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Ullah Khan N, Sadiq A, Khan J, Basharat N, Hassan ZU, Ali I, Shah TA, Bourhia M, Bin Jardan YA, Wondmie GF. Molecular characterization of plasma virome of hepatocellular carcinoma (HCC) patients. AMB Express 2024; 14:46. [PMID: 38664337 PMCID: PMC11045709 DOI: 10.1186/s13568-024-01696-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the most common cancer type, arising from various causes, and responsible for a substantial number of cancer-related fatalities. Recent advancements in viral metagenomics have empowered scientists to delve into the intricate diversity of the virosphere, viral evolution, interactions between viruses and their hosts, and the identification of viral causes behind disease outbreaks, the development of specific symptoms, and their potential role in altering the host's physiology. The present study had the objective of "Molecular Characterization of HBV, HCV, anelloviruses, CMV, SENV-D, SENV-H, HEV, and HPV viruses among individuals suffering from HCC." A total of 381 HCC patients contributed 10 cc of blood each for this study. The research encompassed the assessment of tumor markers, followed by molecular characterization of HBV, HCV, Anelloviruses (TTV, TTMV, and TTMDV), SENV-H and SENV-D viruses, HEV, CMV, and HPV, as well as histopathological examinations. The outcomes of this study revealed that majority of the HCC patients 72.4% (276/381) were male as compared to females. HCV infection, at 76.4% (291 out of 381), exhibited a significant association (p < 0.05) with HCC. Most patients displayed singular lesions in the liver, with Child Pugh Score Type B being the predominant finding in 45.2% of cases. Plasma virome analysis indicated the prevalence of TTMDV (75%), followed by TTMV (70%) and TTV (42.1%) among anelloviruses in HCC patients. Similarly, SENV-H (52%) was followed by SENV-D (20%), with co-infections at 15%. The presence of CMV and HEV among the HCC patients was recorded 5% each however 3.5% of the patients showed the presence of HPV. In conclusion, this study underscores that HCC patients serve as reservoirs for various pathogenic and non-pathogenic viruses, potentially contributing to the development, progression, and severity of the disease.
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Affiliation(s)
- Niamat Ullah Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Asma Sadiq
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Jadoon Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan.
| | - Nosheen Basharat
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Zulfiqar Ul Hassan
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan
| | - Ijaz Ali
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
- Center for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, West Mishref, Kuwait
| | - Tawaf Ali Shah
- College of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, 80060, Morocco.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
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Peña Rodríguez M, Fagan A, Sikaroodi M, Gillevet PM, Bajaj JS. Proton Pump Inhibitor Use and Complications of Cirrhosis Are Linked With Distinct Gut Microbial Bacteriophage and Eukaryotic Viral-Like Particle Signatures in Cirrhosis. Clin Transl Gastroenterol 2024; 15:e00659. [PMID: 37937851 PMCID: PMC10887442 DOI: 10.14309/ctg.0000000000000659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
INTRODUCTION Proton pump inhibitors (PPIs) modulate the progression of cirrhosis to hepatic encephalopathy (HE) and can affect the bacterial microbiome. However, the impact of PPI on the virome in cirrhosis using viral-like particle (VLP) analysis is unclear. METHODS We determined the VLP in the stool microbiome in patients with cirrhosis cross-sectionally (ascites, HE, and PPI use analyzed) who were followed up for 6-month hospitalizations and through 2 clinical trials of PPI withdrawal and initiation. RESULTS In a cross-sectional study, PPI users had greater ascites prevalence and 6-month hospitalizations, but VLP α diversity was similar. Among phages, PPI users had lower Autographviridae and higher Streptococcus phages and Herelleviridae than nonusers, whereas opposite trends were seen in ascites and HE. Trends of eukaryotic viruses (higher Adenoviridae and lower Virgaviridae/Smacoviridae) were similar for PPI, HE, and ascites. Twenty-one percent were hospitalized, mostly due to HE. α Diversity was similar in the hospitalized/nonhospitalized/not groups. Higher Gokushovirinae and lower crAssphages were related to hospitalizations such as HE-related cross-sectional VLP changes. As part of the clinical trial, PPIs were added and withdrawn in 2 different decompensated groups over 14 days. No changes in α diversity were observed. Withdrawal reduced crAssphages, and initiation reduced Gokushovirinae and Bacteroides phages. DISCUSSION In cirrhosis, PPI use has a gut microbial VLP phage signature that is different from that in HE and ascites, and VLP changes are linked with hospitalizations over 6 months, independent of clinical biomarkers. Eukaryotic viral patterns were consistent across PPI use, HE, and ascites, indicating a relationship with the progression of cirrhosis. PPIs alone showed modest VLP changes with withdrawal or initiation. Distinct phage and eukaryotic viral patterns are associated with the use of PPIs in cirrhosis.
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Affiliation(s)
| | - Andrew Fagan
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | | | - Jasmohan S. Bajaj
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
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Wang X, Ding Z, Yang Y, Liang L, Sun Y, Hou C, Zheng Y, Xia Y, Dong L. ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data. Microb Genom 2024; 10:001202. [PMID: 38381034 PMCID: PMC10926697 DOI: 10.1099/mgen.0.001202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers seeking the most up-to-date tools. To address this, we present ViromeFlowX, a user-friendly Nextflow workflow that automates viral genome assembly, identification, classification, and annotation. This streamlined workflow integrates cutting-edge tools for processing raw sequencing data for taxonomic annotation and functional analysis. Application to a dataset of 200 metagenomic samples yielded high-quality viral genomes. ViromeFlowX enables efficient mining of viral genomic data, offering a valuable resource to investigate the gut virome's role in virus-host interactions and virus-related diseases.
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Affiliation(s)
- Xiaokai Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, PR China
| | | | - Ying Yang
- 01Life Institute, Shenzhen, PR China
| | | | | | - Chaojian Hou
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, PR China
| | | | - Yan Xia
- 01Life Institute, Shenzhen, PR China
| | - Lixin Dong
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, PR China
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Fujiki J, Schnabl B. Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases. JHEP Rep 2023; 5:100909. [PMID: 37965159 PMCID: PMC10641246 DOI: 10.1016/j.jhepr.2023.100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/16/2023] Open
Abstract
Phage therapy has been overshadowed by antibiotics for decades. However, it is being revisited as a powerful approach against antimicrobial-resistant bacteria. As bacterial microbiota have been mechanistically linked to gastrointestinal and liver diseases, precise editing of the gut microbiota via the selective bactericidal action of phages has prompted renewed interest in phage therapy. In this review, we summarise the basic virological properties of phages and the latest findings on the composition of the intestinal phageome and the changes associated with liver diseases. We also review preclinical and clinical studies assessing phage therapy for the treatment of gastrointestinal and liver diseases, as well as future prospects and challenges.
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Affiliation(s)
- Jumpei Fujiki
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
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Jinato T, Sikaroodi M, Fagan A, Sterling RK, Lee H, Puri P, Davis BC, Fuchs M, Gavis E, Gillevet PM, Bajaj JS. Alterations in gut virome are associated with cognitive function and minimal hepatic encephalopathy cross-sectionally and longitudinally in cirrhosis. Gut Microbes 2023; 15:2288168. [PMID: 38010871 PMCID: PMC10730154 DOI: 10.1080/19490976.2023.2288168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
Cognitive dysfunction due to minimal hepatic encephalopathy (MHE) adversely impacts patients with cirrhosis and more precise therapies are needed. Gut-brain axis changes are therapeutic targets, but prior studies have largely focused on bacterial changes. Our aim was to determine linkages between individual cognitive testing results and bacteria with the virome using a cross-sectional and longitudinal approach. We included cross-sectional (n = 138) and longitudinal analyses (n = 36) of patients with cirrhosis tested using three cognitive modalities, which were psychometric hepatic encephalopathy score (PHES), inhibitory control test (ICT), Stroop, and all three. Stool metagenomics with virome and bacteriome were analyzed studied cross-sectionally and in a subset followed for development/reversal of MHE repeated at 6 months (longitudinally only using PHES). Cross-sectional: We found no significant changes in α/β diversity in viruses or bacteria regardless of cognitive testing. Cognitively impaired patients were more likely to have higher relative abundance of bacteriophages linked with Streptococcus, Faecalibacterium, and Lactobacillus, which were distinct based on modality. These were also linked with cognition on correlation networks. Longitudinally, 27 patients remained stable while 9 changed their MHE status. Similar changes in phages that are linked with Streptococcus, Faecalibacterium, and Lactobacillus were seen. These phages can influence ammonia, lactate, and short-chain fatty acid generation, which are neuro-active. In conclusion, we found linkages between bacteriophages and cognitive function likely due to impact on bacteria that produce neuroactive metabolites cross-sectionally and longitudinally. These findings could help explore bacteriophages as options to influence treatment for MHE in cirrhosis.
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Affiliation(s)
- Thananya Jinato
- Microbiome Analysis Center, George Mason University, Manassas, VA, USA
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Richard K Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Hannah Lee
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Puneet Puri
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Brian C Davis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
| | | | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA
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6
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Abstract
The trillions of microorganisms in the human intestine are important regulators of health, and disruptions in the gut microbial communities can cause disease. The gut, liver and immune system have a symbiotic relationship with these microorganisms. Environmental factors, such as high-fat diets and alcohol consumption, can disrupt and alter microbial communities. This dysbiosis can lead to dysfunction of the intestinal barrier, translocation of microbial components to the liver and development or progression of liver disease. Changes in metabolites produced by gut microorganisms can also contribute to liver disease. In this Review, we discuss the importance of the gut microbiota in maintenance of health and the alterations in microbial mediators that contribute to liver disease. We present strategies for modulation of the intestinal microbiota and/or their metabolites as potential treatments for liver disease.
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Affiliation(s)
- Cynthia L Hsu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
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7
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Aghara H, Chadha P, Zala D, Mandal P. Stress mechanism involved in the progression of alcoholic liver disease and the therapeutic efficacy of nanoparticles. Front Immunol 2023; 14:1205821. [PMID: 37841267 PMCID: PMC10570533 DOI: 10.3389/fimmu.2023.1205821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
Alcoholic liver disease (ALD) poses a significant threat to human health, with excessive alcohol intake disrupting the immunotolerant environment of the liver and initiating a cascade of pathological events. This progressive disease unfolds through fat deposition, proinflammatory cytokine upregulation, activation of hepatic stellate cells, and eventual development of end-stage liver disease, known as hepatocellular carcinoma (HCC). ALD is intricately intertwined with stress mechanisms such as oxidative stress mediated by reactive oxygen species, endoplasmic reticulum stress, and alcohol-induced gut dysbiosis, culminating in increased inflammation. While the initial stages of ALD can be reversible with diligent care and abstinence, further progression necessitates alternative treatment approaches. Herbal medicines have shown promise, albeit limited by their poor water solubility and subsequent lack of extensive exploration. Consequently, researchers have embarked on a quest to overcome these challenges by delving into the potential of nanoparticle-mediated therapy. Nanoparticle-based treatments are being explored for liver diseases that share similar mechanisms with alcoholic liver disease. It underscores the potential of these innovative approaches to counteract the complex pathogenesis of ALD, providing new avenues for therapeutic intervention. Nevertheless, further investigations are imperative to fully unravel the therapeutic potential and unlock the promise of nanoparticle-mediated therapy specifically tailored for ALD treatment.
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Affiliation(s)
| | | | | | - Palash Mandal
- P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, Gujarat, India
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8
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Aghara H, Chadha P, Zala D, Mandal P. Stress mechanism involved in the progression of alcoholic liver disease and the therapeutic efficacy of nanoparticles. Front Immunol 2023; 14. [DOI: https:/doi.org/10.3389/fimmu.2023.1205821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Alcoholic liver disease (ALD) poses a significant threat to human health, with excessive alcohol intake disrupting the immunotolerant environment of the liver and initiating a cascade of pathological events. This progressive disease unfolds through fat deposition, proinflammatory cytokine upregulation, activation of hepatic stellate cells, and eventual development of end-stage liver disease, known as hepatocellular carcinoma (HCC). ALD is intricately intertwined with stress mechanisms such as oxidative stress mediated by reactive oxygen species, endoplasmic reticulum stress, and alcohol-induced gut dysbiosis, culminating in increased inflammation. While the initial stages of ALD can be reversible with diligent care and abstinence, further progression necessitates alternative treatment approaches. Herbal medicines have shown promise, albeit limited by their poor water solubility and subsequent lack of extensive exploration. Consequently, researchers have embarked on a quest to overcome these challenges by delving into the potential of nanoparticle-mediated therapy. Nanoparticle-based treatments are being explored for liver diseases that share similar mechanisms with alcoholic liver disease. It underscores the potential of these innovative approaches to counteract the complex pathogenesis of ALD, providing new avenues for therapeutic intervention. Nevertheless, further investigations are imperative to fully unravel the therapeutic potential and unlock the promise of nanoparticle-mediated therapy specifically tailored for ALD treatment.
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9
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Ichikawa M, Nakamoto N, Kredo-Russo S, Weinstock E, Weiner IN, Khabra E, Ben-Ishai N, Inbar D, Kowalsman N, Mordoch R, Nicenboim J, Golembo M, Zak N, Jablonska J, Sberro-Livnat H, Navok S, Buchshtab N, Suzuki T, Miyamoto K, Teratani T, Fujimori S, Aoto Y, Konda M, Hayashi N, Chu PS, Taniki N, Morikawa R, Kasuga R, Tabuchi T, Sugimoto S, Mikami Y, Shiota A, Bassan M, Kanai T. Bacteriophage therapy against pathological Klebsiella pneumoniae ameliorates the course of primary sclerosing cholangitis. Nat Commun 2023; 14:3261. [PMID: 37277351 DOI: 10.1038/s41467-023-39029-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
Primary sclerosing cholangitis (PSC) is characterized by progressive biliary inflammation and fibrosis. Although gut commensals are associated with PSC, their causative roles and therapeutic strategies remain elusive. Here we detect abundant Klebsiella pneumoniae (Kp) and Enterococcus gallinarum in fecal samples from 45 PSC patients, regardless of intestinal complications. Carriers of both pathogens exhibit high disease activity and poor clinical outcomes. Colonization of PSC-derived Kp in specific pathogen-free (SPF) hepatobiliary injury-prone mice enhances hepatic Th17 cell responses and exacerbates liver injury through bacterial translocation to mesenteric lymph nodes. We developed a lytic phage cocktail that targets PSC-derived Kp with a sustained suppressive effect in vitro. Oral administration of the phage cocktail lowers Kp levels in Kp-colonized germ-free mice and SPF mice, without off-target dysbiosis. Furthermore, we demonstrate that oral and intravenous phage administration successfully suppresses Kp levels and attenuates liver inflammation and disease severity in hepatobiliary injury-prone SPF mice. These results collectively suggest that using a lytic phage cocktail shows promise for targeting Kp in PSC.
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Affiliation(s)
- Masataka Ichikawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Takahiro Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Sota Fujimori
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Yoshimasa Aoto
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., Tokyo, Japan
| | - Mikiko Konda
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., Tokyo, Japan
| | - Naoki Hayashi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., Tokyo, Japan
| | - Po-Sung Chu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Nobuhito Taniki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Rei Morikawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Ryosuke Kasuga
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Takaya Tabuchi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Shinya Sugimoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Atsushi Shiota
- Department of Microbiology and Immunology, Keio University, Tokyo, Japan
- Microbiopharm Japan, Co. Ltd., Tokyo, Japan
| | | | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University, Tokyo, Japan.
- Japan Agency for Medical Research and Development, AMED, Tokyo, Japan.
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10
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Chen X, Mendes BG, Alves BS, Duan Y. Phage therapy in gut microbiome. Prog Mol Biol Transl Sci 2023; 201:93-118. [PMID: 37770177 DOI: 10.1016/bs.pmbts.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phage therapy, the use of bacteriophage viruses for bacterial infection treatment, has been around for almost a century, but with the increase in antibiotic use, its importance has declined rapidly. There has been renewed interest in revisiting this practice due to the general decline in the effectiveness of antibiotics, combined with improved understanding of human microbiota and advances in sequencing technologies. Phage therapy has been proposed as a clinical alternative to restore the gut microbiota in the absence of an effective treatment. That is due to its immunomodulatory and bactericidal effects against its target bacteria. In the gastrointestinal diseases field, phage therapy has been studied mainly as a promising tool in infectious diseases treatment, such as cholera and diarrhea. However, many studies have been conducted in non-communicable diseases, such as the targeting of adherent invasive Escherichia coli in Crohn's disease, the treatment of Clostridioides difficile in ulcerative colitis, the eradication of Fusobacterium nucleatum in colorectal cancer, the targeting of alcohol-producing Klebsiella pneumoniae in non-alcoholic fatty liver disease, or Enterococcus faecalis in alcohol-associated hepatitis. This review will summarize the changes in the gut microbiota and the phageome in association with some gastrointestinal and liver diseases and highlight the recent scientific advances in phage therapy as a therapeutic tool for their treatment.
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Affiliation(s)
- Xingyao Chen
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Beatriz G Mendes
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Campus Universitário Trindade, Florianópolis, Santa Catarina, Brazil
| | - Bruno Secchi Alves
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Campus Universitário Trindade, Florianópolis, Santa Catarina, Brazil
| | - Yi Duan
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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11
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Chen L, Hou X, Chu H. The Novel Role of Phage Particles in Chronic Liver Diseases. Microorganisms 2023; 11:1181. [PMID: 37317156 DOI: 10.3390/microorganisms11051181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 06/16/2023] Open
Abstract
The gut microbiome is made up of bacteria, fungi, viruses and archaea, all of which are closely related with human health. As the main component of enterovirus, the role of bacteriophages (phages) in chronic liver disease has been gradually recognized. Chronic liver diseases, including alcohol-related liver disease and nonalcoholic fatty liver disease, exhibit alterations of the enteric phages. Phages shape intestinal bacterial colonization and regulate bacterial metabolism. Phages adjoining to intestinal epithelial cells prevent bacteria from invading the intestinal barrier, and mediate intestinal inflammatory response. Phages are also observed increasing intestinal permeability and migrating to peripheral blood and organs, likely contributing to inflammatory injury in chronic liver diseases. By preying on harmful bacteria, phages can improve the gut microbiome of patients with chronic liver disease and thus act as an effective treatment method.
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Affiliation(s)
- Liuying Chen
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Huikuan Chu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
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12
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Abstract
Primary sclerosing cholangitis (PSC) offers unique opportunities to explore the gut-liver axis owing to the close association between liver disease and colonic inflammation. It is well established that the gut microbiota in people with PSC differs from that of healthy individuals, but details of the microbial factors that demarcate PSC from inflammatory bowel disease (IBD) without PSC are poorly understood. In this Review, we aim to provide an overview of the latest literature on the gut microbiome in PSC and PSC with IBD, critically examining hypotheses on how microorganisms could contribute to the pathogenesis of PSC. A particular emphasis will be put on pathogenic features of the gut microbiota that might explain the occurrence of bile duct inflammation and liver disease in the context of IBD, and we postulate the potential existence of a specific yet unknown factor related to the gut-liver axis as causative in PSC. Available data are scrutinized in the perspective of therapeutic approaches related to the gut-liver axis.
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Affiliation(s)
- Johannes R Hov
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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13
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Morrison MA, Artru F, Trovato FM, Triantafyllou E, McPhail MJ. Potential therapies for acute-on-chronic liver failure. Liver Int 2023. [PMID: 36800487 DOI: 10.1111/liv.15545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Acute-on-chronic liver failure (ACLF) is a syndrome that develops in approximately 30% of patients hospitalised with cirrhosis and is characterised by an acute decompensation of liver function associated with extra-hepatic organ failures and a high short-term mortality. At present, no specific therapies are available for ACLF, and current management is limited to treatment of the precipitating event and organ support. Given the high prevalence and high mortality of this severe liver disease, there is an urgent need for targeted treatments. There is increasing evidence of the important role played by systemic inflammation and immune dysfunction in the pathophysiology of ACLF and a better understanding of these immune processes is resulting in new therapeutic targets. The aim of this review is to present an overview of ongoing studies of potentially promising therapies and how they could be utilised in the management of ACLF.
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Affiliation(s)
- Maura A Morrison
- Institute of Liver Studies, King's College Hospital, London, UK
- Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Florent Artru
- Institute of Liver Studies, King's College Hospital, London, UK
- Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Francesca M Trovato
- Institute of Liver Studies, King's College Hospital, London, UK
- Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Evangelos Triantafyllou
- Section of Hepatology and Gastroenterology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Mark J McPhail
- Institute of Liver Studies, King's College Hospital, London, UK
- Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK
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14
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Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023; 186:17-31. [PMID: 36608652 PMCID: PMC9827498 DOI: 10.1016/j.cell.2022.11.017] [Citation(s) in RCA: 103] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill the bacterial host efficiently, and (3) be fully characterized to exclude side effects. Developing therapeutic phages takes a coordinated effort of multiple stakeholders. Herein, we review the state of the art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
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Affiliation(s)
- Steffanie A Strathdee
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA
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15
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Koning M, Herrema H, Nieuwdorp M, Meijnikman AS. Targeting nonalcoholic fatty liver disease via gut microbiome-centered therapies. Gut Microbes 2023; 15:2226922. [PMID: 37610978 PMCID: PMC10305510 DOI: 10.1080/19490976.2023.2226922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/25/2023] Open
Abstract
Humans possess abundant amounts of microorganisms, including bacteria, fungi, viruses, and archaea, in their gut. Patients with nonalcoholic fatty liver disease (NAFLD) exhibit alterations in their gut microbiome and an impaired gut barrier function. Preclinical studies emphasize the significance of the gut microbiome in the pathogenesis of NAFLD. In this overview, we explore how adjusting the gut microbiome could serve as an innovative therapeutic strategy for NAFLD. We provide a summary of current information on untargeted techniques such as probiotics and fecal microbiota transplantation, as well as targeted microbiome-focused therapies including engineered bacteria, prebiotics, postbiotics, and phages for the treatment of NAFLD.
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Affiliation(s)
- Mijra Koning
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences Diabetes, Amsterdam, The Netherlands
| | - Hilde Herrema
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
- Amsterdam Gastroenterology and Metabolism, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences Diabetes, Amsterdam, The Netherlands
| | - Abraham S. Meijnikman
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences Diabetes, Amsterdam, The Netherlands
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16
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Tang W, Yuan M, Li Z, Lin Q, Zhen Y, Li Z, Zhou H, Xia F. Polyphenol-Rich Liupao Tea Extract Prevents High-Fat Diet-Induced MAFLD by Modulating the Gut Microbiota. Nutrients 2022; 14. [PMID: 36432617 DOI: 10.3390/nu14224930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The modulation of gut microbiota dysbiosis might regulate the progression of metabolic-associated fatty liver disease (MAFLD). Here, we found that polyphenol-rich Liupao tea extract (PLE) prevents high-fat diet (HFD)-induced MAFLD in ApoE-/- male mice accompanied by protection of the intestinal barrier and downregulation of lipopolysaccharide (LPS)-related Toll-like receptor 4 (TLR4)-myeloid differentiation primary response 88 (MyD88) signaling in the liver. Fecal microbiome transplantation (FMT) from PLE-and-HFD-treated mice delayed MAFLD development significantly compared with FMT from HFD-treated mice. In this case, 16S rRNA gene sequencing revealed that Rikenellaceae and Odoribacter were significantly enriched and that Helicobacter was significantly decreased in not only the HFD+PLE group but also the HFD+PLE-FMT group. Furthermore, the level of 3-sulfodeoxycholic acid was significantly decreased in the HFD+PLE-FMT group compared with the HFD-FMT group. In conclusion, our data demonstrate that PLE could modulate the MAFLD phenotype in mice and that this effect is partly mediated through modulation of the gut microbiota.
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17
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Abstract
Diarrhea caused by early-weaning-induced stress can increase mortality rates and reduce growth performance of piglets, seriously harming the livestock industry. To date, studies on the gut microbiome of early-weaned piglets have focused almost exclusively on bacteria, while studies on their gut virome are extremely lacking. Here, we used metagenomic and metatranscriptomic sequencing combined with bioinformatic analysis techniques to preliminarily characterize the intestinal virome of early-weaned piglets at different biological classification levels. The alpha diversity of enteroviruses was generally elevated in early-weaned piglets with diarrhea, compared to healthy piglets, whereas the two groups of piglets showed no significant difference in beta diversity. In addition, the species compositions of the gut virome were similar between healthy piglets and piglets with diarrhea, while their respective dominant species were somewhat different. We also identified 58 differential DNA viruses and 16 differential RNA viruses between the two groups of piglets at all biological taxonomic levels. Of these, 1 (family Dhakavirus) and 6 (phylum Artverviricota, class Revtraviricetes, order Ortervirales, family Retroviridae, genus Gammaretrovirus, and species Kirsten murine sarcoma virus) specific viruses disappeared from the intestines of healthy piglets and piglets with diarrhea, respectively. Moreover, we found that some DNA and RNA viruses formed strong correlations among themselves or between them. IMPORTANCE This study systematically reveals the biological diversity, structure, and composition of intestinal DNA and RNA virus profiles in early-weaned piglets. Furthermore, characteristics of differences in gut viromes between early-weaned healthy piglets and piglets with diarrhea were also elucidated. Importantly, some potential biomarkers for early-weaned piglets with diarrhea were identified. These findings fill a gap for the early-weaned piglet gut virome and lay the foundation for the development of strategies to target enteroviruses for the prevention and treatment of early-weaning-induced piglet diarrhea.
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Affiliation(s)
- Shiyu Tao
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huicong Zou
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Li
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong Wei
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
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18
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Chou S, Zhang S, Guo H, Chang YF, Zhao W, Mou X. Targeted Antimicrobial Agents as Potential Tools for Modulating the Gut Microbiome. Front Microbiol 2022; 13:879207. [PMID: 35875544 PMCID: PMC9302920 DOI: 10.3389/fmicb.2022.879207] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 06/13/2022] [Indexed: 12/11/2022] Open
Abstract
The gut microbiome plays a pivotal role in maintaining the health of the hosts; however, there is accumulating evidence that certain bacteria in the host, termed pathobionts, play roles in the progression of diseases. Although antibiotics can be used to eradicate unwanted bacteria, the side effects of antibiotic treatment lead to a great need for more targeted antimicrobial agents as tools to modulate the microbiome more precisely. Herein, we reviewed narrow-spectrum antibiotics naturally made by plants and microorganisms, followed by more targeted antibiotic agents including synthetic peptides, phage, and targeted drug delivery systems, from the perspective of using them as potential tools for modulating the gut microbiome for favorable effects on the health of the host. Given the emerging discoveries on pathobionts and the increasing knowledge on targeted antimicrobial agents reviewed in this article, we anticipate targeted antimicrobial agents will emerge as a new generation of a drug to treat microbiome-involved diseases.
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Affiliation(s)
- Shuli Chou
- Center for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shiqing Zhang
- Center for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Huating Guo
- Center for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yung-fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Wenjing Zhao
- Center for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- *Correspondence: Wenjing Zhao, ;
| | - Xiangyu Mou
- Center for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Xiangyu Mou,
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Li Y, Cao L, Ye M, Xu R, Chen X, Ma Y, Tian RR, Liu FL, Zhang P, Kuang YQ, Zheng YT, Zhang C. Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections. Microbiol Spectr 2022;:e0144722. [PMID: 35758682 DOI: 10.1128/spectrum.01447-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intravenous drug users (IDUs) are a high-risk group for HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, which are the leading causes of death in IDUs. However, the plasma virome of IDUs and how it is influenced by above viral infections remain unclear. Using viral metagenomics, we determined the plasma virome of IDUs and its association with HIV-1, HCV, and/or HBV infections. Compared with healthy individuals, IDUs especially those with major viral infections had higher viral abundance and diversity. Anelloviridae dominated plasma virome. Coinfections of multiple anelloviruses were common, and anelloviruses from the same genus tended to coexist together. In this study, 4,487 anellovirus ORF1 sequences were identified, including 1,620 (36.1%) with less than 69% identity to any known sequences, which tripled the current number. Compared with healthy controls (HC), more anellovirus sequences were observed in neg-IDUs, and HIV-1, HCV, and/or HBV infections further expanded the sequence number in IDUs, which was characterized by the emergence of novel divergent taxons and blooms of resident anelloviruses. Pegivirus was mainly identified in infected IDUs. Five main pegivirus transmission clusters (TCs) were identified by phylogenetic analysis, suggesting a transmission link. Similar anellovirus profiles were observed in IDUs within the same TC, suggesting transmission of anellome among IDUs. Our data suggested that IDUs suffered higher plasma viral burden especially anelloviruses, which was associated with HIV-1, HCV, and/or HBV infections. Blooms in abundance and unprecedented diversity of anellovirus highlighted active evolution and replication of this virus in blood circulation, and an uncharacterized role it may engage with the host. IMPORTANCE Virome is associated with immune status and determines or influences disease progression through both pathogenic and resident viruses. Increased viral burden in IDUs especially those with major viral infections indicated the suboptimal immune status and high infection risks of these population. Blooms in abundance and unprecedented diversity of anellovirus highlighted its active evolution and replication in the blood circulation, and sensitive response to other viral infections. In addition, transmission cluster analysis revealed the transmission link of pegivirus among IDUs, and the individuals with transmission links shared similar anellome profiles. In-depth monitoring of the plasma virome in high-risk populations is not only needed for surveillance for emerging viruses and transmission networks of major and neglected bloodborne viruses, but also important for a better understanding of commensal viruses and their role it may engage with immune system.
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20
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Abstract
Humans harbour large quantities of microbes, including bacteria, fungi, viruses and archaea, in the gut. Patients with liver disease exhibit changes in the intestinal microbiota and gut barrier dysfunction. Preclinical models demonstrate the importance of the gut microbiota in the pathogenesis of various liver diseases. In this review, we discuss how manipulation of the gut microbiota can be used as a novel treatment approach for liver disease. We summarise current data on untargeted approaches, including probiotics and faecal microbiota transplantation, and precision microbiome-centered therapies, including engineered bacteria, postbiotics and phages, for the treatment of liver diseases.
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Affiliation(s)
- Jasmohan S Bajaj
- Department of Medicine, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA.
| | - Siew C Ng
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong; Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
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21
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Manzoor R, Ahmed W, Afify N, Memon M, Yasin M, Memon H, Rustom M, Al Akeel M, Alhajri N. Trust Your Gut: The Association of Gut Microbiota and Liver Disease. Microorganisms 2022; 10:1045. [PMID: 35630487 PMCID: PMC9146349 DOI: 10.3390/microorganisms10051045] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/08/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota composition is important for nutrient metabolism, mucosal barrier function, immunomodulation, and defense against pathogens. Alterations in the gut microbiome can disturb the gut ecosystem. These changes may lead to the loss of beneficial bacteria or an increase in potentially pathogenic bacteria. Furthermore, these have been shown to contribute to the pathophysiology of gastrointestinal and extra-intestinal diseases. Pathologies of the liver, such as non-alcoholic liver disease, alcoholic liver disease, cirrhosis, hepatocellular carcinoma, autoimmune hepatitis, viral hepatitis, and primary sclerosing cholangitis have all been linked to changes in the gut microbiome composition. There is substantial evidence that links gut dysbiosis to the progression and complications of these pathologies. This review article aimed to describe the changes seen in the gut microbiome in liver diseases and the association between gut dysbiosis and liver disease, and finally, explore treatment options that may improve gut dysbiosis in patients with liver disease.
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Affiliation(s)
- Ridda Manzoor
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates; (R.M.); (W.A.); (N.A.); (M.M.); (M.Y.); (H.M.); (M.R.)
| | - Weshah Ahmed
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates; (R.M.); (W.A.); (N.A.); (M.M.); (M.Y.); (H.M.); (M.R.)
| | - Nariman Afify
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates; (R.M.); (W.A.); (N.A.); (M.M.); (M.Y.); (H.M.); (M.R.)
| | - Mashal Memon
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates; (R.M.); (W.A.); (N.A.); (M.M.); (M.Y.); (H.M.); (M.R.)
| | - Maryam Yasin
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates; (R.M.); (W.A.); (N.A.); (M.M.); (M.Y.); (H.M.); (M.R.)
| | - Hamda Memon
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates; (R.M.); (W.A.); (N.A.); (M.M.); (M.Y.); (H.M.); (M.R.)
| | - Mohammad Rustom
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates; (R.M.); (W.A.); (N.A.); (M.M.); (M.Y.); (H.M.); (M.R.)
| | - Mohannad Al Akeel
- Division of Family Medicine, Department of Health, Abu Dhabi P.O. Box 5674, United Arab Emirates;
| | - Noora Alhajri
- Department of Medicine, Sheikh Shakhbout Medical City (SSMC), Abu Dhabi P.O. Box 11001, United Arab Emirates
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22
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Xia Y, Shi H, Qian C, Han H, Lu K, Tao R, Gu R, Zhao Y, Wei Z, Lu Y. Modulation of Gut Microbiota by Magnesium Isoglycyrrhizinate Mediates Enhancement of Intestinal Barrier Function and Amelioration of Methotrexate-Induced Liver Injury. Front Immunol 2022; 13:874878. [PMID: 35634319 PMCID: PMC9134347 DOI: 10.3389/fimmu.2022.874878] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
Background The gut–liver axis plays a crucial role in various liver diseases. Therefore, targeting this crosstalk may provide a new treatment strategy for liver diseases. However, the exact mechanism underlying this crosstalk and its impact on drug-induced liver injury (DILI) requires clarification. Aim This study aimed to investigate the potential mechanism and therapeutic effect of MgIG on MTX-induced liver injury, which is associated with the gut–liver axis and gut microbiota. Methods An MTX-induced liver injury model was generated after 20-mg/kg/3d MTX application for 30 days. Meanwhile, the treatment group was treated with 40-mg/kg MgIG daily. Histological examination, aminotransferase, and aspartate aminotransferase enzyme levels were estimated to evaluate liver function. Immune cells infiltration and inflammatory cytokines were detected to indicate inflammation levels. Colon histological score, intestinal barrier leakage, and expression of tight junctions were employed to assess the intestinal injury. Bacterial translocation was observed using fluorescent in situ hybridisation, colony-forming unit counting, and lipopolysaccharide detection. Alterations in gut microbial composition were analysed using 16s rDNA sequencing and relative quantitative polymerase chain reaction. Short-chain-fatty-acids and lactic acid concentrations were then utilized to validate changes in metabolites of specific bacteria. Lactobacillus sp. supplement and fecal microbiota transplantation were used to evaluate gut microbiota contribution. Results MTX-induced intestinal and liver injuries were significantly alleviated using MgIG treatment. Bacterial translocation resulting from the intestinal barrier disruption was considered a crucial cause of MTX-induced liver injury and the therapeutic target of MgIG. Moreover, MgIG was speculated to have changed the gut microbial composition by up-regulating probiotic Lactobacillus and down-regulating Muribaculaceae, thereby remodelling the intestinal barrier and inhibiting bacterial translocation. Conclusion The MTX-induced intestinal barrier was protected owing to MgIG administration, which reshaped the gut microbial composition and inhibited bacterial translocation into the liver, thus attenuating MTX-related DILI.
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Affiliation(s)
- Yawen Xia
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hang Shi
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Cheng Qian
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongkuan Han
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Keqin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ruizhi Tao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Renjun Gu
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Zhao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Provincial Second Chinese Medicine Hospital, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhonghong Wei
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Zhonghong Wei, ; Yin Lu,
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Zhonghong Wei, ; Yin Lu,
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Abstract
Nonalcoholic fatty liver disease (NAFLD) describes a spectrum of progressive liver diseases ranging from simple steatosis to steatohepatitis and fibrosis. Globally, NAFLD is the leading cause of morbidity and mortality associated with chronic liver disease, and NAFLD patients are at a higher risk of developing cirrhosis and hepatocellular carcinoma. While there is a consensus that inflammation plays a key role in promoting NAFLD progression, the underlying mechanisms are not well understood. Recent clinical and experimental evidence suggest that increased hepatic translocation of gut microbial antigens, secondary to diet-induced impairment of the intestinal barrier may be important in driving hepatic inflammation in NAFLD. Here, we briefly review various endogenous and exogenous factors influencing the intestinal barrier and present recent advances in our understanding of cellular and molecular mechanisms underlying intestinal barrier dysfunction in NAFLD.
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Affiliation(s)
- Biki Gupta
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ravi Rai
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael Oertel
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania,McGowan Institute for Regenerative Medicine, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Reben Raeman
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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24
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Zhou Y, Liu M, Yang J. Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: methods, applications, challenges, and opportunities. Microbiol Res 2022; 260:127023. [DOI: 10.1016/j.micres.2022.127023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/07/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
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25
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Sam Ma Z, Mei J. Stochastic neutral drifts seem prevalent in driving human virome assembly: neutral, near-neutral and non-neutral theoretic analyses. Comput Struct Biotechnol J 2022; 20:2029-2041. [PMID: 35521546 PMCID: PMC9065738 DOI: 10.1016/j.csbj.2022.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 11/26/2022] Open
Abstract
It is estimated that human body is inhabited by approximately 380 trillions of viruses, which exist in the form of viral communities and are collectively termed as human virome. How virome is assembled and what kind of forces maintain the composition and diversity of viral communities is still an open question. The question is of obvious importance because of its implications to human health and diseases. Here we address the question by harnessing the power of Hubbell’s unified neutral theory of biodiversity (UNTB) in terms of three neutral models including standard Hubbell’s neutral model (HNM), Sloan’s near-neutral model (SNM) and Harris et al. (2017) multi-site neutral model (MSN), further augmented by Ning et al. (2019) normalized stochasticity ratio (NSR) and Hammal et al. (2015) power analysis for the neutral test (PNT). With the five models applied to 179 virome samples, we aim to obtain robust findings given both Type-I and Type-II errors are addressed and possible alternative, non-neutral processes are detected. It was found that stochastic neutral drifts seem prevalent: approximately 65–92% at metacommunity/landscape scales and 67–80% at virus species scale. The non-neutral selection is approximately 26–28% at community scale and 23% at species scale. The false negative rate is about 2–3%, which suggested rather limited confounding effects of non-neutral process on neutrality tests. We postulate that prevalence of neutrality in human virome is likely due to extremely simple structure of viruses (stands of DNA/RNA) and their inter-species homogeneities, forming the foundation of species equivalence—the hallmark of neutral theory.
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Abstract
Abstract
Bacteriophages are viruses infecting bacteria and propagating in bacterial cells. They were discovered over 100 years ago, and for decades they played crucial roles as models in genetics and molecular biology and as tools in genetic engineering and biotechnology. Now we also recognize their huge role in natural environment and their importance in human health and disease. Despite our understanding of bacteriophage mechanisms of development, these viruses are described as parasites or predators in the literature. From the biological point of view, there are fundamental differences between parasites and predators. Therefore, in this article, I asked whether bacteriophages should be classified as former or latter biological entities. Analysis of the literature and biological definitions led me to conclude that bacteriophages are parasites rather than predators and should be classified and described as such. If even more precise ecological classification is needed, bacteriophages can perhaps be included in the group of parasitoids. It might be the most appropriate formal classification of these viruses, especially if strictly virulent phages are considered, contrary to phages which lysogenize host cells and those which develop according to the permanent infection mode (or chronic cycle, like filamentous phages) revealing features of classical parasites.
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Affiliation(s)
- Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology , University of Gdańsk , Gdańsk , Poland
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