Anderson R, Groundwater P, Todd A, Worsley A. Antibacterial agents: chemistry, mode of action, mechanisms of resistance and clinical applications. John Wiley & Sons; 2012.
Fischbach MA, Walsh CT. Antibiotics for emerging pathogens. Science. 2009;325(5944):1089–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kamysz W. Are antimicrobial peptides an alternative for conventional antibiotics. Nucl Med Rev Cent East Eur. 2005;8(1):78–86.
PubMed
Google Scholar
Parisien A, Allain B, Zhang J, Mandeville R, Lan C. Novel alternatives to antibiotics: bacteriophages, bacterial cell wall hydrolases, and antimicrobial peptides. J Appl Microbiol. 2008;104(1):1–13.
CAS
PubMed
Google Scholar
Borysowski J, Weber-Dąbrowska B, Górski A. Bacteriophage endolysins as a novel class of antibacterial agents. Exp Biol Med. 2006;231(4):366–77.
CAS
Google Scholar
Kumar A, Kumar S, Kumar D, Mishra A, Dewangan RP, Shrivastava P, Ramachandran S, Taneja B. The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis. Acta Crystallogr Sect D: Biol Crystallogr. 2013;69(12):2543–54.
Article
CAS
Google Scholar
Bush K. Antimicrobial agents targeting bacterial cell walls and cell membranes. Rev Sci Tech. 2012;31(1):43–56.
CAS
PubMed
Google Scholar
Wang S, Shaevitz JW. The mechanics of shape in prokaryotes. Front Biosci (Schol Ed). 2013;5:564–74.
Article
Google Scholar
Meroueh SO, Bencze KZ, Hesek D, Lee M, Fisher JF, Stemmler TL, Mobashery S. Three-dimensional structure of the bacterial cell wall peptidoglycan. Proc Natl Acad Sci U S A. 2006;103(12):4404–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Le Bourhis L, Werts C. Role of Nods in bacterial infection. Microbes Infect. 2007;9(5):629–36.
Article
PubMed
Google Scholar
Reith J, Mayer C. Peptidoglycan turnover and recycling in Gram-positive bacteria. Appl Microbiol Biotechnol. 2011;92(1):1–11.
Article
CAS
PubMed
Google Scholar
Johnson JW, Fisher JF, Mobashery S. Bacterial cell‐wall recycling. Ann N Y Acad Sci. 2013;1277(1):54–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vollmer W, Joris B, Charlier P, Foster S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol Rev. 2008;32(2):259–86.
Article
CAS
PubMed
Google Scholar
Ghuysen J-M, Tipper DJ, Strominger JL. Enzymes that degrade bacterial cell walls. Methods Enzymol. 1966;8:685–99.
Article
CAS
Google Scholar
Frirdich E, Gaynor EC. Peptidoglycan hydrolases, bacterial shape, and pathogenesis. Curr Opin Microbiol. 2013;16(6):767–78.
Article
CAS
PubMed
Google Scholar
Baba T, Schneewind O. Target cell specificity of a bacteriocin molecule: a C-terminal signal directs lysostaphin to the cell wall of Staphylococcus aureus. EMBO J. 1996;15(18):4789.
CAS
PubMed
PubMed Central
Google Scholar
Simmonds R, Pearson L, Kennedy R, Tagg J. Mode of action of a lysostaphin-like bacteriolytic agent produced by Streptococcus zooepidemicus 4881. Appl Environ Microbiol. 1996;62(12):4536–41.
CAS
PubMed
PubMed Central
Google Scholar
Beukes M, Bierbaum G, Sahl H-G, Hastings J. Purification and partial characterization of a murein hydrolase, millericin B, produced by Streptococcus milleri NMSCC 061. Appl Environ Microbiol. 2000;66(1):23–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Loeffler JM, Djurkovic S, Fischetti VA. Phage lytic enzyme Cpl-1 as a novel antimicrobial for pneumococcal bacteremia. Infect Immun. 2003;71(11):6199–204.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nakimbugwe D, Masschalck B, Deckers D, Callewaert L, Aertsen A, Michiels CW. Cell wall substrate specificity of six different lysozymes and lysozyme inhibitory activity of bacterial extracts. FEMS Microbiol Lett. 2006;259(1):41–6.
Article
CAS
PubMed
Google Scholar
Murashova N, Golosova T, Gerasimova L, Gorbuntsova R, Ivanova N. [Lysozyme in the overall therapy of patients with burn trauma]. Antibiotiki. 1975;20(4):369–73.
CAS
PubMed
Google Scholar
Tanaka H, Kitoh Y, Kitabayashi N, Matsumura Y, Okayachi H, Nakatsuji Y, Tanaka K, Kubota K, Namba K, Takemura K. Development of a new delayed healing model of an open skin wound and effects of M-1011G (ointment gauze containing 5 % lysozyme hydrochloride) on the model. Nihon yakurigaku zasshi Folia pharmacologica Japonica. 1994;104(2):121.
Article
CAS
PubMed
Google Scholar
Hoopes JT, Stark CJ, Kim HA, Sussman DJ, Donovan DM, Nelson DC. Use of a bacteriophage lysin, PlyC, as an enzyme disinfectant against Streptococcus equi. Appl Environ Microbiol. 2009;75(5):1388–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoong P, Schuch R, Nelson D, Fischetti VA. Identification of a broadly active phage lytic enzyme with lethal activity against antibiotic-resistant Enterococcus faecalis and Enterococcus faecium. J Bacteriol. 2004;186(14):4808–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nilsen T, Nes IF, Holo H. Enterolysin A, a cell wall-degrading bacteriocin from Enterococcus faecalis LMG 2333. Appl Environ Microbiol. 2003;69(5):2975–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dhalluin A, Bourgeois I, Pestel-Caron M, Camiade E, Raux G, Courtin P, Chapot-Chartier M-P, Pons J-L. Acd, a peptidoglycan hydrolase of Clostridium difficile with N-acetylglucosaminidase activity. Microbiology. 2005;151(7):2343–51.
Article
CAS
PubMed
Google Scholar
Rodríguez-Cerrato V, García P, Huelves L, García E, del Prado G, Gracia M, Ponte C, López R, Soriano F. Pneumococcal LytA autolysin, a potent therapeutic agent in experimental peritonitis-sepsis caused by highly β-lactam-resistant Streptococcus pneumoniae. Antimicrob Agents Chemother. 2007;51(9):3371–3.
Article
PubMed
PubMed Central
Google Scholar
Kashige N, Nakashima Y, Miake F, Watanabe K. Cloning, sequence analysis, and expression of Lactobacillus casei phage PL-1 lysis genes. Arch Virol. 2000;145(8):1521–34.
Article
CAS
PubMed
Google Scholar
Spencer J, Murphy LM, Conners R, Sessions RB, Gamblin SJ. Crystal structure of the LasA virulence factor from Pseudomonas aeruginosa: substrate specificity and mechanism of M23 metallopeptidases. J Mol Biol. 2010;396(4):908–23.
Article
CAS
PubMed
Google Scholar
Kessler E, Safrin M, Blumberg S, Ohman DE. A continuous spectrophotometric assay for Pseudomonas aeruginosa LasA protease (staphylolysin) using a two-stage enzymatic reaction. Anal Biochem. 2004;328(2):225–32.
Article
CAS
PubMed
Google Scholar
Low LY, Yang C, Perego M, Osterman A, Liddington RC. Structure and lytic activity of a Bacillus anthracis prophage endolysin. J Biol Chem. 2005;280(42):35433–9.
Article
CAS
PubMed
Google Scholar
Mellroth P, Steiner H. PGRP-SB1: an N-acetylmuramoyl L-alanine amidase with antibacterial activity. Biochem Biophys Res Commun. 2006;350(4):994–9.
Article
CAS
PubMed
Google Scholar
García-Cano I, Campos-Gómez M, Contreras-Cruz M, Serrano-Maldonado CE, González-Canto A, Peña-Montes C, Rodríguez-Sanoja R, Sánchez S, Farrés A. Expression, purification, and characterization of a bifunctional 99-kDa peptidoglycan hydrolase from Pediococcus acidilactici ATCC 8042. Appl Microbiol Biotechnol. 2015;99(20):8563–8573.
Article
PubMed
Google Scholar
Szweda P, Schielmann M, Kotlowski R, Gorczyca G, Zalewska M, Milewski S. Peptidoglycan hydrolases-potential weapons against Staphylococcus aureus. Appl Microbiol Biotechnol. 2012;96(5):1157–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hughey V, Johnson E. Antimicrobial activity of lysozyme against bacteria involved in food spoilage and food-borne disease. Appl Environ Microbiol. 1987;53(9):2165–70.
CAS
PubMed
PubMed Central
Google Scholar
Callewaert L, Walmagh M, Michiels CW, Lavigne R. Food applications of bacterial cell wall hydrolases. Curr Opin Biotechnol. 2011;22(2):164–71.
Article
CAS
PubMed
Google Scholar
Schmelcher M, Waldherr F, Loessner MJ. Listeria bacteriophage peptidoglycan hydrolases feature high thermoresistance and reveal increased activity after divalent metal cation substitution. Appl Microbiol Biotechnol. 2012;93(2):633–43.
Article
CAS
PubMed
Google Scholar
Fenton M, McAuliffe O, O’Mahony J, Coffey A. Recombinant bacteriophage lysins as antibacterials. Bioeng Bugs. 2010;1(1):9–16.
Article
PubMed
PubMed Central
Google Scholar
Fischetti VA. Bacteriophage lysins as effective antibacterials. Curr Opin Microbiol. 2008;11(5):393–400.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rodríguez-Rubio L, Martínez B, Rodríguez A, Donovan DM, García P. Enhanced staphylolytic activity of the Staphylococcus aureus bacteriophage vB_SauS-phiIPLA88 HydH5 virion-associated peptidoglycan hydrolase: fusions, deletions, and synergy with LysH5. Appl Environ Microbiol. 2012;78(7):2241–8.
Article
PubMed
PubMed Central
Google Scholar
García‐Cano I, Velasco‐Pérez L, Rodríguez‐Sanoja R, Sánchez S, Mendoza‐Hernández G, Llorente‐Bousquets A, Farrés A. Detection, cellular localization and antibacterial activity of two lytic enzymes of Pediococcus acidilactici ATCC 8042. J Appl Microbiol. 2011;111(3):607–15.
Article
PubMed
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 2006;34(suppl 1):D187–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957–63.
Article
PubMed
PubMed Central
Google Scholar
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31(10):1674–6.
Article
PubMed
Google Scholar
Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38(12):e132.
Article
PubMed
PubMed Central
Google Scholar
Sharma AK, Gupta A, Kumar S, Dhakan DB, Sharma VK. Woods: a fast and accurate functional annotator and classifier of genomic and metagenomic sequences. Genomics. 2015;106(1):1–6.
Article
CAS
PubMed
Google Scholar
Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH. The WEKA data mining software: an update. ACM SIGKDD Explorations Newsletter. 2009;11(1):10–8.
Article
Google Scholar
Chang C-C, Lin C-J. LIBSVM: a library for support vector machines. ACM TIST. 2011;2(3):27.
Google Scholar
Bottou L, Lin C-J. Support vector machine solvers. Large scale kernel machines. 2007;301-20.
Gupta A, Kapil R, Dhakan DB, Sharma VK. MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data. PLoS One. 2014;9(4):e93907.
Article
PubMed
PubMed Central
Google Scholar
Breiman L. Random forests. Mach Learn. 2001;45(1):5–32.
Article
Google Scholar
Chaudhary N, Sharma AK, Agarwal P, Gupta A, Sharma VK. 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets. PLoS One. 2015;10(2):e0116106.
Article
PubMed
PubMed Central
Google Scholar
Touw WG, Bayjanov JR, Overmars L, Backus L, Boekhorst J, Wels M, van Hijum SA. Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? Brief Bioinform. 2013;14(3):315–26.
Article
PubMed
PubMed Central
Google Scholar