Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease.
Alcoholism
/ complications
Animals
Bacteriophages
/ physiology
Enterococcus faecalis
/ isolation & purification
Ethanol
/ adverse effects
Fatty Liver
/ complications
Feces
/ microbiology
Female
Gastrointestinal Microbiome
Germ-Free Life
Hepatitis, Alcoholic
/ complications
Hepatocytes
/ drug effects
Humans
Liver
/ drug effects
Male
Mice
Mice, Inbred C57BL
Perforin
/ metabolism
Phage Therapy
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
11 2019
11 2019
Historique:
received:
09
04
2019
accepted:
02
10
2019
pubmed:
15
11
2019
medline:
22
4
2020
entrez:
15
11
2019
Statut:
ppublish
Résumé
Chronic liver disease due to alcohol-use disorder contributes markedly to the global burden of disease and mortality
Identifiants
pubmed: 31723265
doi: 10.1038/s41586-019-1742-x
pii: 10.1038/s41586-019-1742-x
pmc: PMC6872939
mid: NIHMS1540838
doi:
Substances chimiques
Perforin
126465-35-8
Ethanol
3K9958V90M
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
505-511Subventions
Organisme : NIAAA NIH HHS
ID : R01 AA020703
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001863
Pays : United States
Organisme : BLRD VA
ID : I01 BX004594
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK120515
Pays : United States
Organisme : NIAAA NIH HHS
ID : R01 AA024726
Pays : United States
Organisme : Wellcome Trust
ID : 093869
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : T32 GM070421
Pays : United States
Organisme : NIAAA NIH HHS
ID : P50 AA011999
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIDDK NIH HHS
ID : P30 DK034989
Pays : United States
Organisme : NIAAA NIH HHS
ID : U01 AA026939
Pays : United States
Organisme : NIAAA NIH HHS
ID : U01 AA021908
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK120531
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : CommentIn
Type : CommentIn
Type : CommentIn
Type : CommentIn
Références
Lozano, R. et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 380, 2095–2128 (2012).
pubmed: 23245604
pmcid: 23245604
Lee, B. P., Vittinghoff, E., Dodge, J. L., Cullaro, G. & Terrault, N. A. National trends and long-term outcomes of liver transplant for alcohol-associated liver disease in the United States. JAMA Intern. Med. 179, 340–348 (2019).
pubmed: 30667468
pmcid: 6439700
Rehm, J. et al. Burden of disease associated with alcohol use disorders in the United States. Alcohol. Clin. Exp. Res. 38, 1068–1077 (2014).
pubmed: 24428196
pmcid: 4147870
Llopis, M. et al. Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease. Gut 65, 830–839 (2016).
pubmed: 26642859
Ike, Y., Clewell, D. B., Segarra, R. A. & Gilmore, M. S. Genetic analysis of the pAD1 hemolysin/bacteriocin determinant in Enterococcus faecalis: Tn917 insertional mutagenesis and cloning. J. Bacteriol. 172, 155–163 (1990).
pubmed: 2152897
pmcid: 208413
Tang, W. & van der Donk, W. A. The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry. Nat. Chem. Biol. 9, 157–159 (2013).
pubmed: 23314913
pmcid: 3578037
Maddrey, W. C. et al. Corticosteroid therapy of alcoholic hepatitis. Gastroenterology 75, 193–199 (1978).
pubmed: 352788
Dominguez, M. et al. A new scoring system for prognostic stratification of patients with alcoholic hepatitis. Am. J. Gastroenterol. 103, 2747–2756 (2008).
pubmed: 18721242
Thursz, M. R. et al. Prednisolone or pentoxifylline for alcoholic hepatitis. N. Engl. J. Med. 372, 1619–1628 (2015).
pubmed: 25901427
Mathurin, P. & Lucey, M. R. Management of alcoholic hepatitis. J. Hepatol. 56, S39–S45 (2012).
pubmed: 22300464
Llorente, C. et al. Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus. Nat. Commun. 8, 837 (2017).
pubmed: 29038503
pmcid: 5643518
Gilmore, M. S. et al. Genetic structure of the Enterococcus faecalis plasmid pAD1-encoded cytolytic toxin system and its relationship to lantibiotic determinants. J. Bacteriol. 176, 7335–7344 (1994).
pubmed: 7961506
pmcid: 197123
Cox, C. R., Coburn, P. S. & Gilmore, M. S. Enterococcal cytolysin: a novel two component peptide system that serves as a bacterial defense against eukaryotic and prokaryotic cells. Curr. Protein Pept. Sci. 6, 77–84 (2005).
pubmed: 15638770
Van Tyne, D., Martin, M. J. & Gilmore, M. S. Structure, function, and biology of the Enterococcus faecalis cytolysin. Toxins 5, 895–911 (2013).
Bertola, A., Mathews, S., Ki, S. H., Wang, H. & Gao, B. Mouse model of chronic and binge ethanol feeding (the NIAAA model). Nat. Protoc. 8, 627–637 (2013).
pubmed: 23449255
Ogilvie, L. A. & Jones, B. V. The human gut virome: a multifaceted majority. Front. Microbiol. 6, 918 (2015).
pubmed: 26441861
pmcid: 4566309
Chatterjee, A. et al. Bacteriophage resistance alters antibiotic-mediated intestinal expansion of enterococci. Infect. Immun. 87, e00085-19 (2019).
pubmed: 30936157
Poindexter, J. S. Biological properties and classification of the Caulobacter group. Bacteriol. Rev. 28, 231–295 (1964).
pubmed: 14220656
pmcid: 441226
Shin, J. et al. Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Sci. Rep. 6, 29681 (2016).
pubmed: 27411898
pmcid: 4944186
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).
Marcuk, L. M. et al. Clinical studies of the use of bacteriophage in the treatment of cholera. Bull. World Health Organ. 45, 77–83 (1971).
pubmed: 4946956
pmcid: 2427894
Sarker, S. A. et al. Oral phage therapy of acute bacterial diarrhea with two coliphage preparations: a randomized trial in children from Bangladesh. EBioMedicine 4, 124–137 (2016).
pubmed: 26981577
pmcid: 4776075
Dalmasso, M., Hill, C. & Ross, R. P. Exploiting gut bacteriophages for human health. Trends Microbiol. 22, 399–405 (2014).
pubmed: 24656964
Ujmajuridze, A. et al. Adapted bacteriophages for treating urinary tract infections. Front. Microbiol. 9, 1832 (2018).
pubmed: 30131795
pmcid: 6090023
Khawaldeh, A. et al. Bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection. J. Med. Microbiol. 60, 1697–1700 (2011).
pubmed: 21737541
Schooley, R. T. et al. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob. Agents Chemother. 61, e00954-17 (2017).
pubmed: 28807909
pmcid: 5610518
Dedrick, R. M. et al. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat. Med. 25, 730–733 (2019).
pubmed: 31068712
pmcid: 31068712
Fish, R. et al. Compassionate use of bacteriophage therapy for foot ulcer treatment as an effective step for moving toward clinical trials. Methods Mol. Biol. 1693, 159–170 (2018).
pubmed: 29119440
Górski, A. et al. Phages and immunomodulation. Future Microbiol. 12, 905–914 (2017).
pubmed: 28434234
Brandl, K. et al. Dysregulation of serum bile acids and FGF19 in alcoholic hepatitis. J. Hepatol. 69, 396–405 (2018).
pubmed: 29654817
pmcid: 6054564
Gao, B. et al. Serum and fecal oxylipins in patients with alcohol-related liver disease. Dig. Dis. Sci. 64, 1878–1892 (2019).
pubmed: 31076986
Lang, S. et al. Intestinal fungal dysbiosis and systemic immune response to fungi in patients with alcoholic hepatitis. Hepatology (2019).
Ball, S. A., Tennen, H., Poling, J. C., Kranzler, H. R. & Rounsaville, B. J. Personality, temperament, and character dimensions and the DSM-IV personality disorders in substance abusers. J. Abnorm. Psychol. 106, 545–553 (1997).
pubmed: 9358685
Krieg, L. et al. Mutation of the gastric hydrogen-potassium ATPase alpha subunit causes iron-deficiency anemia in mice. Blood 118, 6418–6425 (2011).
pubmed: 21976678
pmcid: 3236123
Gill, J. J. et al. The Caulobacter crescentus phage phiCbK: genomics of a canonical phage. BMC Genomics 13, 542 (2012).
pubmed: 23050599
pmcid: 3556154
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb. Genom. 3, e000132 (2017).
pubmed: 29177090
pmcid: 5695209
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput. Biol. 13, e1005595 (2017).
pubmed: 28594827
pmcid: 5481147
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
pubmed: 25409509
pmcid: 4237348
Santiago-Rodriguez, T. M. et al. Transcriptome analysis of bacteriophage communities in periodontal health and disease. BMC Genomics 16, 549 (2015).
pubmed: 26215258
pmcid: 4515923
Haft, D. H. et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res. 46, D851–D860 (2018).
pubmed: 29112715
Tatusova, T. et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614–6624 (2016).
pubmed: 27342282
pmcid: 5001611
Fouts, D. E. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 34, 5839–5851 (2006).
pubmed: 17062630
pmcid: 1635311
Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).
pubmed: 27323842
pmcid: 4915045
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
pubmed: 30016406
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).
pubmed: 27095192
pmcid: 27095192
Valentine, R. C., Shapiro, B. M. & Stadtman, E. R. Regulation of glutamine synthetase. XII. Electron microscopy of the enzyme from Escherichia coli. Biochemistry 7, 2143–2152 (1968).
pubmed: 4873173
Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494–504 (2011).
pubmed: 21212162
pmcid: 3044863
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA 108 (Suppl 1), 4516–4522 (2011).
Chen, P. et al. Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice. Gastroenterology 148, 203–214.e16 (2015).
pubmed: 25239591
Ryu, H. et al. Development of quantitative PCR assays targeting the 16S rRNA genes of Enterococcus spp. and their application to the identification of enterococcus species in environmental samples. Appl. Environ. Microbiol. 79, 196–204 (2013).
pubmed: 23087032
pmcid: 3536114
Haas, W., Shepard, B. D. & Gilmore, M. S. Two-component regulator of Enterococcus faecalis cytolysin responds to quorum-sensing autoinduction. Nature 415, 84–87 (2002).
pubmed: 11780122
Page, A. J. et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb. Genom. 2, e000083 (2016).
pubmed: 28348874
pmcid: 5320598
Chen, L. et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 33, D325–D328 (2005).
pubmed: 15608208
Jia, B. et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573 (2017)
pubmed: 27789705
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
pubmed: 24451623
pmcid: 24451623
Tang, W., Bobeica, S. C., Wang, L. & van der Donk, W. A. CylA is a sequence-specific protease involved in toxin biosynthesis. J. Ind. Microbiol. Biotechnol. 46, 537–549 (2019).
pubmed: 30484123
Iwaisako, K. et al. Protection from liver fibrosis by a peroxisome proliferator-activated receptor δ agonist. Proc. Natl Acad. Sci. USA 109, E1369–E1376 (2012).
pubmed: 22538808
Clarke, T. H., Brinkac, L. M., Sutton, G. & Fouts, D. E. GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models. Bioinformatics 34, 3032–3034 (2018).
pubmed: 29668840
pmcid: 6129299