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Ignat M, Stefanescu H. Non-Invasive Biomarkers for Differentiating Alcohol Associated Hepatitis from Acute Decompensation in Patients with ALD. J Clin Med 2024; 13:3747. [PMID: 38999313 PMCID: PMC11242687 DOI: 10.3390/jcm13133747] [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: 05/19/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024] Open
Abstract
Alcohol-associated hepatitis (AH) is the most severe form of alcohol-related liver disease. The natural course of alcohol-related liver disease is influenced by heavy alcohol consumption and abstinence periods. Differentiating between AH and decompensated cirrhosis (DC) could be extremely challenging in clinical practice due to clinical and bioclinical similarities. The severity of AH is made on bioclinical grounds, the severe form necessitating corticotherapy treatment. Liver biopsy is still the standard of care for establishing the diagnosis in atypical presentations. The pathogenesis of AH is an interplay between gene expression, cytokine dysregulation, the immune system and the gut microbiota. Non-invasive tests are increasingly and widely used for the purpose of early diagnosis and reliable prognostication. The non-invasive tests are emerging in concordance with disease pathogenesis. In this review, we describe the non-invasive tools that can distinguish AH from DC. We outline the available cut-offs and their performance in diagnosis and prognosis, as well as in assessing the treatment response to corticotherapy. Promising circulating biomarkers like keratin 18, microRNAs and sphingolipids will be in the review.
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Affiliation(s)
- Mina Ignat
- Regional Institute of Gastroenterology and Hepatology "Prof. Dr. O. Fodor", 400394 Cluj-Napoca, Romania
- Faculty of Medicine, University of Medicine and Pharmacy "Iuliu Hatieganu", 400347 Cluj-Napoca, Romania
| | - Horia Stefanescu
- Regional Institute of Gastroenterology and Hepatology "Prof. Dr. O. Fodor", 400394 Cluj-Napoca, Romania
- Faculty of Medicine, University of Medicine and Pharmacy "Iuliu Hatieganu", 400347 Cluj-Napoca, Romania
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2
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Liu J, MacNaughtan J, Kerbert AJC, Portlock T, Martínez Gonzalez J, Jin Y, Clasen F, Habtesion A, Ji H, Jin Q, Phillips A, De Chiara F, Ingavle G, Jimenez C, Zaccherini G, Husi K, Rodriguez Gandia MA, Cordero P, Soeda J, McConaghy L, Oben J, Church K, Li JV, Wu H, Jalan A, Gines P, Solà E, Eaton S, Morgan C, Kowalski M, Green D, Gander A, Edwards LA, Cox IJ, Cortez-Pinto H, Avery T, Wiest R, Durand F, Caraceni P, Elosua R, Vila J, Pavesi M, Arroyo V, Davies N, Mookerjee RP, Vargas V, Sandeman S, Mehta G, Shoaie S, Marchesi J, Albillos A, Andreola F, Jalan R. Clinical, experimental and pathophysiological effects of Yaq-001: a non-absorbable, gut-restricted adsorbent in models and patients with cirrhosis. Gut 2024; 73:1183-1198. [PMID: 38621924 DOI: 10.1136/gutjnl-2023-330699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVE Targeting bacterial translocation in cirrhosis is limited to antibiotics with risk of antimicrobial resistance. This study explored the therapeutic potential of a non-absorbable, gut-restricted, engineered carbon bead adsorbent, Yaq-001 in models of cirrhosis and acute-on-chronic liver failure (ACLF) and, its safety and tolerability in a clinical trial in cirrhosis. DESIGN Performance of Yaq-001 was evaluated in vitro. Two-rat models of cirrhosis and ACLF, (4 weeks, bile duct ligation with or without lipopolysaccharide), receiving Yaq-001 for 2 weeks; and two-mouse models of cirrhosis (6-week and 12-week carbon tetrachloride (CCl4)) receiving Yaq-001 for 6 weeks were studied. Organ and immune function, gut permeability, transcriptomics, microbiome composition and metabolomics were analysed. The effect of faecal water on gut permeability from animal models was evaluated on intestinal organoids. A multicentre, double-blind, randomised, placebo-controlled clinical trial in 28 patients with cirrhosis, administered 4 gr/day Yaq-001 for 3 months was performed. RESULTS Yaq-001 exhibited rapid adsorption kinetics for endotoxin. In vivo, Yaq-001 reduced liver injury, progression of fibrosis, portal hypertension, renal dysfunction and mortality of ACLF animals significantly. Significant impact on severity of endotoxaemia, hyperammonaemia, liver cell death, systemic inflammation and organ transcriptomics with variable modulation of inflammation, cell death and senescence in the liver, kidneys, brain and colon was observed. Yaq-001 reduced gut permeability in the organoids and impacted positively on the microbiome composition and metabolism. Yaq-001 regulated as a device met its primary endpoint of safety and tolerability in the clinical trial. CONCLUSIONS This study provides strong preclinical rationale and safety in patients with cirrhosis to allow clinical translation. TRIAL REGISTRATION NUMBER NCT03202498.
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Affiliation(s)
- Jinxia Liu
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jane MacNaughtan
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Annarein J C Kerbert
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Javier Martínez Gonzalez
- Hospital Ramón y Cajal, IRYCIS, CIBEREHD, Universidad de Alcalá, Madrid, Spain
- Liver Unit, Hospital Vall d'Hebron, Universitat Autónoma, CIBERehd, Barcelona, Spain
| | - Yi Jin
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Frederick Clasen
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Abeba Habtesion
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Huoyan Ji
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Qin Jin
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Alexandra Phillips
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Francesco De Chiara
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Ganesh Ingavle
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton, UK
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
| | - Cesar Jimenez
- Liver Unit, Hospital Vall d'Hebron, Universitat Autónoma, CIBERehd, Barcelona, Spain
| | - Giacomo Zaccherini
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Unit of Semeiotics, Liver and Alcohol-related Diseases, University of Bologna Hospital of Bologna Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Katherine Husi
- Department of Gastroenterology, Inselspital University Hospital Bern, Bern, Switzerland
| | | | - Paul Cordero
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
| | - Junpei Soeda
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Lynda McConaghy
- Yaqrit Discovery Limited. The Elms Courtyard, Bromesberrow, Ledbury, UK
| | - Jude Oben
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Karen Church
- Yaqrit Discovery Limited. The Elms Courtyard, Bromesberrow, Ledbury, UK
| | - Jia V Li
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Haifeng Wu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | | | - Pere Gines
- Liver Unit, Hospital Clinic of Barcelona, IDIBAPS, Faculty of Medicine and Health sciences, University of Barcelona, Barcelona, Spain
| | - Elsa Solà
- Liver Unit, Hospital Clinic of Barcelona, IDIBAPS, Faculty of Medicine and Health sciences, University of Barcelona, Barcelona, Spain
| | - Simon Eaton
- Institute of Child Health, University College London, London, UK
| | - Carrie Morgan
- Yaqrit Discovery Limited. The Elms Courtyard, Bromesberrow, Ledbury, UK
| | - Michal Kowalski
- Yaqrit Discovery Limited. The Elms Courtyard, Bromesberrow, Ledbury, UK
| | - Daniel Green
- Yaqrit Discovery Limited. The Elms Courtyard, Bromesberrow, Ledbury, UK
| | - Amir Gander
- Tissue Access for Patient Benefit, University College London, London, UK
| | - Lindsey A Edwards
- Centre for Host Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, Guy's Tower, Guy's Hospital, King's College London, London, UK
- Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - I Jane Cox
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Helena Cortez-Pinto
- Clínica Universitária de Gastrenterologia, Laboratório de Nutrição, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Reiner Wiest
- UVCM Gastroenterology, University Bern, Bern, Switzerland
| | - Francois Durand
- Hepatology and Liver Intensive Care, Hospital Beaujon, Clichy, University paris Cité, Paris, France
| | - Paolo Caraceni
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Unit of Semeiotics, Liver and Alcohol Related Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | | | - Marco Pavesi
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), Barcelona, Spain
| | - Vicente Arroyo
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), Barcelona, Spain
| | - Nathan Davies
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Rajeshwar P Mookerjee
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Victor Vargas
- Liver Unit, Hospital Vall d'Hebron, Universitat Autónoma, CIBERehd, Barcelona, Spain
| | - Susan Sandeman
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton, UK
| | - Gautam Mehta
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Julian Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital, Imperial College London, London, UK
| | - Agustín Albillos
- Department of Gastroenterology and Hepatology, Hospital Universitario Ramon y Cajal, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Fausto Andreola
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
| | - Rajiv Jalan
- Liver Failure Group, UCL Institute for Liver & Digestive Health, Division of Medicine, London, UK
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), Barcelona, Spain
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3
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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [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: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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4
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Odenwald MA, Lin H, Lehmann C, Dylla NP, Cole CG, Mostad JD, Pappas TE, Ramaswamy R, Moran A, Hutchison AL, Stutz MR, Dela Cruz M, Adler E, Boissiere J, Khalid M, Cantoral J, Haro F, Oliveira RA, Waligurski E, Cotter TG, Light SH, Beavis KG, Sundararajan A, Sidebottom AM, Reddy KG, Paul S, Pillai A, Te HS, Rinella ME, Charlton MR, Pamer EG, Aronsohn AI. Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease. Nat Microbiol 2023; 8:2033-2049. [PMID: 37845315 PMCID: PMC11059310 DOI: 10.1038/s41564-023-01493-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/08/2023] [Indexed: 10/18/2023]
Abstract
Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen in humans and mice, which, in combination, can reduce the growth of antibiotic-resistant bacteria such as vancomycin-resistant Enterococcus faecium in vitro. Our studies suggest that lactulose and bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.
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Affiliation(s)
- Matthew A Odenwald
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA.
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Christopher Lehmann
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, USA
| | - Nicholas P Dylla
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Cody G Cole
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Jake D Mostad
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Téa E Pappas
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - Angelica Moran
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Alan L Hutchison
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Matthew R Stutz
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cook County Health, Chicago, IL, USA
| | - Mark Dela Cruz
- Section of Cardiology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Emerald Adler
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jaye Boissiere
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Maryam Khalid
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jackelyn Cantoral
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita A Oliveira
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Thomas G Cotter
- Division of Digestive and Liver Diseases, UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | | | | | - K Gautham Reddy
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Sonali Paul
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Anjana Pillai
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Helen S Te
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Mary E Rinella
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Michael R Charlton
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Andrew I Aronsohn
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
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5
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Bao Z, Wei R, Zheng X, Zhang T, Bi Y, Shen S, Zou P, Zhang J, Yan H, Li MD, Yang Z, Gao H. Landscapes of gut microbiome and bile acid signatures and their interaction in HBV-associated acute-on-chronic liver failure. Front Microbiol 2023; 14:1185993. [PMID: 37275140 PMCID: PMC10233926 DOI: 10.3389/fmicb.2023.1185993] [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: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Submassive hepatic necrosis (SMHN, defined as necrosis of 15-90% of the entire liver on explant) is a likely characteristic pathological feature of ACLF in patients with hepatitis B cirrhosis. We aimed to comprehensively explore microbiome and bile acids patterns across enterhepatic circulation and build well-performing machine learning models to predict SMHN status. Methods Based on the presence or absence of SMHN, 17 patients with HBV-related end-stage liver disease who received liver transplantation were eligible for inclusion. Serum, portal venous blood, and stool samples were collected for comparing differences of BA spectra and gut microbiome and their interactions. We adopted the random forest algorithm with recursive feature elimination (RF-RFE) to predict SMHN status. Results By comparing total BA spectrum between SMHN (-) and SMHN (+) patients, significant changes were detected only in fecal (P = 0.015). Compared with the SMHN (+) group, the SMHN (-) group showed that UDCA, 7-KLCA, 3-DHCA, 7-KDCA, ISOLCA and α-MCA in feces, r-MCA, 7-KLCA and 7-KDCA in serum, γ-MCA and 7-KLCA in portal vein were enriched, and TUDCA in feces was depleted. PCoA analysis showed significantly distinct overall microbial composition in two groups (P = 0.026). Co-abundance analysis showed that bacterial species formed strong and broad relationships with BAs. Among them, Parabacteroides distasonis had the highest node degree. We further identified a combinatorial marker panel with a high AUC of 0.92. Discussion Our study demonstrated the changes and interactions of intestinal microbiome and BAs during enterohepatic circulation in ACLF patients with SMHN. In addition, we identified a combinatorial marker panel as non-invasive biomarkers to distinguish the SMHN status with high AUC.
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Affiliation(s)
- Zhiwei Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Runan Wei
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoping Zheng
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Ting Zhang
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Yunjiao Bi
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Sijia Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengfei Zou
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Junjie Zhang
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Huadong Yan
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Ming D. Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China
| | - Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hainv Gao
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
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6
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Bajaj JS, Peña-Rodriguez M, La Reau A, Phillips W, Fuchs M, Davis BC, Sterling RK, Sikaroodi M, Fagan A, Shamsaddini A, Henseler Z, Ward T, Puri P, Lee H, Gillevet PM. Longitudinal transkingdom gut microbial approach towards decompensation in outpatients with cirrhosis. Gut 2023; 72:759-771. [PMID: 36343978 PMCID: PMC9998342 DOI: 10.1136/gutjnl-2022-328403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE First decompensation development is a critical milestone that needs to be predicted. Transkingdom gut microbial interactions, including archaeal methanogens, may be important targets and predictors but a longitudinal approach is needed. DESIGN Cirrhosis outpatients who provided stool twice were included. Group 1: compensated, group 2: 1 decompensation (decomp), group 3: >1 decompensationwere followed and divided into those who remained stable or decompensated. Bacteria, viral and archaeal presence, α/β diversity and taxa changes over time adjusted for clinical variables were analysed. Correlation networks between kingdoms were analysed. RESULTS 157 outpatients (72 group 1, 33 group 2 and 52 group 3) were followed and 28%-47% developed outcomes. Baseline between those who remained stable/developed outcome: While no α/β diversity differences were seen, commensals were lower and pathobionts were higher in those who decompensated. After decompensation: those experiencing their first decompensation showed greater decrease in α/β-diversity, bacterial change (↑Lactobacillus spp, Streptococcus parasanguinis and ↓ beneficial Lachnospiraceae and Eubacterium hallii) and viral change (↑Siphoviridae, ↓ Myoviridae) versus those with further decompensation. Archaea: 19% had Methanobacter brevii, which was similar between/within groups. Correlation networks: Baseline archaeal-viral-bacterial networks were denser and more homogeneous in those who decompensated versus the rest. Archaea-bacterial correlations collapsed post first decompensation. Lactobacillus phage Lc Nu and C2-like viruses were negatively linked with beneficial bacteria. CONCLUSION In this longitudinal study of cirrhosis outpatients, the greatest transkingdom gut microbial changes were seen in those reaching the first decompensation, compared with subsequent decompensating events. A transkingdom approach may refine prediction and provide therapeutic targets to prevent cirrhosis progression.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | | | | | | | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Brian C Davis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Richard K Sterling
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Andrew Fagan
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | | | | | - Tonya Ward
- Diversigen Inc, New Brighton, Minnesota, USA
| | - Puneet Puri
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Hannah Lee
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Health System, Richmond, Virginia, USA
- GI Section, Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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7
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Roosan D, Wu Y, Tran M, Huang Y, Baskys A, Roosan MR. Opportunities to integrate nutrigenomics into clinical practice and patient counseling. Eur J Clin Nutr 2023; 77:36-44. [PMID: 35444269 DOI: 10.1038/s41430-022-01146-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND Little progress has been made in translating nutrigenomics knowledge into clinical counseling in the past decade. Currently, clinicians are overwhelmed by nutrigenomics information without the proper scientific guidelines on patient counseling. METHODS In this study, we conducted a scoping review of the primary literature to assess the current evidence of nutrigenomics counseling. A literature search using PRISMA guidelines identified the current challenges and opportunities facing nutrigenomics counseling in clinical practice. RESULTS We identified four main themes: inadequate training, lack of awareness, underdeveloped nutrigenomics counseling skills, and unreliable evidence-based practice information. Many clinicians did not have the necessary knowledge to perform nutrigenomic counseling and were unaware of the available scientific information source. Moreover, there are no guidelines in the scientific community to counsel patients on nutrigenomics testing. CONCLUSION Opportunities exist for government and non-government entities to create an evidence-based information platform using clinical guidelines to integrate nutrigenomics knowledge from bench to bedside successfully.
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Affiliation(s)
- Don Roosan
- College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA.
| | - Yanting Wu
- College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Michael Tran
- College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Ying Huang
- College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Andrius Baskys
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA
| | - Moom R Roosan
- School of Pharmacy, Chapman University, Irvine, CA, USA
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8
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Li SL, Zheng SQ, Tang YZ, Liu HM, Mao Q. Progress in understanding of relationship between duodenal mucosal microecology and hepatitis B virus related acute-on-chronic liver failure. Shijie Huaren Xiaohua Zazhi 2022; 30:1074-1078. [DOI: 10.11569/wcjd.v30.i24.1074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
According to statistics, the rate of hepatitis B virus (HBV) infection is still high in China, and the mortality of acute-on-chronic liver failure (ACLF) is also high. In recent years, studies on the fecal flora of patients with HBV related ACLF have found that intestinal microecology affects the occurrence, development, and prognosis of HBV related ACLF. However, fecal flora cannot completely replace the whole intestinal microecology, and duodenal mucosal microecology may be a new research direction. This review discusses the influence of duodenal mucosal flora on the clinical outcome of HBV-ACLF with regard to mechanism, physiology, and anatomical characteristics.
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Affiliation(s)
- Shi-Lian Li
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing Key Laboratory of Infectious Disease Research, Chongqing 400038, China
| | - Shao-Qin Zheng
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing Key Laboratory of Infectious Disease Research, Chongqing 400038, China
| | - Ying-Zi Tang
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing Key Laboratory of Infectious Disease Research, Chongqing 400038, China
| | - Hui-Min Liu
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing Key Laboratory of Infectious Disease Research, Chongqing 400038, China
| | - Qing Mao
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing Key Laboratory of Infectious Disease Research, Chongqing 400038, China
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9
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Won SM, Oh KK, Gupta H, Ganesan R, Sharma SP, Jeong JJ, Yoon SJ, Jeong MK, Min BH, Hyun JY, Park HJ, Eom JA, Lee SB, Cha MG, Kwon GH, Choi MR, Kim DJ, Suk KT. The Link between Gut Microbiota and Hepatic Encephalopathy. Int J Mol Sci 2022; 23:ijms23168999. [PMID: 36012266 PMCID: PMC9408988 DOI: 10.3390/ijms23168999] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatic encephalopathy (HE) is a serious complication of cirrhosis that causes neuropsychiatric problems, such as cognitive dysfunction and movement disorders. The link between the microbiota and the host plays a key role in the pathogenesis of HE. The link between the gut microbiome and disease can be positively utilized not only in the diagnosis area of HE but also in the treatment area. Probiotics and prebiotics aim to resolve gut dysbiosis and increase beneficial microbial taxa, while fecal microbiota transplantation aims to address gut dysbiosis through transplantation (FMT) of the gut microbiome from healthy donors. Antibiotics, such as rifaximin, aim to improve cognitive function and hyperammonemia by targeting harmful taxa. Current treatment regimens for HE have achieved some success in treatment by targeting the gut microbiota, however, are still accompanied by limitations and problems. A focused approach should be placed on the establishment of personalized trial designs and therapies for the improvement of future care. This narrative review identifies factors negatively influencing the gut–hepatic–brain axis leading to HE in cirrhosis and explores their relationship with the gut microbiome. We also focused on the evaluation of reported clinical studies on the management and improvement of HE patients with a particular focus on microbiome-targeted therapy.
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10
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Nie K, Ma K, Luo W, Shen Z, Yang Z, Xiao M, Tong T, Yang Y, Wang X. Roseburia intestinalis: A Beneficial Gut Organism From the Discoveries in Genus and Species. Front Cell Infect Microbiol 2021; 11:757718. [PMID: 34881193 PMCID: PMC8647967 DOI: 10.3389/fcimb.2021.757718] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
Roseburia intestinalis is an anaerobic, Gram-positive, slightly curved rod-shaped flagellated bacterium that produces butyrate in the colon. R. intestinalis has been shown to prevent intestinal inflammation and maintain energy homeostasis by producing metabolites. Evidence shows that this bacterium contributes to various diseases, such as inflammatory bowel disease, type 2 diabetes mellitus, antiphospholipid syndrome, and atherosclerosis. This review reveals the potential therapeutic role of R. intestinalis in human diseases. Patients with inflammatory bowel disease exhibit significant changes in R. intestinalis abundance, and they may benefit a lot from modulations targeting R. intestinalis. The data reviewed here demonstrate that R. intestinalis plays its role in regulating barrier homeostasis, immune cells, and cytokine release through its metabolite butyrate, flagellin and other. Recent advancements in the application of primary culture technology, culture omics, single-cell sequencing, and metabonomics technology have improved research on Roseburia and revealed the benefits of this bacterium in human health and disease treatment.
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Affiliation(s)
- Kai Nie
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Kejia Ma
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Weiwei Luo
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Zhaohua Shen
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Zhenyu Yang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Mengwei Xiao
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Ting Tong
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Yuanyuan Yang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
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11
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Kim SE, Park JW, Kim HS, Jang MK, Suk KT, Kim DJ. The Role of Gut Dysbiosis in Acute-on-Chronic Liver Failure. Int J Mol Sci 2021; 22:ijms222111680. [PMID: 34769109 PMCID: PMC8584227 DOI: 10.3390/ijms222111680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Acute-on-chronic liver failure (ACLF) is an important syndrome of liver failure that has a high risk of short-term mortality in patients with chronic liver disease. The development of ACLF is associated with proinflammatory precipitating events, such as infection, alcoholic hepatitis, and intense systemic inflammation. Recently, the role of the gut microbiome has increasingly emerged in human health and disease. Additionally, the gut microbiome might have a major role in the development of liver disease. In this review, we examine evidence to support the role of gut dysbiosis in cirrhosis and ACLF. Additionally, we explore the mechanism by which the gut microbiome contributes to the development of ACLF, with a focus on alcohol-induced liver disease.
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Affiliation(s)
- Sung-Eun Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon 24252, Korea; (S.-E.K.); (J.W.P.); (H.S.K.); (M.-K.J.); (K.T.S.)
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
| | - Ji Won Park
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon 24252, Korea; (S.-E.K.); (J.W.P.); (H.S.K.); (M.-K.J.); (K.T.S.)
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
| | - Hyung Su Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon 24252, Korea; (S.-E.K.); (J.W.P.); (H.S.K.); (M.-K.J.); (K.T.S.)
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
| | - Myoung-Kuk Jang
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon 24252, Korea; (S.-E.K.); (J.W.P.); (H.S.K.); (M.-K.J.); (K.T.S.)
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
| | - Ki Tae Suk
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon 24252, Korea; (S.-E.K.); (J.W.P.); (H.S.K.); (M.-K.J.); (K.T.S.)
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
| | - Dong Joon Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon 24252, Korea; (S.-E.K.); (J.W.P.); (H.S.K.); (M.-K.J.); (K.T.S.)
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
- Correspondence: ; Tel.: +82–33–240–5646
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12
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Shamsaddini A, Gillevet PM, Acharya C, Fagan A, Gavis E, Sikaroodi M, McGeorge S, Khoruts A, Albhaisi S, Fuchs M, Sterling RK, Bajaj JS. Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis. Gastroenterology 2021; 161:508-521.e7. [PMID: 33857456 PMCID: PMC9069394 DOI: 10.1053/j.gastro.2021.04.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes. METHODS In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning. RESULTS A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs. CONCLUSIONS Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.
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Affiliation(s)
| | | | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | | | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Alexander Khoruts
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Somaya Albhaisi
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Richard K. Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
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13
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Transition to decompensation and acute-on-chronic liver failure: Role of predisposing factors and precipitating events. J Hepatol 2021; 75 Suppl 1:S36-S48. [PMID: 34039491 DOI: 10.1016/j.jhep.2020.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
The transition from compensated to decompensated cirrhosis results from a complex interplay of predisposing and precipitating factors and represents an inflection point in the probability of a patient surviving. With the progression of cirrhosis, patients accumulate multiple disorders (e.g. altered liver architecture, portal hypertension, local and systemic inflammation, bacterial translocation, gut dysbiosis, kidney vasoconstriction) that predispose them to decompensation. On the background of these factors, precipitating events (e.g. bacterial infection, alcoholic hepatitis, variceal haemorrhage, drug-induced liver injury, flare of liver disease) lead to acute decompensation (ascites, hepatic encephalopathy, variceal bleeding, jaundice) and/or organ failures, which characterise acute-on-chronic liver failure. In this review paper, we will discuss the current hypotheses and latest evidences regarding predisposing and precipitating factors associated with the transition to decompensated liver disease.
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14
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Bajaj JS, Sikaroodi M, Shamsaddini A, Henseler Z, Santiago-Rodriguez T, Acharya C, Fagan A, Hylemon PB, Fuchs M, Gavis E, Ward T, Knights D, Gillevet PM. Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy. Gut 2021; 70:1162-1173. [PMID: 32998876 DOI: 10.1136/gutjnl-2020-322470] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/18/2020] [Accepted: 08/30/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Altered bacterial composition is associated with disease progression in cirrhosis but the role of virome, especially phages, is unclear. DESIGN Cross-sectional and pre/post rifaximin cohorts were enrolled. Cross-sectional: controls and cirrhotic outpatients (compensated, on lactulose (Cirr-L), on rifaximin (Cirr-LR)) were included and followed for 90-day hospitalisations. Pre/post: compensated cirrhotics underwent stool collection pre/post 8 weeks of rifaximin. Stool metagenomics for bacteria and phages and their correlation networks were analysed in controls versus cirrhosis, within cirrhotics, hospitalised/not and pre/post rifaximin. RESULTS Cross-sectional: 40 controls and 163 cirrhotics (63 compensated, 43 Cirr-L, 57 Cirr-LR) were enrolled. Cirr-L/LR groups were similar on model for end-stage liver disease (MELD) score but Cirr-L developed greater hospitalisations versus Cirr-LR (56% vs 30%, p=0.008). Bacterial alpha/beta diversity worsened from controls through Cirr-LR. While phage alpha diversity was similar, beta diversity was different between groups. Autochthonous bacteria linked negatively, pathobionts linked positively with MELD but only modest phage-MELD correlations were seen. Phage-bacterial correlation network complexity was highest in controls, lowest in Cirr-L and increased in Cirr-LR. Microviridae and Faecalibacterium phages were linked with autochthonous bacteria in Cirr-LR, but not Cirr-L hospitalised patients had greater pathobionts, lower commensal bacteria and phages focused on Streptococcus, Lactococcus and Myoviridae. Pre/post: No changes in alpha/beta diversity of phages or bacteria were seen postrifaximin. Phage-bacterial linkages centred around urease-producing Streptococcus species collapsed postrifaximin. CONCLUSION Unlike bacteria, faecal phages are sparsely linked with cirrhosis characteristics and 90-day outcomes. Phage and bacterial linkages centred on urease-producing, ammonia-generating Streptococcus species were affected by disease progression and rifaximin therapy and were altered in patients who experienced 90-day hospitalisations.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | | | | | | | - Chathur Acharya
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Andrew Fagan
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Phillip B Hylemon
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Edith Gavis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Tonya Ward
- Diversigen, New Brighton, Minnesota, USA
| | - Dan Knights
- Diversigen, New Brighton, Minnesota, USA.,Department of Computer Science and Engineering, U, University of Minnesota, Minneapolis, MN, USA.,Minnesota Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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15
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Research progress on gut microbiota in patients with gastric cancer, esophageal cancer, and small intestine cancer. Appl Microbiol Biotechnol 2021; 105:4415-4425. [PMID: 34037843 DOI: 10.1007/s00253-021-11358-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 12/12/2022]
Abstract
The pathogenesis of gut microbiota in humans can be indicated due to the wide application of techniques, such as 16S rRNA sequencing. Presently, several studies have found a significant difference in fecal flora between normal individuals and patients with gastric cancer. Although clinical research on the feedback mechanism of gastric flora and gut microbiota is lacking, clarifying the relationship between gut microbiota and the characteristics of cancer is significant for the early diagnosis of gastric cancer. This study was conducted to review the results of several studies in the past 5 years and analyze the intestinal bacteria in patients with gastric cancer and compare them with those in patients with esophageal and small intestine cancers. It was found that the gut microbiota in patients with gastric cancer was similar to that in patients with esophageal cancer. However, making an analysis and comparing the gut microbiota in patients with small intestine and gastric cancers was impossible due to the low incidence of small intestinal cancer. Our review summarized the research progress on using the gut microbiota for early screening for gastric cancer, and the results of this study will provide a further direction in this field. KEY POINTS: • We reviewed several relative mechanisms of the gut microbiota related to gastric cancer. • The gut microbiota in gastric, esophageal, and small intestine cancers are significantly different in types and quantity, and we have provided some tips for further research. • A prospective review of sequencing methods and study results on the gut microbiota in gastric, esophageal, and small intestine cancers was described.
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16
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Gui QF, Jin HL, Zhu F, Lu HF, Zhang Q, Xu J, Yang YM, Xiao C. Gut microbiota signatures in Schistosoma japonicum infection-induced liver cirrhosis patients: a case-control study. Infect Dis Poverty 2021; 10:43. [PMID: 33771232 PMCID: PMC8004463 DOI: 10.1186/s40249-021-00821-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background Several studies have assessed the role of gut microbiota in various cirrhosis etiologies, however, none has done so in the context of Schistosoma japonicum infection in humans. We, therefore, sought to determine whether gut microbiota is associated with S. japonicum infection-induced liver cirrhosis. Methods From December 2017 to November 2019, 24 patients with S. japonicum infection-induced liver cirrhosis, as well as 25 age- and sex-matched controls from the Zhejiang Province, China, were enrolled. Fecal samples were collected and used for 16S rRNA gene sequencing (particularly, the hypervariable V4 region) using the Illumina MiSeq system. Wilcoxon Rank-Sum and PERMANOVA tests were used for analysis. Results Eight hundred and seven operational taxonomic units (OTUs) were detected, of which, 491 were common between the two groups, whereas 123 and 193 were unique to the control and cirrhosis groups, respectively. Observed species, Chao, ACE, Shannon, Simpson, and Good’s coverage indexes, used for alpha diversity analysis, showed values of 173.4 ± 63.8, 197.7 ± 73.0, 196.3 ± 68.9, 2.96 ± 0.57, 0.13 ± 0.09, and 1.00 ± 0.00, respectively, in the control group and 154.0 ± 68.1, 178.6 ± 75.1, 179.9 ± 72.4, 2.68 ± 0.76, 0.19 ± 0.18, and 1.00 ± 0.00, respectively, in the cirrhosis group, with no significant differences observed between the groups. Beta diversity was evaluated by weighted UniFrac distances, with values of 0.40 ± 0.13 and 0.40 ± 0.11 in the control and cirrhosis groups, respectively (P > 0.05). PCA data also confirmed this similarity (P > 0.05). Meanwhile, the relative abundance of species belonging to the Bacilli class was higher in cirrhosis patients [median: 2.74%, interquartile range (IQR): 0.18–7.81%] than healthy individuals (median: 0.15%, IQR: 0.47–0.73%; P < 0.01), and that of Lactobacillales order was also higher in cirrhosis patients (median: 2.73%, IQR: 0.16–7.80%) than in healthy individuals (median: 0.12%, IQR: 0.03–0.70%; P < 0.05). Conclusions Cumulatively, our results suggest that the gut microbiota of S. japonicum infection-induced liver cirrhosis patients is similar to that of healthy individuals, indicating that bacterial taxa cannot be used as non-invasive biomarkers for S. japonicum infection-induced liver cirrhosis. ![]()
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Affiliation(s)
- Qi-Feng Gui
- Department of Geriatrics, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-Chemical Injury Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Hui-Lin Jin
- Department of Geriatrics, Wangdian People's Hospital, Jiaxing, Zhejiang, People's Republic of China
| | - Feng Zhu
- Department of Geriatrics, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-Chemical Injury Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Hai-Feng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Qin Zhang
- Department of Geriatrics, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-Chemical Injury Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jia Xu
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-Chemical Injury Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Department of Emergency Medicine, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yun-Mei Yang
- Department of Geriatrics, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China. .,Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-Chemical Injury Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
| | - Chi Xiao
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People's Republic of China.
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Acharya C, Bajaj JS. Chronic Liver Diseases and the Microbiome-Translating Our Knowledge of Gut Microbiota to Management of Chronic Liver Disease. Gastroenterology 2021; 160:556-572. [PMID: 33253686 PMCID: PMC9026577 DOI: 10.1053/j.gastro.2020.10.056] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
Abstract
Chronic liver disease is reaching epidemic proportions with the increasing prevalence of obesity, nonalcoholic liver disease, and alcohol overuse worldwide. Most patients are not candidates for liver transplantation even if they have end-stage liver disease. There is growing evidence of a gut microbial basis for many liver diseases, therefore, better diagnostic, prognostic, and therapeutic approaches based on knowledge of gut microbiota are needed. We review the questions that need to be answered to successfully translate our knowledge of the intestinal microbiome and the changes associated with liver disease into practice.
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Bajaj JS, Reddy KR, O'Leary JG, Vargas HE, Lai JC, Kamath PS, Tandon P, Wong F, Subramanian RM, Thuluvath P, Fagan A, White MB, Gavis EA, Sehrawat T, de la Rosa Rodriguez R, Thacker LR, Sikaroodi M, Garcia-Tsao G, Gillevet PM. Serum Levels of Metabolites Produced by Intestinal Microbes and Lipid Moieties Independently Associated With Acute-on-Chronic Liver Failure and Death in Patients With Cirrhosis. Gastroenterology 2020; 159:1715-1730.e12. [PMID: 32687928 PMCID: PMC7680282 DOI: 10.1053/j.gastro.2020.07.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Inpatients with cirrhosis have high rates of acute-on-chronic failure (ACLF) development and high mortality within 30 days of admission to the hospital. Better biomarkers are needed to predict these outcomes. We performed metabolomic analyses of serum samples from patients with cirrhosis at multiple centers to determine whether metabolite profiles might identify patients at high risk for ACLF and death. METHODS We performed metabolomic analyses, using liquid chromatography, of serum samples collected at time of admission to 12 North American tertiary hepatology centers from 602 patients in the North American Consortium for the Study of End-Stage Liver Disease sites from 2015 through 2017 (mean age, 56 years; 61% men; mean model for end-stage liver disease score, 19.5). We performed analysis of covariance, adjusted for model for end-stage liver disease at time of hospital admission, serum levels of albumin and sodium, and white blood cell count, to identify metabolites that differed between patients who did vs did not develop ACLF and patients who did vs did not die during hospitalization and within 30 days. We performed random forest analysis to identify specific metabolite(s) that were associated with outcomes and area under the curve (AUC) analyses to analyze them in context of clinical parameters. We analyzed microbiomes of stool samples collected from 133 patients collected at the same time and examined associations with serum metabolites. RESULTS Of the 602 patients analyzed, 88 developed ACLF (15%), 43 died in the hospital (7%), and 72 died within 30 days (12%). Increased levels of compounds of microbial origin (aromatic compounds, secondary or sulfated bile acids, and benzoate) and estrogen metabolites, as well as decreased levels of phospholipids, were associated with development of ACLF, inpatient, and 30-day mortality and were also associated with fecal microbiomes. Random forest analysis and logistic regression showed that levels of specific microbially produced metabolites identified patients who developed ACLF with an AUC of 0.84 (95% confidence interval [CI] 0.78-0.88; P = .001), patients who died while in the hospital with an AUC of 0.81 (95% CI 0.74-0.85; P = .002), and patients who died within 30 days with an AUC of 0.77 (95% CI 0.73-0.81; P = .02). The metabolites were significantly additive to clinical parameters for predicting these outcomes. Metabolites associated with outcomes were also correlated with microbiomes of stool samples. CONCLUSIONS In an analysis of serum metabolites and fecal microbiomes of patients hospitalized with cirrhosis at multiple centers, we associated metabolites of microbial origin and lipid moieties with development of ACLF and death as an inpatient or within 30 days, after controlling for clinical features.
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Affiliation(s)
- Jasmohan S Bajaj
- Department of Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia.
| | - K Rajender Reddy
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Hugo E Vargas
- Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Jennifer C Lai
- Department of Medicine, University of California, San Francisco, California
| | | | - Puneeta Tandon
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Florence Wong
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Paul Thuluvath
- Department of Medicine, Mercy Medical Center, Baltimore, Maryland
| | - Andrew Fagan
- Department of Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Melanie B White
- Department of Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Edith A Gavis
- Department of Medicine, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | | | | | - Leroy R Thacker
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
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Mücke MM, Rüschenbaum S, Mayer A, Mücke VT, Schwarzkopf KM, Zeuzem S, Kehrmann J, Scholtysik R, Lange CM. Stool and sputum microbiome during quinolone prophylaxis of spontaneous bacterial peritonitis: an exploratory study. Gut Pathog 2020; 12:51. [PMID: 33133240 PMCID: PMC7596951 DOI: 10.1186/s13099-020-00389-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Quinolone prophylaxis is recommended for patients with advanced cirrhosis at high risk of spontaneous bacterial peritonitis (SBP) or with prior SBP. Yet, the impact of long-term antibiotic prophylaxis on the microbiome of these patients is poorly characterized. METHODS Patients with liver cirrhosis receiving long-term quinolone prophylaxis to prevent SBP were prospectively included and sputum and stool samples were obtained at baseline, 1, 4 and 12 weeks thereafter. Both bacterial DNA and RNA were assessed with 16S rRNA sequencing. Relative abundance, alpha and beta diversity were calculated and correlated with clinical outcome. RESULTS Overall, 35 stool and 19 sputum samples were obtained from 11 patients. Two patients died (day 9 and 12) all others were followed for 180 days. Reduction of Shannon diversity and bacterial richness was insignificant after initiation of quinolone prophylaxis (p > 0.05). Gut microbiota were significantly different between patients (p < 0.001) but non-significantly altered between the different time points before and after initiation of antibiotic prophylaxis (p > 0.05). A high relative abundance of Enterobacteriaceae > 20% during quinolone prophylaxis was found in three patients. Specific clinical scenarios (development of secondary infections during antibiotic prophylaxis or the detection of multidrug-resistant Enterobacteriaceae) characterized these patients. Sputum microbiota were not significantly altered in individuals during prophylaxis. CONCLUSION The present exploratory study with small sample size showed that inter-individual differences in diversity of gut microbiota were high at baseline, yet quinolone prophylaxis had only a moderate impact. High relative abundances of Enterobacteriaceae during follow-up might indicate failure of or non-adherence to quinolone prophylaxis. However, our results may not be clinically significant given the limitations of the study and therefore future studies are needed to further investigate this phenomenon.
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Affiliation(s)
- Marcus M. Mücke
- Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Sabrina Rüschenbaum
- Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Present Address: Department for Gastroenterology and Hepatology, University Hospital Essen and University of Duisburg-Essen, Essen, Germany
| | - Amelie Mayer
- Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Victoria T. Mücke
- Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Katharina M. Schwarzkopf
- Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Stefan Zeuzem
- Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - René Scholtysik
- Institute of Cell Biology, University Hospital Essen and University of Duisburg-Essen, Essen, Germany
| | - Christian M. Lange
- Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Present Address: Department for Gastroenterology and Hepatology, University Hospital Essen and University of Duisburg-Essen, Essen, Germany
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Yan C, Duan G, Wu FX, Pan Y, Wang J. BRWMDA:Predicting Microbe-Disease Associations Based on Similarities and Bi-Random Walk on Disease and Microbe Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1595-1604. [PMID: 30932846 DOI: 10.1109/tcbb.2019.2907626] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Many current studies have evidenced that microbes play important roles in human diseases. Therefore, discovering the associations between microbes and diseases is beneficial to systematically understanding the mechanisms of diseases, diagnosing, and treating complex diseases. It is well known that finding new potential microbe-disease associations via biological experiments is a time-consuming and expensive process. However, the computation methods can provide an opportunity to effectively predict microbe-disease associations. In recent years, efforts toward predicting microbe-disease associations are not in proportional to the importance of microbes to human diseases. In this study, we develop a method (called BRWMDA) to predict new microbe-disease associations based on similarity and improving bi-random walk on the disease and microbe networks. BRWMDA integrates microbe network, disease network, and known microbe-disease associations into a single network. After calculating the Gaussian Interaction Profile (GIP) kernel similarity of microbes based on known microbe-disease associations, the microbe network is obtained by adjusting the similarity with the logistics function. In addition, the disease network is computed by the similarity network fusion (SNF) method with the symptom-based similarity and the GIP kernel similarity based on known microbe-disease associations. Then, these two networks of microbe and disease are connected by known microbe-disease associations. Based on the assumption that similar microbes are normally associated with similar diseases and vice versa, BRWMDA is employed to predict new potential microbe-disease associations via random walk with different steps on microbe and disease networks, which reasonably uses the similarity of microbe network and disease network. The 5-fold cross validation and Leave One Out Cross Validation (LOOCV) are adopted to assess the prediction performance of our BRWMDA algorithm, as well as other competing methods for comparison. 5-fold cross validation experiments show that BRWMDA obtained the maximum AUC value of 0.9087, which is again superior to other methods of 0.9025(NGRHMDA), 0.8797 (LRLSHMDA), 0.8571 (KATZHMDA), 0.7782 (HGBI), and 0.5629 (NBI). In addition, BRWMDA also outperforms other methods in terms of LOOCV, whose AUC value is 0.9397, which is superior to other methods of 0.9111(NGRHMDA), 0.8909 (LRLSHMDA), 0.8644 (KATZHMDA), 0.7866 (HGBI), and 0.5553 (NBI). Case studies also illustrate that BRWMDA is an effective method to predict microbe-disease associations.
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Bajaj JS, Khoruts A. Microbiota changes and intestinal microbiota transplantation in liver diseases and cirrhosis. J Hepatol 2020; 72:1003-1027. [PMID: 32004593 DOI: 10.1016/j.jhep.2020.01.017] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023]
Abstract
Patients with chronic liver disease and cirrhosis demonstrate a global mucosal immune impairment, which is associated with altered gut microbiota composition and functionality. These changes progress along with the advancing degree of cirrhosis and can be linked with hepatic encephalopathy, infections and even prognostication independent of clinical biomarkers. Along with compositional changes, functional alterations to the microbiota, related to short-chain fatty acids, bioenergetics and bile acid metabolism, are also associated with cirrhosis progression and outcomes. Altering the functional and structural profile of the microbiota is partly achieved by medications used in patients with cirrhosis such as rifaximin, lactulose, proton pump inhibitors and other antibiotics. However, the role of faecal or intestinal microbiota transplantation is increasingly being recognised. Herein, we review the challenges, opportunities and road ahead for the appropriate and safe use of intestinal microbiota transplantation in liver disease.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA.
| | - Alexander Khoruts
- Division of Gastroenterology Hepatology and Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
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Bajaj JS, Acharya C, Sikaroodi M, Gillevet PM, Thacker LR. Cost-effectiveness of integrating gut microbiota analysis into hospitalisation prediction in cirrhosis. GASTROHEP 2020; 2:79-86. [PMID: 33071650 PMCID: PMC7567123 DOI: 10.1002/ygh2.390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Admissions in cirrhosis are expensive and often unpredictable based on purely clinical variables. Admissions could be related to complications associated with gut microbial changes, which can improve prognostication. However, the cost-effectiveness is unclear. AIMS Determine cost-effectiveness of adding gut microbiota analysis to clinical parameters in prediction and subsequent reduction of admissions in cirrhosis. METHODS Using a Markov model of 1000 cirrhosis patients over 90 days, we modeled microbiota testing using 16srRNA ($250/sample), low-depth ($350/sample) and high-depth ($650/sample) metagenomics added to standard-of-care (SOC) for prevention of admissions using standard outcome costs and rates of development. We generated quality of life years (QALY) and Incremental cost-effectiveness ratios (ICER) for the base scenarios and performed sensitivity analyses by varying costs for outcomes (transplant, death, admission) and admission rates (40%, range 25%-60%). RESULTS Using fixed costs of outcomes and outcome rates, microbiota analysis was cost-saving ($47K-$97K) at $250 and $350/sample if admissions were reduced by 5%over SOC and >10% with $650/sample. When costs of LT, death and admissions were varied, these cost-savings remained robust provided there was >2.1% reduction (range 1.3%-3.2%) for $250/sample, >2.9% (range 1.8%-4.4%) for $350/sample and >5.4% (range 3.3%-8.2%) for $650/sample. These cost-savings remained robust even when the assumed admission rate was varied for all sample cost values. CONCLUSIONS Gut microbiota analysis is cost-effective for predicting and potentially preventing 90-day admissions in cirrhosis over current standard of care. This cost-saving remained robust even after sensitivity analyses that varied the background admission rates.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | | | | | - Leroy R Thacker
- Department of Biostatistics, Virginia Commonwealth University Medical Center, Richmond, Virginia
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Advances in Gut Microbiota of Viral Hepatitis Cirrhosis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9726786. [PMID: 31886272 PMCID: PMC6893240 DOI: 10.1155/2019/9726786] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023]
Abstract
Although gut dysbiosis appears in 20%-75% of cirrhotic patients, there are limited data on microbiota profiles in viral hepatitis cirrhotics and its role in progression to cirrhosis. Further understanding on the relationship between gut dysbiosis and cirrhosis presents a unique opportunity in not only predicting the development of cirrhosis but also discovering new therapies. Recent advances have been made on identifying unique microbiota in viral hepatitis cirrhotics and adopting the microbiota index to predict cirrhosis. Therapeutic intervention with microbiome-modulating has been explored. Cirrhosis from viral infection has unique bacterial or fungal profiles, which include increased numbers of Prevotella, Streptococcus, Staphylococcaceae, and Enterococcus, as well as decreased Ruminococcus and Clostridium. In addition, the gut microbiota can stimulate liver immunity, effectively helping hepatitis virus clearance. In clinical settings, CDR, GDI, Basidiomycota/Ascomycota, specific POD, and so forth are efficient microbiota indexes to diagnose or prognosticate cirrhosis from viral hepatitis. FMT, probiotics, and prebiotics can restore microbial diversity in cirrhotic patients with viral hepatitis, decrease ammonia serum or endotoxemia levels, prevent complications, reduce rehospitalization rate, and improve prognosis. Cirrhotics from viral hepatitis had unique bacterial or fungal profiles, associated with specific metabolic, immune, and endocrinological statuses. Such profiles are modifiable with medical treatment. The role of gut archaea and virome, implementation of FMT, microbiota metabolites as adjuvant immunotherapy, and microbiota indexes for prognostication deserve attention.
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Serum and urinary metabolomics and outcomes in cirrhosis. PLoS One 2019; 14:e0223061. [PMID: 31560724 PMCID: PMC6764675 DOI: 10.1371/journal.pone.0223061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cirrhosis can alter several metabolic pathways. Metabolomics could prognosticate outcomes like hepatic encephalopathy (HE), transplant, hospitalization and death. AIM Determine changes in serum and urine metabolomics in cirrhotics who develop outcomes. METHODS Cirrhotic outpatients underwent data, serum/urine collection and were followed for 90 days. Demographics, cirrhosis details and medications were collected. Metabolomics was performed on urine/serum using GC/MS with subsequent bioinformatics analyses (ChemRICH, MetaMAPP and PLS-DA). Logistic regression adjusting for covariates (demographics, alcohol etiology, prior HE, PPI, SBP prophylaxis, rifaximin/lactulose) were performed and ROC curves comparing MELD to adjusted serum & urine metabolites were created. RESULTS 211 patients gave serum, of which 64 were hospitalized, 19 developed HE, 13 were transplanted and 11 died. 164 patients gave urine of which 56 were hospitalized, 18 developed HE, 12 were transplanted and 11 died. Metabolomics: Saturated fatty acids, amino acids and bioenergetics-related metabolites differentiated patients with/without outcomes. After regression, 232, 228, 284 and 229 serum metabolites were significant for hospitalization, HE, death and transplant. In urine 290, 284, 227 & 285 metabolites were significant for hospitalization, HE, death and transplant respectively. AUC was higher for serum metabolites vs MELD for HE (0.85 vs.0.76), death (0.99 vs.0.88), transplant (0.975 vs.0.94) and hospitalizations (0.84 vs.0.83). Similarly, urinary metabolite AUC was also higher than MELD for HE (0.87 vs.0.72), death (0.92 vs 0.86), transplant (0.99 vs.0.90) and hospitalizations (0.89 vs.0.84). CONCLUSIONS In this exploratory study, serum and metabolites focused on lipid, bioenergetics and amino acid metabolism are altered in cirrhotics who develop negative outcomes.
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Jiang L, Chen L, Zhu L. Electrically conductive membranes for anti-biofouling in membrane distillation with two novel operation modes: Capacitor mode and resistor mode. WATER RESEARCH 2019; 161:297-307. [PMID: 31203035 DOI: 10.1016/j.watres.2019.06.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/29/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
This study evaluated the anti-biofouling efficacy of capacitor mode and resistor mode in membrane distillation (MD). Polytetrafluoroethylene (PTFE) membrane coated with carbon nanotube (CNT) was adopted as the electrically conductive membrane. The biofouling formation on the pre-treatment membrane was systematically analyzed, and the results showed that both operation modes had obvious inhabitation on bacteria, especially the capacitor mode exhibited stronger prevention capability on biomass accumulation than resistor mode. NMDs analysis of microbial communities further revealed that the anti-biofouling effect mainly occurred on the membrane surface, and gram-positive biomarkers which can survive better in external electric field was distinctively found in capacitor mode through LEfSE analysis. Hypothesis was introduced to explain the anti-fouling function of two modes that in the capacitor mode, the competitive electrostatic repulsion of bacteria cells on negative electrode associated by the cell-disruption effect of electro-catalyzed reactive oxygen species (ROS) generation, while the anti-fouling function of resistor mode was a result of temperature increment on membrane surface caused by Joule heating effects. This article attempts to provide an insight of anti-fouling mechanism of electric field applied in MD and to prove the feasibility of above-mentioned operation modes as non-chemical methods for optimization of membrane-based water treatment process.
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Affiliation(s)
- Longjie Jiang
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Lin Chen
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China.
| | - Liang Zhu
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
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Zhong H, Ren H, Lu Y, Fang C, Hou G, Yang Z, Chen B, Yang F, Zhao Y, Shi Z, Zhou B, Wu J, Zou H, Zi J, Chen J, Bao X, Hu Y, Gao Y, Zhang J, Xu X, Hou Y, Yang H, Wang J, Liu S, Jia H, Madsen L, Brix S, Kristiansen K, Liu F, Li J. Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics. EBioMedicine 2019; 47:373-383. [PMID: 31492563 PMCID: PMC6796533 DOI: 10.1016/j.ebiom.2019.08.048] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022] Open
Abstract
Background The gut microbiota plays important roles in modulating host metabolism. Previous studies have demonstrated differences in the gut microbiome of T2D and prediabetic individuals compared to healthy individuals, with distinct disease-related microbial profiles being reported in groups of different age and ethnicity. However, confounding factors such as anti-diabetic medication hamper identification of the gut microbial changes in disease development. Method We used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naïve type 2 diabetic (TN-T2D, n = 77), pre-diabetic (Pre-DM, n = 80), and normal glucose tolerant (NGT, n = 97) individuals to investigate compositional and functional changes of the gut microbiota and the faecal content of microbial and host proteins in Pre-DM and treatment-naïve T2D individuals to elucidate possible host-microbial interplays characterizing different disease stages. Findings We observed distinct differences characterizing the gut microbiota of these three groups and validated several key features in an independent TN-T2D cohort. We also demonstrated that the content of several human antimicrobial peptides and pancreatic enzymes differed in faecal samples between three groups. Interpretation Our findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and point to the value of metaproteomics to gain further insight into interplays between the gut microbiota and the host. Fund The study was supported by the National Natural Science Foundation of China (No. 31601073), the National Key Research and Development Program of China (No. 2017YFC0909703) and the Shenzhen Municipal Government of China (No. JCYJ20170817145809215). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Huanzi Zhong
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Huahui Ren
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Yan Lu
- Suzhou Centre for Disease Control and Prevention, Suzhou 215007, China
| | - Chao Fang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Guixue Hou
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Ziyi Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Bing Chen
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Fangming Yang
- BGI-Shenzhen, Shenzhen 518083, China; BGI Education Centre, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Yue Zhao
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Zhun Shi
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Baojin Zhou
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Jiegen Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hua Zou
- BGI-Shenzhen, Shenzhen 518083, China; BGI Education Centre, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Jiayu Chen
- China National GeneBank, Shenzhen 518120, China
| | - Xiao Bao
- China National GeneBank, Shenzhen 518120, China
| | - Yihe Hu
- Suzhou Centre for Disease Control and Prevention, Suzhou 215007, China
| | - Yan Gao
- Suzhou Centre for Disease Control and Prevention, Suzhou 215007, China
| | - Jun Zhang
- Suzhou Centre for Disease Control and Prevention, Suzhou 215007, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China
| | - Lise Madsen
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark; Institute of Marine Research, P.O. Box 7800, 5020 Bergen, Norway
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Fang Liu
- Suzhou Centre for Disease Control and Prevention, Suzhou 215007, China.
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, Shenzhen 518120, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
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Amornphimoltham P, Yuen PST, Star RA, Leelahavanichkul A. Gut Leakage of Fungal-Derived Inflammatory Mediators: Part of a Gut-Liver-Kidney Axis in Bacterial Sepsis. Dig Dis Sci 2019; 64:2416-2428. [PMID: 30863955 DOI: 10.1007/s10620-019-05581-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/06/2019] [Indexed: 02/07/2023]
Abstract
Sepsis is a life-threatening response to systemic infection. In addition to frank gastrointestinal (GI) rupture/puncture, sepsis can also be exacerbated by translocation of pathogen-associated molecular patterns (PAMPs) from the GI tract to the systemic circulation (gut origin of sepsis). In the human gut, Gram-negative bacteria and Candida albicans are abundant, along with their major PAMP components, endotoxin (LPS) and (1 → 3)-β-D-glucan (BG). Whereas the influence of LPS in bacterial sepsis has been studied extensively, exploration of the role of BG in bacterial sepsis is limited. Post-translocation, PAMPs enter the circulation through lymphatics and the portal vein, and are detoxified and then excreted via the liver and the kidney. Sepsis-induced liver and kidney injury might therefore affect the kinetics and increase circulating PAMPs. In this article, we discuss the current knowledge of the impact of PAMPs from both gut mycobiota and microbiota, including epithelial barrier function and the "gut-liver-kidney axis," on bacterial sepsis severity.
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Affiliation(s)
| | - Peter S T Yuen
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert A Star
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Asada Leelahavanichkul
- Immunology Unit, Department of Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand. .,Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Chulalongkorn University, Bangkok, Thailand.
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Koontz JM, Dancy BCR, Horton CL, Stallings JD, DiVito VT, Lewis JA. The Role of the Human Microbiome in Chemical Toxicity. Int J Toxicol 2019; 38:251-264. [PMID: 31220972 DOI: 10.1177/1091581819849833] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is overwhelming evidence that the microbiome must be considered when evaluating the toxicity of chemicals. Disruption of the normal microbial flora is a known effect of toxic exposure, and these disruptions may lead to human health effects. In addition, the biotransformation of numerous compounds has been shown to be dependent on microbial enzymes, with the potential for different host health outcomes resulting from variations in the microbiome. Evidence suggests that such metabolism of environmental chemicals by enzymes from the host's microbiota can affect the toxicity of that chemical to the host. Chemical-microbial interactions can be categorized into two classes: Microbiome Modulation of Toxicity (MMT) and Toxicant Modulation of the Microbiome (TMM). MMT refers to transformation of a chemical by microbial enzymes or metabolites to modify the chemical in a way that makes it more or less toxic. TMM is a change in the microbiota that results from a chemical exposure. These changes span a large magnitude of effects and may vary from microbial gene regulation, to inhibition of a specific enzyme, to the death of the microbes. Certain microbiomes or microbiota may become associated with different health outcomes, such as resistance or susceptibility to exposure to certain toxic chemicals, the ability to recover following a chemical-induced injury, the presence of disease-associated phenotypes, and the effectiveness of immune responses. Future work in toxicology will require an understanding of how the microbiome interacts with toxicants to fully elucidate how a compound will affect a diverse, real-world population.
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Affiliation(s)
- Jason M Koontz
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | - Blair C R Dancy
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | | | | | - Valerie T DiVito
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | - John A Lewis
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
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Association Between Intestinal Microbiota Collected at Hospital Admission and Outcomes of Patients With Cirrhosis. Clin Gastroenterol Hepatol 2019; 17:756-765.e3. [PMID: 30036646 DOI: 10.1016/j.cgh.2018.07.022] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Inpatients with cirrhosis are prone to develop acute-on-chronic liver failure (ACLF). ACLF is associated with dysbiosis of the intestinal microbiota, which might serve as a prognostic factor. We investigated whether features of the intestinal microbiota associate organ failure, transfer to intensive care, and mortality within 30 days in patients admitted to the hospital with cirrhosis. METHODS Stool samples were collected from 181 patients with cirrhosis (age 56 years; mean model for end-stage liver disease score, 21; 43% with infections) at time of admission, from multiple hospitals in North America. Patients were followed for 30 days for development of ACLF, extra-hepatic organ failures, and death or hospice care. Microbiota were analyzed by 16s rRNA sequencing for alpha diversity (within groups), beta diversity (between groups), cirrhosis dysbiosis ratio (CDR), and taxa that differed between groups with vs without negative outcomes (individual organ failures, transfer to intensive care, ACLF, death, or hospice). Regression analyses were performed using microbial and clinical variables for each outcome. RESULTS ACLF developed in 8% of study subjects; 16% were transferred to intensive care and 21% died. Beta diversity of the intestinal microbiome was significantly different, whereas alpha diversity was similar, between subjects with vs without outcomes. The CDR was lower in subjects who developed ACLF, especially among those with renal failure. Taxa belonging to phylum Proteobacteria (Enterobacteriaceae, Campylobacteriaceae, and Pasteurellaceae) and Firmicutes (Enterococcaceae and Streptococcaceae) were associated with development of negative outcomes, whereas other Firmicutes members (Lachnospiraceae and Clostridiales) reduced risk of negative outcomes. Changes in the microbiota associated with extra-hepatic organ failure, transfer to intensive care, ACLF, and death, independently on logistic regression analyses. CONCLUSION In hospitalized patients with cirrhosis, dysbiosis of the intestinal microbiota on admission (particularly changes in Protebacteria constituents) associates with increased risk of extra-hepatic organ failure, ACLF, and death, independent of clinical factors. Strategies to reduce gut dysbiosis might improve outcomes of patients with cirrhosis.
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Acharya C, Bajaj JS. Altered Microbiome in Patients With Cirrhosis and Complications. Clin Gastroenterol Hepatol 2019; 17:307-321. [PMID: 30099098 PMCID: PMC6314917 DOI: 10.1016/j.cgh.2018.08.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/06/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023]
Abstract
In patients with cirrhosis, the gut microbiome are affected by multiple gut and systemic alterations. These changes lead to dysbiosis in the microbiota of different parts of the body, resulting in inflammation. The constant immune stimulation resulting in part from dysbiosis is associated with morbidity in patients with cirrhosis. Dysbiosis as a dynamic event worsens with decompensation such as with hepatic encephalopathy, infections or acute-on-chronic liver failure (ACLF). These microbial patterns could be applied as diagnostic and prognostic measures in cirrhosis in the outpatient and inpatient setting. Current therapies for cirrhosis have differing impacts on gut microbial composition and functionality. Dietary modifications and the oral cavity have emerged as newer targetable factors to modulate the microbiome, which could affect inflammation and, potentially improve outcomes. Additionally, fecal microbial transplant is being increasingly studied to provide compositional and functional modulation of the microbiome. Ultimately, a combination of targeted therapies may be needed to provide an optimal gut milieu to improve outcomes in cirrhosis.
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