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Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

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Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease
  • 1.

    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).

  • 2.

    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).

  • 3.

    Rehm, J. et al. Burden of disease associated with alcohol use disorders in the United States. Alcohol. Clin. Exp. Res. 38, 1068–1077 (2014).

  • 4.

    Llopis, M. et al. Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease. Gut 65, 830–839 (2016).

  • 5.

    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).

  • 6.

    Tang, W. & van der Donk, W. A. The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry. Nat. Chem. Biol. 9, 157–159 (2013).

  • 7.

    Maddrey, W. C. et al. Corticosteroid therapy of alcoholic hepatitis. Gastroenterology 75, 193–199 (1978).

  • 8.

    Dominguez, M. et al. A new scoring system for prognostic stratification of patients with alcoholic hepatitis. Am. J. Gastroenterol. 103, 2747–2756 (2008).

  • 9.

    Thursz, M. R. et al. Prednisolone or pentoxifylline for alcoholic hepatitis. N. Engl. J. Med. 372, 1619–1628 (2015).

  • 10.

    Mathurin, P. & Lucey, M. R. Management of alcoholic hepatitis. J. Hepatol. 56, S39–S45 (2012).

  • 11.

    Llorente, C. et al. Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus. Nat. Commun. 8, 837 (2017).

  • 12.

    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).

  • 13.

    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).

  • 14.

    Van Tyne, D., Martin, M. J. & Gilmore, M. S. Structure, function, and biology of the Enterococcus faecalis cytolysin. Toxins 5, 895–911 (2013).

  • 15.

    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).

  • 16.

    Ogilvie, L. A. & Jones, B. V. The human gut virome: a multifaceted majority. Front. Microbiol. 6, 918 (2015).

  • 17.

    Chatterjee, A. et al. Bacteriophage resistance alters antibiotic-mediated intestinal expansion of enterococci. Infect. Immun. 87, e00085-19 (2019).

  • 18.

    Poindexter, J. S. Biological properties and classification of the Caulobacter group. Bacteriol. Rev. 28, 231–295 (1964).

  • 19.

    Shin, J. et al. Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Sci. Rep. 6, 29681 (2016).

  • 20.

    Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

  • 21.

    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).

  • 22.

    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).

  • 23.

    Dalmasso, M., Hill, C. & Ross, R. P. Exploiting gut bacteriophages for human health. Trends Microbiol. 22, 399–405 (2014).

  • 24.

    Ujmajuridze, A. et al. Adapted bacteriophages for treating urinary tract infections. Front. Microbiol. 9, 1832 (2018).

  • 25.

    Khawaldeh, A. et al. Bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection. J. Med. Microbiol. 60, 1697–1700 (2011).

  • 26.

    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).

  • 27.

    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).

  • 28.

    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).

  • 29.

    Górski, A. et al. Phages and immunomodulation. Future Microbiol. 12, 905–914 (2017).

  • 30.

    Brandl, K. et al. Dysregulation of serum bile acids and FGF19 in alcoholic hepatitis. J. Hepatol. 69, 396–405 (2018).

  • 31.

    Gao, B. et al. Serum and fecal oxylipins in patients with alcohol-related liver disease. Dig. Dis. Sci. 64, 1878–1892 (2019).

  • 32.

    Lang, S. et al. Intestinal fungal dysbiosis and systemic immune response to fungi in patients with alcoholic hepatitis. Hepatology (2019).

  • 33.

    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).

  • 34.

    Krieg, L. et al. Mutation of the gastric hydrogen-potassium ATPase alpha subunit causes iron-deficiency anemia in mice. Blood 118, 6418–6425 (2011).

  • 35.

    Gill, J. J. et al. The Caulobacter crescentus phage phiCbK: genomics of a canonical phage. BMC Genomics 13, 542 (2012).

  • 36.

    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).

  • 37.

    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).

  • 38.

    Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).

  • 39.

    Santiago-Rodriguez, T. M. et al. Transcriptome analysis of bacteriophage communities in periodontal health and disease. BMC Genomics 16, 549 (2015).

  • 40.

    Haft, D. H. et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res. 46, D851–D860 (2018).

  • 41.

    Tatusova, T. et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614–6624 (2016).

  • 42.

    Fouts, D. E. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 34, 5839–5851 (2006).

  • 43.

    Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).

  • 44.

    Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).

  • 45.

    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).

  • 46.

    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).

  • 47.

    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).

  • 48.

    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).

  • 49.

    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).

  • 50.

    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).

  • 51.

    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).

  • 52.

    Page, A. J. et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb. Genom. 2, e000083 (2016).

  • 53.

    Chen, L. et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 33, D325–D328 (2005).

  • 54.

    Jia, B. et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573 (2017)

  • 55.

    Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

  • 56.

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

  • 57.

    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).

  • 58.

    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).

  • 59.

    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).

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