drug therapy. Conventional ways of personalized medication, such as pharmacogenomics and therapeutic drug monitoring (TDM), can only be implemented from a single perspective. The development of pharmacometabolomics provides a research method for the realization of precise drug administration, which integrates the environmental and genetic factors, and applies metabolomics technology to study how to predict different drug therapeutic responses of organisms based on baseline metabolic levels. The published research on pharmacometabolomics has achieved satisfactory results in predicting the pharmacokinetics, pharmacodynamics, and the discovery of biomarkers of drugs. Among them, the pharmacokinetics related to pharmacometabolomics are used to explore individual variability in drug metabolism from the level of metabolism of the drugs in vivo and the level of endogenous metabolite changes. By searching for relevant literature with the keyword "pharmacometabolomics" on the two major literature retrieval websites, PubMed and Web of Science, from 2006 to 2023, we reviewed articles in the field of pharmacometabolomics that incorporated pharmacokinetics into their research. This review explains the therapeutic effects of drugs on the body from the perspective of endogenous metabolites and pharmacokinetic principles, and reports the latest advances in pharmacometabolomics related to pharmacokinetics to provide research ideas and methods for advancing the implementation of personalized medication.
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Affiliation(s)
- Jingai Jian
- School of Medicine, Shanghai University, Shanghai 200444, China; (J.J.); (D.H.)
| | - Donglin He
- School of Medicine, Shanghai University, Shanghai 200444, China; (J.J.); (D.H.)
| | - Songyan Gao
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China;
| | - Xia Tao
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Xin Dong
- School of Medicine, Shanghai University, Shanghai 200444, China; (J.J.); (D.H.)
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18
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Khezri MR, Esmaeili A, Ghasemnejad-Berenji M. Role of Bmal1 and Gut Microbiota in Alzheimer's Disease and Parkinson's Disease Pathophysiology: The Probable Effect of Melatonin on Their Association. ACS Chem Neurosci 2023; 14:3883-3893. [PMID: 37823531 DOI: 10.1021/acschemneuro.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
In recent years, the role of new factors in the pathophysiology of neurodegenerative diseases has been investigated. Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative diseases worldwide. Although pathological changes such as the accumulation of aggregated proteins in the brain and inflammatory responses are known as the main factors involved in the development of these diseases, new studies show the role of gut microbiota and circadian rhythm in the occurrence of these changes. However, the association between circadian rhythm and gut microbiota in AD and PD has not yet been investigated. Recent results propose that alterations in circadian rhythm regulators, mainly Bmal1, may regulate the abundance of gut microbiota. This correlation has been linked to the regulation of the expression of immune-related genes and Bmal-1 mediated oscillation of IgA and hydrogen peroxide production. These data seem to provide new insight into the molecular mechanism of melatonin inhibiting the progression of AD and PD. Therefore, this manuscript aims to review the role of the gut microbiota and circadian rhythm in health and AD and PD and also presents a hypothesis on the effect of melatonin on their communication.
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Affiliation(s)
- Mohammad Rafi Khezri
- Faculty of Pharmacy. Urmia University of Medical Sciences, Urmia 571478334, Iran
| | - Ayda Esmaeili
- Department of Clinical Pharmacy, School of Pharmacy, Urmia University of Medical Sciences, Urmia 5715799313, Iran
| | - Morteza Ghasemnejad-Berenji
- Department of Pharmacology and Toxicology, School of Pharmacy, Urmia University of Medical Sciences, Urmia 5715799313, Iran
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Wohlgemuth R. Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems. Metabolites 2023; 13:1097. [PMID: 37887422 PMCID: PMC10608848 DOI: 10.3390/metabo13101097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland;
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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20
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Aboushaala K, Wong AYL, Barajas JN, Lim P, Al-Harthi L, Chee A, Forsyth CB, Oh CD, Toro SJ, Williams FMK, An HS, Samartzis D. The Human Microbiome and Its Role in Musculoskeletal Disorders. Genes (Basel) 2023; 14:1937. [PMID: 37895286 PMCID: PMC10606932 DOI: 10.3390/genes14101937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Musculoskeletal diseases (MSDs) are characterized as injuries and illnesses that affect the musculoskeletal system. MSDs affect every population worldwide and are associated with substantial global burden. Variations in the makeup of the gut microbiota may be related to chronic MSDs. There is growing interest in exploring potential connections between chronic MSDs and variations in the composition of gut microbiota. The human microbiota is a complex community consisting of viruses, archaea, bacteria, and eukaryotes, both inside and outside of the human body. These microorganisms play crucial roles in influencing human physiology, impacting metabolic and immunological systems in health and disease. Different body areas host specific types of microorganisms, with facultative anaerobes dominating the gastrointestinal tract (able to thrive with or without oxygen), while strict aerobes prevail in the nasal cavity, respiratory tract, and skin surfaces (requiring oxygen for development). Together with the immune system, these bacteria have coevolved throughout time, forming complex biological relationships. Changes in the microbial ecology of the gut may have a big impact on health and can help illnesses develop. These changes are frequently impacted by lifestyle choices and underlying medical disorders. The potential for safety, expenses, and efficacy of microbiota-based medicines, even with occasional delivery, has attracted interest. They are, therefore, a desirable candidate for treating MSDs that are chronic and that may have variable progression patterns. As such, the following is a narrative review to address the role of the human microbiome as it relates to MSDs.
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Affiliation(s)
- Khaled Aboushaala
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Arnold Y. L. Wong
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China;
| | - Juan Nicolas Barajas
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Perry Lim
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA;
| | - Ana Chee
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Christopher B. Forsyth
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA;
| | - Chun-do Oh
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Sheila J. Toro
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | | | - Howard S. An
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Dino Samartzis
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
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21
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Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
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Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
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Emencheta SC, Olovo CV, Eze OC, Kalu CF, Berebon DP, Onuigbo EB, Vila MMDC, Balcão VM, Attama AA. The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health. Pharmaceutics 2023; 15:2416. [PMID: 37896176 PMCID: PMC10609668 DOI: 10.3390/pharmaceutics15102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophages (phages) are nano-sized viruses characterized by their inherent ability to live off bacteria. They utilize diverse mechanisms to absorb and gain entry into the bacterial cell wall via the release of viral genetic material, which uses the replication mechanisms of the host bacteria to produce and release daughter progeny virions that attack the surrounding host cells. They possess specific characteristics, including specificity for particular or closely related bacterial species. They have many applications, including as potential alternatives to antibiotics against multi-resistant bacterial pathogens and as control agents in bacteria-contaminated environments. They are ubiquitously abundant in nature and have diverse biota, including in the gut. Gut microbiota describes the community and interactions of microorganisms within the intestine. As with bacteria, parasitic bacteriophages constantly interact with the host bacterial cells within the gut system and have obvious implications for human health. However, it is imperative to understand these interactions as they open up possible applicable techniques to control gut-implicated bacterial diseases. Thus, this review aims to explore the interactions of bacteriophages with bacterial communities in the gut and their current and potential impacts on human health.
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Affiliation(s)
- Stephen C. Emencheta
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Chinasa V. Olovo
- Department of Microbiology, University of Nigeria, Nsukka 410001, Nigeria;
| | - Osita C. Eze
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Chisom F. Kalu
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Dinebari P. Berebon
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Ebele B. Onuigbo
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
| | - Anthony A. Attama
- Department of Pharmaceutics, University of Nigeria, Nsukka 410001, Nigeria
- Institute for Drug-Herbal Medicine-Excipient Research and Development, University of Nigeria, Nsukka 410001, Nigeria
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23
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Cai J, Auster A, Cho S, Lai Z. Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage. J Adv Res 2023; 52:171-201. [PMID: 37419381 PMCID: PMC10555929 DOI: 10.1016/j.jare.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND The gut microbiome is a diverse system within the gastrointestinal tract composed of trillions of microorganisms (gut microbiota), along with their genomes. Accumulated evidence has revealed the significance of the gut microbiome in human health and disease. Due to its ability to alter drug/xenobiotic pharmacokinetics and therapeutic outcomes, this once-forgotten "metabolic organ" is receiving increasing attention. In parallel with the growing microbiome-driven studies, traditional analytical techniques and technologies have also evolved, allowing researchers to gain a deeper understanding of the functional and mechanistic effects of gut microbiome. AIM OF REVIEW From a drug development perspective, microbial drug metabolism is becoming increasingly critical as new modalities (e.g., degradation peptides) with potential microbial metabolism implications emerge. The pharmaceutical industry thus has a pressing need to stay up-to-date with, and continue pursuing, research efforts investigating clinical impact of the gut microbiome on drug actions whilst integrating advances in analytical technology and gut microbiome models. Our review aims to practically address this need by comprehensively introducing the latest innovations in microbial drug metabolism research- including strengths and limitations, to aid in mechanistically dissecting the impact of the gut microbiome on drug metabolism and therapeutic impact, and to develop informed strategies to address microbiome-related drug liability and minimize clinical risk. KEY SCIENTIFIC CONCEPTS OF REVIEW We present comprehensive mechanisms and co-contributing factors by which the gut microbiome influences drug therapeutic outcomes. We highlight in vitro, in vivo, and in silico models for elucidating the mechanistic role and clinical impact of the gut microbiome on drugs in combination with high-throughput, functionally oriented, and physiologically relevant techniques. Integrating pharmaceutical knowledge and insight, we provide practical suggestions to pharmaceutical scientists for when, why, how, and what is next in microbial studies for improved drug efficacy and safety, and ultimately, support precision medicine formulation for personalized and efficacious therapies.
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Affiliation(s)
- Jingwei Cai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA.
| | - Alexis Auster
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Sungjoon Cho
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Zijuan Lai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
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24
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Mengoli M, Conti G, Fabbrini M, Candela M, Brigidi P, Turroni S, Barone M. Microbiota-gut-brain axis and ketogenic diet: how close are we to tackling epilepsy? MICROBIOME RESEARCH REPORTS 2023; 2:32. [PMID: 38045924 PMCID: PMC10688818 DOI: 10.20517/mrr.2023.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 12/05/2023]
Abstract
The microbiota-gut-brain axis refers to the intricate bidirectional communication between commensal microorganisms residing in the digestive tract and the central nervous system, along neuroendocrine, metabolic, immune, and inflammatory pathways. This axis has been suggested to play a role in several neurological disorders, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, and epilepsy, paving the way for microbiome-based intervention strategies for the mitigation and treatment of symptoms. Epilepsy is a multifaceted neurological condition affecting more than 50 million individuals worldwide, 30% of whom do not respond to conventional pharmacological therapies. Among the first-hand microbiota modulation strategies, nutritional interventions represent an easily applicable option in both clinical and home settings. In this narrative review, we summarize the mechanisms underlying the microbiota-gut-brain axis involvement in epilepsy, discuss the impact of antiepileptic drugs on the gut microbiome, and then the impact of a particular dietary pattern, the ketogenic diet, on the microbiota-gut-brain axis in epileptic patients. The investigation of the microbiota response to non-pharmacological therapies is an ever-expanding field with the potential to allow the design of increasingly accessible and successful intervention strategies.
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Affiliation(s)
- Mariachiara Mengoli
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
| | - Gabriele Conti
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
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25
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Amini Khiabani S, Asgharzadeh M, Samadi Kafil H. Chronic kidney disease and gut microbiota. Heliyon 2023; 9:e18991. [PMID: 37609403 PMCID: PMC10440536 DOI: 10.1016/j.heliyon.2023.e18991] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Chronic kidney disease (CKD) refers to a range of various pathophysiological processes correlated with abnormal renal function and a progressive loss in GFR. Just as dysbiosis and altered pathology of the gut are accompanied with hypertension, which is a significant CKD risk factor. Gut dysbiosis in CKD patients is associated with an elevated levels of uremic toxins, which in turn increases the CKD progression. According to research results, the gut-kidney axis has a role in the formation of kidney stones, also in IgAN. A number of researchers have categorized the gut microbiota as enterotypes, and others, skeptical of theory of enterotypes, have suggested biomarkers to describe taxa that related to lifestyle, nutrition, and disease status. Metabolome-microbiome studies have been used to investigate the interactions of host-gut microbiota in terms of the involvement of metabolites in these interactions and are yielded promising results. The correlation between gut microbiota and CKD requires further multi-omic researches. Also, with regard to systems biology, studies on the communication network of proteins and transporters such as SLC and ABC, can help us achieve a deeper understanding of the gut-liver-kidney axis communication and can thus provide promising new horizons in the treatment of CKD patients. Probiotic-based treatment is an approach to reduce uremic poisoning, which is accomplished by swallowing microbes those can catalyze URS in the gut. If further comprehensive studies are carried out, we will know about the probiotics impact in slowing the renal failure progression and reducing inflammatory markers.
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Affiliation(s)
- Siamak Amini Khiabani
- Research center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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26
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Lodge S, Lawler NG, Gray N, Masuda R, Nitschke P, Whiley L, Bong SH, Yeap BB, Dwivedi G, Spraul M, Schaefer H, Gil-Redondo R, Embade N, Millet O, Holmes E, Wist J, Nicholson JK. Integrative Plasma Metabolic and Lipidomic Modelling of SARS-CoV-2 Infection in Relation to Clinical Severity and Early Mortality Prediction. Int J Mol Sci 2023; 24:11614. [PMID: 37511373 PMCID: PMC10380980 DOI: 10.3390/ijms241411614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
An integrative multi-modal metabolic phenotyping model was developed to assess the systemic plasma sequelae of SARS-CoV-2 (rRT-PCR positive) induced COVID-19 disease in patients with different respiratory severity levels. Plasma samples from 306 unvaccinated COVID-19 patients were collected in 2020 and classified into four levels of severity ranging from mild symptoms to severe ventilated cases. These samples were investigated using a combination of quantitative Nuclear Magnetic Resonance (NMR) spectroscopy and Mass Spectrometry (MS) platforms to give broad lipoprotein, lipidomic and amino acid, tryptophan-kynurenine pathway, and biogenic amine pathway coverage. All platforms revealed highly significant differences in metabolite patterns between patients and controls (n = 89) that had been collected prior to the COVID-19 pandemic. The total number of significant metabolites increased with severity with 344 out of the 1034 quantitative variables being common to all severity classes. Metabolic signatures showed a continuum of changes across the respiratory severity levels with the most significant and extensive changes being in the most severely affected patients. Even mildly affected respiratory patients showed multiple highly significant abnormal biochemical signatures reflecting serious metabolic deficiencies of the type observed in Post-acute COVID-19 syndrome patients. The most severe respiratory patients had a high mortality (56.1%) and we found that we could predict mortality in this patient sub-group with high accuracy in some cases up to 61 days prior to death, based on a separate metabolic model, which highlighted a different set of metabolites to those defining the basic disease. Specifically, hexosylceramides (HCER 16:0, HCER 20:0, HCER 24:1, HCER 26:0, HCER 26:1) were markedly elevated in the non-surviving patient group (Cliff's delta 0.91-0.95) and two phosphoethanolamines (PE.O 18:0/18:1, Cliff's delta = -0.98 and PE.P 16:0/18:1, Cliff's delta = -0.93) were markedly lower in the non-survivors. These results indicate that patient morbidity to mortality trajectories is determined relatively soon after infection, opening the opportunity to select more intensive therapeutic interventions to these "high risk" patients in the early disease stages.
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Affiliation(s)
- Samantha Lodge
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Nathan G. Lawler
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Nicola Gray
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Reika Masuda
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
| | - Philipp Nitschke
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
| | - Luke Whiley
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Sze-How Bong
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
| | - Bu B. Yeap
- Medical School, University of Western Australia, Perth, WA 6150, Australia; (B.B.Y.); (G.D.)
- Department of Endocrinology and Diabetes, Fiona Stanley Hospital, Perth, WA 6150, Australia
| | - Girish Dwivedi
- Medical School, University of Western Australia, Perth, WA 6150, Australia; (B.B.Y.); (G.D.)
- Department of Cardiology, Fiona Stanley Hospital, Perth, WA 6150, Australia
| | | | | | - Rubén Gil-Redondo
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Parque Tecnológico de Bizkaia, Bld. 800, 48160 Derio, Spain; (R.G.-R.); (N.E.); (O.M.)
| | - Nieves Embade
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Parque Tecnológico de Bizkaia, Bld. 800, 48160 Derio, Spain; (R.G.-R.); (N.E.); (O.M.)
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Parque Tecnológico de Bizkaia, Bld. 800, 48160 Derio, Spain; (R.G.-R.); (N.E.); (O.M.)
| | - Elaine Holmes
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
| | - Julien Wist
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Chemistry Department, Universidad del Valle, Cali 76001, Colombia
| | - Jeremy K. Nicholson
- Australian National Phenome Center, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia; (S.L.); (N.G.L.); (N.G.); (R.M.); (P.N.); (L.W.); (S.-H.B.); (E.H.)
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Institute of Global Health Innovation, Faculty of Medicine, Imperial College London, Faculty Building, South Kensington Campus, London SW7 2NA, UK
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Abstract
Live biotherapeutic products (LBPs), including symbiotic and genetically engineered bacteria, are a promising class of emerging therapeutics that are widely investigated both preclinically and clinically for their oral delivery to the gastrointestinal (GI) tract. One emergent delivery strategy involves the direct functionalization of LBP surfaces through noncovalent or covalent modifications to control LBP interactions with the GI microenvironment, thereby improving their viability, attachment, or therapeutic effect. However, unlike other therapeutic modalities, LBPs are living organisms which present two unique challenges for surface modifications: (1) this approach can directly interfere with key LBP biological processes (e.g., colonization, metabolite secretion) and (2) modification can be variable due to the dynamic nature of LBP surfaces. Collectively, these factors remain uncharacterized as they relate to the oral delivery of LBPs. Herein, we leverage our previously reported surface modification platform, which enables LBP surface-presentation of targeting ligands, to broadly evaluate and characterize surface modifications on LBPs. Specifically, we evaluate how LBP growth affects the dilution of surface-presented targeting ligands and the subsequent loss of specific target attachment over time. Next, we describe key surface modification parameters (e.g., concentration, residence time) that can be optimized to facilitate LBP target attachment. We then characterize how bioconjugation influences the suitability of LBPs for oral delivery by evaluating their growth, viability, storage, toxicity against mammalian cells, and in vivo colonization. Broadly, we describe key parameters that influence the performance of surface modified LBPs and subsequently outline an experimental pipeline for characterizing and evaluating their suitability for oral delivery.
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Affiliation(s)
- Ava M. Vargason
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aaron C. Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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28
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Zaidi S, Ali K, Khan AU. It's all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention. Arch Microbiol 2023; 205:257. [PMID: 37280443 DOI: 10.1007/s00203-023-03589-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
Concept of microorganisms has largely been perceived from their pathogenic view point. Nevertheless, it is being gradually revisited in terms of its significance to human health and now appears to be the most dominant force that shapes the immune system of the human body and also determines an individual's predisposition to diseases. Human inhabits bacterial diversity (which is predominant among all microbial communities in human body) occupying 0.3% of body mass, known as microbiota. On birth, a part of microbiota that child obtains is essentially a mother's legacy. So, the review was initiated with this critical topic of microbiotal inheritance. Since, each body site has distinct physiological specifications; therefore, they contain discrete microbiome composition that has been separately discussed along with dysbiosis-induced pathologies originating in different body organs. Factors affecting microbiome composition and may cause dysbiosis like antibiotics, delivery, feeding method etc. as well as the strategies that immune system adopts to prevent dysbiosis have been highlighted. We also tried to bring into attention the topic of dysbiosis induced biofilms, that enables cohort to survive stresses, evolve, disseminate and infection resurgence that is still in dormancy. Eventually, we put spotlight on microbiome significance in medical therapeutics. We didn't merely confine article to gut microbiota, that is being studied more extensively. Numerous community forms at diverse body sites are inter-related, and being exposed to awfully variable perturbations appear to be challenging to evaluate perturbation risks holistically. All aspects have been elaborately discussed to achieve a global depiction of human microbiota in order to meet urgent necessity for protocol standardisation. Demonstrates that environmental challenges (antibiotic use, alterations in diet, stress, smoking etc.) might cause dysbiosis i.e. transition of healthy microbiome composition to the one in which pathogenic microorganisms become more abundant, and eventually results in an infected state.
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Affiliation(s)
- Sahar Zaidi
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Khursheed Ali
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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29
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Wang J, Dong P, Zheng S, Mai Y, Ding J, Pan P, Tang L, Wan Y, Liang H. Advances in gut microbiome in metabonomics perspective: based on bibliometrics methods and visualization analysis. Front Cell Infect Microbiol 2023; 13:1196967. [PMID: 37325519 PMCID: PMC10266355 DOI: 10.3389/fcimb.2023.1196967] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Background and aims Gastrointestinal microbial metabolomics is closely related to the state of the organism and has significant interaction with the pathogenesis of many diseases. Based on the publications in Web of Science Core Collection(WoSCC) from 2004 to 2022, this study conducted a bibliometric analysis of this field, aiming to understand its development trend and frontier, and provide basic information and potential points for in-depth exploration of this field. Methods All articles on gastrointestinal flora and metabolism published from 2004 to 2022 were collected and identified in WoCSS. CiteSpace v.6.1 and VOSviewer v.1.6.15.0 were used to calculate bibliometric indicators, including number of publications and citations, study categories, countries/institutions, authors/co-cited authors, journals/co-cited journals, co-cited references, and keywords. A map was drawn to visualize the data based on the analysis results for a more intuitive view. Results There were 3811 articles in WoSCC that met our criteria. Analysis results show that the number of publications and citations in this field are increasing year by year. China is the country with the highest number of publications and USA owns the highest total link strength and citations. Chinese Acad Sci rank first for the number of institutional publications and total link strength. Journal of Proteome Research has the most publications. Nicholson, Jeremy K. is one of the most important scholars in this field. The most cited reference is "Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease". Burst detection indicates that Urine, spectroscopy, metabonomic and gut microflora are long-standing hot topics in this field, while autism spectrum disorder and omics are likely to be at the forefront of research. The study of related metabolic small molecules and the application of gastrointestinal microbiome metabolomics in various diseases are currently emerging research directions and frontier in this field. Conclusion This study is the first to make a bibliometric analysis of the studies related to gastrointestinal microbial metabolomics and reveal the development trends and current research hotspots in this field. This can contribute to the development of the field by providing relevant scholars with valuable and effective information about the current state of the field.
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Affiliation(s)
- Jieyan Wang
- Department of Urology, The People's Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzen, China
| | - Peng Dong
- College of Anesthesiology, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Shuqian Zheng
- School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Yiyin Mai
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jianan Ding
- School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Pinfei Pan
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Liugang Tang
- Tendon and Injury Department, Sichuan Provincial Orthopedics Hospital, Chengdu, China
| | - Yantong Wan
- Guangdong Provincial Key Laboratory of Proteomics, Southern Medical University, Guangzhou, China
| | - Hui Liang
- Department of Urology, The People's Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzen, China
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30
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Pabst O, Hornef MW, Schaap FG, Cerovic V, Clavel T, Bruns T. Gut-liver axis: barriers and functional circuits. Nat Rev Gastroenterol Hepatol 2023:10.1038/s41575-023-00771-6. [PMID: 37085614 DOI: 10.1038/s41575-023-00771-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 04/23/2023]
Abstract
The gut and the liver are characterized by mutual interactions between both organs, the microbiome, diet and other environmental factors. The sum of these interactions is conceptualized as the gut-liver axis. In this Review we discuss the gut-liver axis, concentrating on the barriers formed by the enterohepatic tissues to restrict gut-derived microorganisms, microbial stimuli and dietary constituents. In addition, we discuss the establishment of barriers in the gut and liver during development and their cooperative function in the adult host. We detail the interplay between microbial and dietary metabolites, the intestinal epithelium, vascular endothelium, the immune system and the various host soluble factors, and how this interplay establishes a homeostatic balance in the healthy gut and liver. Finally, we highlight how this balance is disrupted in diseases of the gut and liver, outline the existing therapeutics and describe the cutting-edge discoveries that could lead to the development of novel treatment approaches.
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Affiliation(s)
- Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany.
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH Aachen University, Aachen, Germany
| | - Frank G Schaap
- Department of General, Visceral and Transplantation Surgery, RWTH Aachen University, Aachen, Germany
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Vuk Cerovic
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH Aachen University, Aachen, Germany
| | - Tony Bruns
- Department of Internal Medicine III, RWTH Aachen University, Aachen, Germany
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31
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Shen G, Moua KTY, Perkins K, Johnson D, Li A, Curtin P, Gao W, McCune JS. Precision sirolimus dosing in children: The potential for model-informed dosing and novel drug monitoring. Front Pharmacol 2023; 14:1126981. [PMID: 37021042 PMCID: PMC10069443 DOI: 10.3389/fphar.2023.1126981] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/14/2023] [Indexed: 04/07/2023] Open
Abstract
The mTOR inhibitor sirolimus is prescribed to treat children with varying diseases, ranging from vascular anomalies to sporadic lymphangioleiomyomatosis to transplantation (solid organ or hematopoietic cell). Precision dosing of sirolimus using therapeutic drug monitoring (TDM) of sirolimus concentrations in whole blood drawn at the trough (before the next dose) time-point is the current standard of care. For sirolimus, trough concentrations are only modestly correlated with the area under the curve, with R 2 values ranging from 0.52 to 0.84. Thus, it should not be surprising, even with the use of sirolimus TDM, that patients treated with sirolimus have variable pharmacokinetics, toxicity, and effectiveness. Model-informed precision dosing (MIPD) will be beneficial and should be implemented. The data do not suggest dried blood spots point-of-care sampling of sirolimus concentrations for precision dosing of sirolimus. Future research on precision dosing of sirolimus should focus on pharmacogenomic and pharmacometabolomic tools to predict sirolimus pharmacokinetics and wearables for point-of-care quantitation and MIPD.
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Affiliation(s)
- Guofang Shen
- Department of Hematologic Malignancies Translational Sciences, City of Hope, and Department of Hematopoietic Cell Transplantation, City of Hope Medical Center, Duarte, CA, United States
| | - Kao Tang Ying Moua
- Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kathryn Perkins
- Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, United States
| | - Deron Johnson
- Clinical Informatics, City of Hope Medical Center, Duarte, CA, United States
| | - Arthur Li
- Division of Biostatistics, City of Hope, Duarte, CA, United States
| | - Peter Curtin
- Department of Hematologic Malignancies Translational Sciences, City of Hope, and Department of Hematopoietic Cell Transplantation, City of Hope Medical Center, Duarte, CA, United States
| | - Wei Gao
- Division of Engineering and Applied Science, Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Jeannine S. McCune
- Department of Hematologic Malignancies Translational Sciences, City of Hope, and Department of Hematopoietic Cell Transplantation, City of Hope Medical Center, Duarte, CA, United States
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Rashid F, Dubinkina V, Ahmad S, Maslov S, Irudayaraj JMK. Gut Microbiome-Host Metabolome Homeostasis upon Exposure to PFOS and GenX in Male Mice. TOXICS 2023; 11:281. [PMID: 36977046 PMCID: PMC10051855 DOI: 10.3390/toxics11030281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
Alterations of the normal gut microbiota can cause various human health concerns. Environmental chemicals are one of the drivers of such disturbances. The aim of our study was to examine the effects of exposure to perfluoroalkyl and polyfluoroalkyl substances (PFAS)-specifically, perfluorooctane sulfonate (PFOS) and 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy) propanoic acid (GenX)-on the microbiome of the small intestine and colon, as well as on liver metabolism. Male CD-1 mice were exposed to PFOS and GenX in different concentrations and compared to controls. GenX and PFOS were found to have different effects on the bacterial community in both the small intestine and colon based on 16S rRNA profiles. High GenX doses predominantly led to increases in the abundance of Clostridium sensu stricto, Alistipes, and Ruminococcus, while PFOS generally altered Lactobacillus, Limosilactobacillus, Parabacteroides, Staphylococcus, and Ligilactobacillus. These treatments were associated with alterations in several important microbial metabolic pathways in both the small intestine and colon. Untargeted LC-MS/MS metabolomic analysis of the liver, small intestine, and colon yielded a set of compounds significantly altered by PFOS and GenX. In the liver, these metabolites were associated with the important host metabolic pathways implicated in the synthesis of lipids, steroidogenesis, and in the metabolism of amino acids, nitrogen, and bile acids. Collectively, our results suggest that PFOS and GenX exposure can cause major perturbations in the gastrointestinal tract, aggravating microbiome toxicity, hepatotoxicity, and metabolic disorders.
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Affiliation(s)
- Faizan Rashid
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Veronika Dubinkina
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Saeed Ahmad
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sergei Maslov
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph Maria Kumar Irudayaraj
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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Shamsuzzaman M, Ahsan T, Rahman H, Das KC, Salimullah. Integration of pharmacogenomic and pharmacomicrobiomic data for personalized medicine. PRECISION MEDICAL SCIENCES 2023. [DOI: 10.1002/prm2.12095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Affiliation(s)
- Muhammad Shamsuzzaman
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Tamim Ahsan
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Hadisur Rahman
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Salimullah
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
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Paine H, Jones F, Kinross J. Preparing the Bowel (Microbiome) for Surgery: Surgical Bioresilience. Clin Colon Rectal Surg 2023; 36:138-145. [PMID: 36844712 PMCID: PMC9946716 DOI: 10.1055/s-0042-1760675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The preparation of the bowel for radical surgery is a corner stone of elective colorectal practice. The evidence for this intervention is of variable quality and it is often contradictory, yet there is now a global move toward the adoption of oral antibiotic therapy for the reduction of perioperative infective complications, such as surgical site infections. The gut microbiome is a critical mediator of the systemic inflammatory response to surgical injury, wound healing, and perioperative gut function. The loss of critical microbial symbiotic functions caused by bowel preparation and surgery has an adverse impact on surgical outcomes, yet the mechanisms through which this occurs are poorly defined. In this review, the evidence for bowel preparation strategies is critically appraised in the context of the gut microbiome. The impact of antibiotic therapy on the surgical gut microbiome and the importance of the intestinal "resistome" to surgical recovery is described. Data to support the augmentation of the microbiome through diet, probiotic and symbiotic approaches, as well as fecal transplantation are also appraised. Finally, we propose a novel strategy of bowel preparation defined as " surgical bioresilience " and define areas or prioritization in this emerging field. This describes the optimization of surgical intestinal homeostasis and core surgical exposome-microbiome interactions that regulate the wound immune microenvironment, the systemic inflammatory response to surgical injury, and gut function across the perioperative time course.
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Affiliation(s)
- Heidi Paine
- Division of General Surgery, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Faye Jones
- Division of General Surgery, King Edward VII Hospital, London, United Kingdom
| | - James Kinross
- Division of Colorectal Surgery, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
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McCune JS, Navarro SL, Baker KS, Risler LJ, Phillips BR, Randolph TW, Shireman L, Schoch G, Deeg HJ, Zhang Y, Men A, Maton L, Huitema ADR. Prediction of Busulfan Clearance by Predose Plasma Metabolomic Profiling. Clin Pharmacol Ther 2023; 113:370-379. [PMID: 36369996 PMCID: PMC9888309 DOI: 10.1002/cpt.2794] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Intravenous busulfan doses are often personalized to a target plasma exposure (targeted busulfan) using an individual's busulfan clearance (BuCL). We evaluated whether BuCL could be predicted by a predose plasma panel of 841 endogenous metabolomic compounds (EMCs). In this prospective cohort of 132 hematopoietic cell transplantation (HCT) patients, all had samples collected immediately before busulfan administration (preBU) and 96 had samples collected 2 weeks before busulfan (2-week-preBU). BuCL was significantly associated with 37 EMCs after univariate linear regression analysis and controlling for false discovery (< 0.05) in the 132 preBU samples. In parallel, with preBU samples, we included all 841 EMCs in a least absolute shrinkage and selection operator-penalized regression which selected 13 EMCs as predominantly associated with BuCL. Then, we constructed a prediction model by estimating coefficients for these 13 EMCs, along with sex, using ordinary least-squares. When the resulting linear prediction model was applied to the 2-week-preBU samples, it explained 40% of the variation in BuCL (adjusted R2 = 0.40). Pathway enrichment analysis revealed 18 pathways associated with BuCL. Lysine degradation followed by steroid biosynthesis, which aligned with the univariate analysis, were the top two pathways. BuCL can be predicted before busulfan administration with a linear regression model of 13 EMCs. This pharmacometabolomics method should be prioritized over use of a busulfan test dose or pharmacogenomics to guide busulfan dosing. These results highlight the potential of pharmacometabolomics as a precision medicine tool to improve or replace pharmacokinetics to personalize busulfan doses.
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Affiliation(s)
- Jeannine S. McCune
- City of Hope, Department of Hematologic Malignancies Translational Sciences, Duarte, California (CA), 91010, United States of America (USA)
| | - Sandi L. Navarro
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (WA), 98109, USA
| | - K. Scott Baker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (WA), 98109, USA,Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Linda J. Risler
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA
| | - Brian R. Phillips
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA
| | - Timothy W. Randolph
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (WA), 98109, USA
| | - Laura Shireman
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA
| | - Gary Schoch
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (WA), 98109, USA
| | - H. Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (WA), 98109, USA,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Yuzheng Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (WA), 98109, USA
| | - Alex Men
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA
| | - Loes Maton
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Alwin D. R. Huitema
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands,Department of Pharmacology, Princes Maxima & Pharmacology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands,Department of Clinical Pharmacy, University Medical Center Utrecht, The Netherlands
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Levitan O, Ma L, Giovannelli D, Burleson DB, McCaffrey P, Vala A, Johnson DA. The gut microbiome–Does stool represent right? Heliyon 2023; 9:e13602. [PMID: 37101508 PMCID: PMC10123208 DOI: 10.1016/j.heliyon.2023.e13602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner-colonic microbiome. To test this hypothesis, we conducted prospective clinical studies with up to 20 patients undergoing an FDA-cleared gravity-fed colonic lavage without oral purgative pre-consumption. The objective of this study was to present the analysis of inner-colonic microbiota obtained non-invasively during the lavage and how these results differ from stool samples. The inner-colonic samples represented the descending, transverse, and ascending colon. All samples were analyzed for 16S rRNA and shotgun metagenomic sequences. The taxonomic, phylogenetic, and biosynthetic gene cluster analyses showed a distinctive biogeographic gradient and revealed differences between the sample types, especially in the proximal colon. The high percentage of unique information found only in the inner-colonic effluent highlights the importance of these samples and likewise the importance of collecting them using a method that can preserve these distinctive signatures. We proposed that these samples are imperative for developing future biomarkers, targeted therapeutics, and personalized medicine.
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Gao Z, Zhou W, Lv X, Wang X. Metabolomics as a Critical Tool for Studying Clinical Surgery. Crit Rev Anal Chem 2023:1-14. [PMID: 36592066 DOI: 10.1080/10408347.2022.2162810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Metabolomics enables the analysis of metabolites within an organism, which offers the closest direct measurement of the physiological activity of the organism, and has advanced efforts to characterize metabolic states, identify biomarkers, and investigate metabolic pathways. A high degree of innovation in analytical techniques has promoted the application of metabolomics, especially in the study of clinical surgery. Metabolomics can be employed as a clinical testing method to maximize therapeutic outcomes, and has been applied in rapid diagnosis of diseases, timely postoperative monitoring, prognostic assessment, and personalized medicine. This review focuses on the use of mass spectrometry and nuclear magnetic resonance-based metabolomics in clinical surgery, including identifying metabolic changes before and after surgery, finding disease-associated biomarkers, and exploring the potential of personalized therapy. Challenges and opportunities of metabolomics in organ transplantation are also discussed, with a particular emphasis on metabolomics in donor organ evaluation and protection, prognostic outcome prediction, as well as postoperative adverse reaction monitoring. In the end, current limitations of metabolomics in clinical surgery and future research directions are presented.
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Affiliation(s)
- Zhenye Gao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenxiu Zhou
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xiaoyuan Lv
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xin Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
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Cho S, Yang X, Won KJ, Leone VA, Chang EB, Guzman G, Ko Y, Bae ON, Lee H, Jeong H. Phenylpropionic acid produced by gut microbiota alleviates acetaminophen-induced hepatotoxicity. Gut Microbes 2023; 15:2231590. [PMID: 37431867 PMCID: PMC10337503 DOI: 10.1080/19490976.2023.2231590] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
The gut microbiota affects hepatic drug metabolism. However, gut microbial factors modulating hepatic drug metabolism are largely unknown. In this study, using a mouse model of acetaminophen (APAP)-induced hepatotoxicity, we identified a gut bacterial metabolite that controls the hepatic expression of CYP2E1 that catalyzes the conversion of APAP to a reactive, toxic metabolite. By comparing C57BL/6 substrain mice from two different vendors, Jackson (6J) and Taconic (6N), which are genetically similar but harbor different gut microbiotas, we established that the differences in the gut microbiotas result in differential susceptibility to APAP-induced hepatotoxicity. 6J mice exhibited lower susceptibility to APAP-induced hepatotoxicity than 6N mice, and such phenotypic difference was recapitulated in germ-free mice by microbiota transplantation. Comparative untargeted metabolomic analysis of portal vein sera and liver tissues between conventional and conventionalized 6J and 6N mice led to the identification of phenylpropionic acid (PPA), the levels of which were higher in 6J mice. PPA supplementation alleviated APAP-induced hepatotoxicity in 6N mice by lowering hepatic CYP2E1 levels. Moreover, PPA supplementation also reduced carbon tetrachloride-induced liver injury mediated by CYP2E1. Our data showed that previously known PPA biosynthetic pathway is responsible for PPA production. Surprisingly, while PPA in 6N mouse cecum contents is almost undetectable, 6N cecal microbiota produces PPA as well as 6J cecal microbiota in vitro, suggesting that PPA production in the 6N gut microbiota is suppressed in vivo. However, previously known gut bacteria harboring the PPA biosynthetic pathway were not detected in either 6J or 6N microbiota, suggesting the presence of as-yet-unidentified PPA-producing gut microbes. Collectively, our study reveals a novel biological function of the gut bacterial metabolite PPA in the gut-liver axis and presents a critical basis for investigating PPA as a modulator of CYP2E1-mediated liver injury and metabolic diseases.
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Affiliation(s)
- Sungjoon Cho
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Xiaotong Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyoung-Jae Won
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Vanessa A Leone
- Department of Animal & Dairy Sciences, College of Agriculture & Life Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Eugene B Chang
- Section of Gastroenterology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL, USA
| | - Grace Guzman
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yeonju Ko
- College of Pharmacy, Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Ok-Nam Bae
- College of Pharmacy, Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Hyunwoo Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN, USA
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Hyunyoung Jeong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN, USA
- Department of Pharmacy Practice, College of Pharmacy, Purdue University, West Lafayette, IN, USA
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Chemotherapy-Induced Peripheral Neuropathy. Handb Exp Pharmacol 2023; 277:299-337. [PMID: 36253554 DOI: 10.1007/164_2022_609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating side effect of many common anti-cancer agents that can lead to dose reduction or treatment discontinuation, which decrease chemotherapy efficacy. Long-term CIPN can interfere with activities of daily living and diminish the quality of life. The mechanism of CIPN is not yet fully understood, and biomarkers are needed to identify patients at high risk and potential treatment targets. Metabolomics can capture the complex behavioral and pathophysiological processes involved in CIPN. This chapter is to review the CIPN metabolomics studies to find metabolic pathways potentially involved in CIPN. These potential CIPN metabolites are then investigated to determine whether there is evidence from studies of other neuropathy etiologies such as diabetic neuropathy and Leber hereditary optic neuropathy to support the importance of these pathways in peripheral neuropathy. Six potential biomarkers and their putative mechanisms in peripheral neuropathy were reviewed. Among these biomarkers, histidine and phenylalanine have clear roles in neurotransmission or neuroinflammation in peripheral neuropathy. Further research is needed to discover and validate CIPN metabolomics biomarkers in large clinical studies.
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Nabeh OA. Gut microbiota and cardiac arrhythmia: a pharmacokinetic scope. Egypt Heart J 2022; 74:87. [PMID: 36583819 PMCID: PMC9803803 DOI: 10.1186/s43044-022-00325-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Dealing with cardiac arrhythmia is a difficult challenge. Choosing between different anti-arrhythmic drugs (AADs) while being cautious about the pro-arrhythmic characteristics of some of these drugs and their diverse interaction with other drugs is a real obstacle. MAIN BODY Gut microbiota (GM), in our bodies, are now being considered as a hidden organ which can regulate our immune system, digest complex food, and secrete bioactive compounds. Yet, GM are encountered in the pathophysiology of arrhythmia and can affect the pharmacokinetics of AADs, as well as some anti-thrombotics, resulting in altering their bioavailability, therapeutic function and may predispose to some of their unpleasant adverse effects. CONCLUSIONS Knowledge of the exact role of GM in the pharmacokinetics of these drugs is now essential for better understanding of the art of arrhythmia management. Also, it will help deciding when to consider probiotics as an adjunctive therapy while treating arrhythmia. This should be discovered in the near future.
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Affiliation(s)
- Omnia Azmy Nabeh
- grid.7776.10000 0004 0639 9286Department of Medical Pharmacology, Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt
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Conti G, D’Amico F, Fabbrini M, Brigidi P, Barone M, Turroni S. Pharmacomicrobiomics in Anticancer Therapies: Why the Gut Microbiota Should Be Pointed Out. Genes (Basel) 2022; 14:55. [PMID: 36672796 PMCID: PMC9859289 DOI: 10.3390/genes14010055] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Anticancer treatments have shown a variable therapeutic outcome that may be partly attributable to the activity of the gut microbiota on the pathology and/or therapies. In recent years, microbiota-drug interactions have been extensively investigated, but most of the underlying molecular mechanisms still remain unclear. In this review, we discuss the relationship between the gut microbiota and some of the most commonly used drugs in oncological diseases. Different strategies for manipulating the gut microbiota layout (i.e., prebiotics, probiotics, antibiotics, and fecal microbiota transplantation) are then explored in order to optimize clinical outcomes in cancer patients. Anticancer technologies that exploit tumor-associated bacteria to target tumors and biotransform drugs are also briefly discussed. In the field of pharmacomicrobiomics, multi-omics strategies coupled with machine and deep learning are urgently needed to bring to light the interaction among gut microbiota, drugs, and host for the development of truly personalized precision therapies.
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Affiliation(s)
- Gabriele Conti
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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Talapko J, Včev A, Meštrović T, Pustijanac E, Jukić M, Škrlec I. Homeostasis and Dysbiosis of the Intestinal Microbiota: Comparing Hallmarks of a Healthy State with Changes in Inflammatory Bowel Disease. Microorganisms 2022; 10:microorganisms10122405. [PMID: 36557658 PMCID: PMC9781915 DOI: 10.3390/microorganisms10122405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota, which represent a community of different microorganisms in the human intestinal tract, are crucial to preserving human health by participating in various physiological functions and acting as a metabolic organ. In physiological conditions, microbiota-host partnership exerts homeostatic stability; however, changes in intestinal microbiota composition (dysbiosis) are an important factor in the pathogenesis of inflammatory bowel disease and its two main disease entities: ulcerative colitis and Crohn's disease. The incidence and prevalence of these inflammatory conditions have increased rapidly in the last decade, becoming a significant problem for the healthcare system and a true challenge in finding novel therapeutic solutions. The issue is that, despite numerous studies, the etiopathogenesis of inflammatory bowel disease is not completely clear. Based on current knowledge, chronic intestinal inflammation occurs due to altered intestinal microbiota and environmental factors, as well as a complex interplay between the genetic predisposition of the host and an inappropriate innate and acquired immune response. It is important to note that the development of biological and immunomodulatory therapy has led to significant progress in treating inflammatory bowel disease. Certain lifestyle changes and novel approaches-including fecal microbiota transplantation and nutritional supplementation with probiotics, prebiotics, and synbiotics-have offered solutions for dysbiosis management and paved the way towards restoring a healthy microbiome, with only minimal long-term unfavorable effects.
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Affiliation(s)
- Jasminka Talapko
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Aleksandar Včev
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Tomislav Meštrović
- University Centre Varaždin, University North, 42000 Varaždin, Croatia
- Institute for Health Metrics and Evaluation and the Department of Health Metrics Sciences, University of Washington, Seattle, WA 98195, USA
- Correspondence: (T.M.); (I.Š.)
| | - Emina Pustijanac
- Faculty of Natural Sciences, Juraj Dobrila University of Pula, 52100 Pula, Croatia
| | - Melita Jukić
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
- General Hospital Vukovar, Županijska 35, 32000 Vukovar, Croatia
| | - Ivana Škrlec
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
- Correspondence: (T.M.); (I.Š.)
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Gulnaz A, Chang JE, Maeng HJ, Shin KH, Lee KR, Chae YJ. A mechanism-based understanding of altered drug pharmacokinetics by gut microbiota. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2022. [DOI: 10.1007/s40005-022-00600-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Steiner HE, Patterson HK, Giles JB, Karnes JH. Bringing pharmacomicrobiomics to the clinic through well-designed studies. Clin Transl Sci 2022; 15:2303-2315. [PMID: 35899413 PMCID: PMC9579385 DOI: 10.1111/cts.13381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 01/25/2023] Open
Abstract
Pharmacomicrobiomic studies investigate drug-microbiome interactions, such as the effect of microbial variation on drug response and disposition. Studying and understanding the interactions between the gut microbiome and drugs is becoming increasingly relevant to clinical practice due to its potential for avoiding adverse drug reactions or predicting variability in drug response. The highly variable nature of the human microbiome presents significant challenges to assessing microbes' influence. Studies aiming to explore drug-microbiome interactions should be well-designed to account for variation in the microbiome over time and collect data on confounders such as diet, disease, concomitant drugs, and other environmental factors. Here, we assemble a set of important considerations and recommendations for the methodological features required for performing a pharmacomicrobiomic study in humans with a focus on the gut microbiome. Consideration of these factors enable discovery, reproducibility, and more accurate characterization of the relationships between a given drug and the microbiome. Furthermore, appropriate interpretation and dissemination of results from well-designed studies will push the field closer to clinical relevance and implementation.
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Affiliation(s)
- Heidi E. Steiner
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Hayley K. Patterson
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Jason B. Giles
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Jason H. Karnes
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA,Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
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Effect of DSS-Induced Ulcerative Colitis and Butyrate on the Cytochrome P450 2A5: Contribution of the Microbiome. Int J Mol Sci 2022; 23:ijms231911627. [PMID: 36232929 PMCID: PMC9569822 DOI: 10.3390/ijms231911627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Several studies have indicated the beneficial anti-inflammatory effect of butyrate in inflammatory bowel disease (IBD) therapy implying attempts to increase butyrate production in the gut through orally administered dietary supplementation. Through the gut-liver axis, however, butyrate may reach directly the liver and influence the drug-metabolizing ability of hepatic enzymes, and, indirectly, also the outcome of applied pharmacotherapy. The focus of our study was on the liver microsomal cytochrome P450 (CYP) 2A5, which is a mouse orthologue of human CYP2A6 responsible for metabolism of metronidazole, an antibiotic used to treat IBD. Our findings revealed that specific pathogen-free (SPF) and germ-free (GF) mice with dextran sulfate sodium (DSS)-induced colitis varied markedly in enzyme activity of CYP2A and responded differently to butyrate pre-treatment. A significant decrease (to 50%) of the CYP2A activity was observed in SPF mice with colitis; however, an administration of butyrate prior to DSS reversed this inhibition effect. This phenomenon was not observed in GF mice. The results highlight an important role of gut microbiota in the regulation of CYP2A under inflammatory conditions. Due to the role of CYP2A in metronidazole metabolism, this phenomenon may have an impact on the IBD therapy. Butyrate administration, hence, brings promising therapeutic potential for improving symptoms of gut inflammation; however, possible interactions with drug metabolism need to be further studied.
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Fu L, Qian Y, Shang Z, Sun X, Kong X, Gao Y. Antibiotics enhancing drug-induced liver injury assessed for causality using Roussel Uclaf Causality Assessment Method: Emerging role of gut microbiota dysbiosis. Front Med (Lausanne) 2022; 9:972518. [PMID: 36160154 PMCID: PMC9500153 DOI: 10.3389/fmed.2022.972518] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Drug-induced liver injury (DILI) is a disease that remains difficult to predict and prevent from a clinical perspective, as its occurrence is hard to fully explain by the traditional mechanisms. In recent years, the risk of the DILI for microbiota dysbiosis has been recognized as a multifactorial process. Amoxicillin-clavulanate is the most commonly implicated drug in DILI worldwide with high causality gradings based on the use of RUCAM in different populations. Antibiotics directly affect the structure and diversity of gut microbiota (GM) and changes in metabolites. The depletion of probiotics after antibiotics interference can reduce the efficacy of hepatoprotective agents, also manifesting as liver injury. Follow-up with liver function examination is essential during the administration of drugs that affect intestinal microorganisms and their metabolic activities, such as antibiotics, especially in patients on a high-fat diet. In the meantime, altering the GM to reconstruct the hepatotoxicity of drugs by exhausting harmful bacteria and supplementing with probiotics/prebiotics are potential therapeutic approaches. This review will provide an overview of the current evidence between gut microbiota and DILI events, and discuss the potential mechanisms of gut microbiota-mediated drug interactions. Finally, this review also provides insights into the “double-edged sword” effect of antibiotics treatment against DILI and the potential prevention and therapeutic strategies.
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Affiliation(s)
- Lihong Fu
- Central Laboratory, Department of Liver Diseases, ShuGuang Hospital, Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
- Institute of Infection Diseases, Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Yihan Qian
- Central Laboratory, Department of Liver Diseases, ShuGuang Hospital, Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Zhi Shang
- Central Laboratory, Department of Liver Diseases, ShuGuang Hospital, Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Xuehua Sun
- Central Laboratory, Department of Liver Diseases, ShuGuang Hospital, Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Xiaoni Kong
- Central Laboratory, Department of Liver Diseases, ShuGuang Hospital, Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
- *Correspondence: Xiaoni Kong,
| | - Yueqiu Gao
- Central Laboratory, Department of Liver Diseases, ShuGuang Hospital, Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
- Institute of Infection Diseases, Shanghai University of Chinese Traditional Medicine, Shanghai, China
- Yueqiu Gao,
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Brahma S, Naik A, Lordan R. Probiotics: A gut response to the COVID-19 pandemic but what does the evidence show? Clin Nutr ESPEN 2022; 51:17-27. [PMID: 36184201 PMCID: PMC9393107 DOI: 10.1016/j.clnesp.2022.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/13/2022] [Accepted: 08/17/2022] [Indexed: 11/08/2022]
Abstract
Since the global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), research has focused on understanding the etiology of coronavirus disease 2019 (COVID-19). Identifying and developing prophylactic and therapeutics strategies to manage the pandemic is still of critical importance. Among potential targets, the role of the gut and lung microbiomes in COVID-19 has been questioned. Consequently, probiotics were touted as potential prophylactics and therapeutics for COVID-19. In this review we highlight the role of the gut and lung microbiome in COVID-19 and potential mechanisms of action of probiotics. We also discuss the progress of ongoing clinical trials for COVID-19 that aim to modulate the microbiome using probiotics in an effort to develop prophylactic and therapeutic strategies. To date, despite the large interest in this area of research, there is promising but limited evidence to suggest that probiotics are an effective prophylactic or treatment strategy for COVID-19. However, the role of the microbiome in pathogenesis and as a potential target for therapeutics of COVID-19 cannot be discounted.
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Laue HE, Shen Y, Bloomquist TR, Wu H, Brennan KJM, Cassoulet R, Wilkie E, Gillet V, Desautels AS, Abdelouahab N, Bellenger JP, Burris HH, Coull BA, Weisskopf MG, Zhang W, Takser L, Baccarelli AA. In Utero Exposure to Caffeine and Acetaminophen, the Gut Microbiome, and Neurodevelopmental Outcomes: A Prospective Birth Cohort Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9357. [PMID: 35954712 PMCID: PMC9367926 DOI: 10.3390/ijerph19159357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023]
Abstract
Pregnant individuals are exposed to acetaminophen and caffeine, but it is unknown how these exposures interact with the developing gut microbiome. We aimed to determine whether acetaminophen and/or caffeine relate to the childhood gut microbiome and whether features of the gut microbiome alter the relationship between acetaminophen/caffeine and neurodevelopment. Forty-nine and 85 participants provided meconium and stool samples at 6-7, respectively, for exposure and microbiome assessment. Fecal acetaminophen and caffeine concentrations were quantified, and fecal DNA underwent metagenomic sequencing. Caregivers and study staff assessed the participants' motor and cognitive development using standardized scales. Prenatal exposures had stronger associations with the childhood microbiome than concurrent exposures. Prenatal acetaminophen exposure was associated with a trend of lower gut bacterial diversity in childhood [β = -0.17 Shannon Index, 95% CI: (-0.31, -0.04)] and was marginally associated with differences in the relative abundances of features of the gut microbiome at the phylum (Firmicutes, Actinobacteria) and gene pathway levels. Among the participants with a higher relative abundance of Proteobacteria, prenatal exposure to acetaminophen and caffeine was associated with lower scores on WISC-IV subscales. Acetaminophen during bacterial colonization of the naïve gut is associated with lasting alterations in childhood microbiome composition. Future studies may inform our understanding of downstream health effects.
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Affiliation(s)
- Hannah E. Laue
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Yike Shen
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (Y.S.); (T.R.B.); (H.W.); (K.J.M.B.); (A.A.B.)
| | - Tessa R. Bloomquist
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (Y.S.); (T.R.B.); (H.W.); (K.J.M.B.); (A.A.B.)
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (Y.S.); (T.R.B.); (H.W.); (K.J.M.B.); (A.A.B.)
| | - Kasey J. M. Brennan
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (Y.S.); (T.R.B.); (H.W.); (K.J.M.B.); (A.A.B.)
| | - Raphael Cassoulet
- Département de Chimie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (R.C.); (J.P.B.)
| | - Erin Wilkie
- Département de Pédiatrie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (E.W.); (V.G.); (A.-S.D.); (N.A.); (L.T.)
| | - Virginie Gillet
- Département de Pédiatrie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (E.W.); (V.G.); (A.-S.D.); (N.A.); (L.T.)
| | - Anne-Sandrine Desautels
- Département de Pédiatrie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (E.W.); (V.G.); (A.-S.D.); (N.A.); (L.T.)
| | - Nadia Abdelouahab
- Département de Pédiatrie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (E.W.); (V.G.); (A.-S.D.); (N.A.); (L.T.)
| | - Jean Philippe Bellenger
- Département de Chimie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (R.C.); (J.P.B.)
| | - Heather H. Burris
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brent A. Coull
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
| | - Marc G. Weisskopf
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Larissa Takser
- Département de Pédiatrie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; (E.W.); (V.G.); (A.-S.D.); (N.A.); (L.T.)
- Département de Psychiatrie, Faculté de Médicine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (Y.S.); (T.R.B.); (H.W.); (K.J.M.B.); (A.A.B.)
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Cox TO, Lundgren P, Nath K, Thaiss CA. Metabolic control by the microbiome. Genome Med 2022; 14:80. [PMID: 35906678 PMCID: PMC9338551 DOI: 10.1186/s13073-022-01092-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 07/15/2022] [Indexed: 12/20/2022] Open
Abstract
The interaction between the metabolic activities of the intestinal microbiome and its host forms an important part of health. The basis of this interaction is in part mediated by the release of microbially-derived metabolites that enter the circulation. These products of microbial metabolism thereby interface with the immune, metabolic, or nervous systems of the host to influence physiology. Here, we review the interactions between the metabolic activities of the microbiome and the systemic metabolism of the host. The concept that the endocrine system includes more than just the eukaryotic host component enables the rational design of exogenous interventions that shape human metabolism. An improved mechanistic understanding of the metabolic microbiome-host interaction may therefore pioneer actionable microbiota-based diagnostics or therapeutics that allow the control of host systemic metabolism via the microbiome.
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Affiliation(s)
- Timothy O Cox
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick Lundgren
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kirti Nath
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christoph A Thaiss
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Pant A, Maiti TK, Mahajan D, Das B. Human Gut Microbiota and Drug Metabolism. MICROBIAL ECOLOGY 2022:1-15. [PMID: 35869999 PMCID: PMC9308113 DOI: 10.1007/s00248-022-02081-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 07/18/2022] [Indexed: 05/31/2023]
Abstract
The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.
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Affiliation(s)
- Archana Pant
- Molecular Genetics Lab, National Institute of Immunology, New Delhi, Delhi-110067, India
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121001, India
- Molecular Genetics Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO box, Gurgaon Expressway, #04 Faridabad-121001, Haryana, India
| | - Tushar K Maiti
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121001, India
| | - Dinesh Mahajan
- Chemistry and Pharmacology Lab, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO box, Gurgaon Expressway, #04 Faridabad-121001, Haryana, India.
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