Abstract
The article is dedicated to microbial diversity in nature, methods of investigation, identification and classification of bacteria and bacteriophages, as well as their applications in biotechnology. Microbial culture collections and the strategies for preservation of microbial diversity are considered.
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References
Abedon ST (2017) Phage companies. http://companies.phage.org. Accessed 31 May 2017
Abuladze T, Li M, Menetrez MY, Dean T, Senecal A, Sulakvelidze A (2008) Bacteriophages reduce experimental contamination of hard surfaces, tomato, spinach, broccoli and ground beef by Escherichia coli O157:H7. Appl Environ Microbiol 74:6230–6238. https://doi.org/10.1128/AEM.01465-08
Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6(6):431–440. https://doi.org/10.1038/nrmicro1872
Ackermann HW (1996) Frequency of morphological phage descriptions in 1995. Arch Virol 141(2):209–218. https://doi.org/10.1007/BF01718394
Ackermann HW (2005) Bacteriophage classification. In: Kutter E, Sulakvelidze A (eds) Bacteriophages: biology and applications. CRC Press, Boca Raton, pp 67–90
Ackermann HW (2006) Classification of bacteriophages. In: Calendar R (ed) The bacteriophages. Oxford University Press, Oxford, pp 8–16
Ackermann HW (2009) Phage classification and characterization. In: Clokie MRJ, Kropinski A (eds) Bacteriophages. Methods and protocols, vol 1: isolation, characterization, and interactions. Humana Press, New York, pp 127–140. https://doi.org/10.1007/978-1-60327-164-6
Ackermann HW (2011) Bacteriophage taxonomy. Microbiol Australia 32(2):90–94
Ackermann HW, Eisenstark A (1974) The present state of phage taxonomy. Intervirology 3(4):201–219. https://doi.org/10.1159/000149758
Ackermann HW, Prangishvili D (2012) Prokaryote viruses studied by electron microscopy. Arch Virol 157(10):1843–1849. https://doi.org/10.1007/s00705-012-1383-y
Ackermann HW, Tremblay D, Moineau S (2004) Long-term bacteriophage preservation. World Fed Cult Collection Newslett 38:35–40
Adams MH, Wade E (1954) Classification of bacterial viruses: the relationship of two Serratia phages to coli-dysentery phages T3, T7, and D44. J Bacteriol 68:320–325
Anany H, Chen W, Pelton R, Griffiths MW (2011) Biocontrol of Listeria monocytogenes and Escherichia coli O157:H7 in meat by using phages immobilized on modified cellulose membranes. Appl Environ Microbiol 77:6379–6387. https://doi.org/10.1128/AEM.05493-11
Angert ER, Clements KD, Pace NR (1993) The largest bacterium. Nature 362:239–241. https://doi.org/10.1038/362239a0
Annear DI (1956) The preservation of bacteria by drying in peptone plugs. J Hyg 54(4):487–508
Annear DI (1957) The preservation of bacteriophage by drying. J Appl Microbiol 20(1):21–22. https://doi.org/10.1111/j.1365-2672.1957.tb04510.x
Ashbolt NJ, Grabow WO, Snozzi M (2001) Indicators of microbial water quality. In: Fewtrell L, Bartram J (eds) Water quality: guidelines, standards and health. IWA Publishing, London, pp 289–316
Atlas RM, Hazen TC (2011) Oil biodegradation and bioremediation: a tale of the two worst spills in U.S. history. Environ Sci Technol 45(16):6709–6715. https://doi.org/10.1021/es2013227
Babalova EG, Katsitadze KT, Sakvarelidze LA Imnaishvili NS, Sharashidze TG, Badashvili VA, Kiknadze GP, Meĭpariani AN, Gendzekhadze ND, Machavariani EV, Gogoberidze KL, Gozalov EI, Dekanosidze NG (1968) Preventive value of dried dysentery bacteriophage. Zh mikrobiol Epidemiol Immunobiol 45:143–145
Bagyaraj DJ, Rangaswami G (2007) Agricultural microbiology. Prentice Hall, New Delhi
Baird A (2011) Gene transfer into mammalian cells using targeted filamentous bacteriophage. Cold Spring Harb Protoc 2011:950–957. https://doi.org/10.1101/pdb.prot5653
Barry T, Colleran G, Glennon M, Dunican LK, Gannon F (1991) The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl 1:51–56. https://doi.org/10.1101/gr.1.1.51
Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, Stahl DA, Cherni A (2004) Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. J Clin Microbiol 42:3711–3730. https://doi.org/10.1128/JCM.42.8.3711-3730.2004
Bazan J, Całkosiński I, Gamian A (2012a) Phage display – a powerful technique for immunotherapy: 1. Introduction and potential of therapeutic applications. Hum Vaccin Immunother 8(12):1817–1828. https://doi.org/10.4161/hv.21703
Bazan J, Całkosiński I, Gamian A (2012b) Phage display – a powerful technique for immunotherapy: 2. Vaccine delivery. Hum Vaccin Immunother 8(12):1829–1835. https://doi.org/10.4161/hv.21704
Bergh O, Børsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467–468. https://doi.org/10.1038/340467a0
Biswas B, Adhya S, Washart P, Paul B, Trostel AN, Powell B, Carlton R, Merril CR (2002) Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Infect Immun 70:204–210. https://doi.org/10.1128/IAI.70.1.204-210.2002
Bordenstein SR, Bordenstein SR (2016) Eukaryotic association module in phage WO genomes from Wolbachia. Nat Commun 7:13155. https://doi.org/10.1038/ncomms13155
Borysowski J, Górski A (2008) Is phage therapy acceptable in the immunocompromised host? Int J Infect Dis 12:466–471. https://doi.org/10.1016/j.ijid.2008.01.006
Bradley DE (1967) Ultrastructure of bacteriophage and bacteriocins. Bacteriol Rev 31:230–314
Bruynoghe R, Maisin J (1921) Essais de thérapeutique au moyen du bacteriophage du Staphylocoque. C R Soc Biol 85:1120–1121
Burnet FM (1933a) The classification of dysentery – coli bacteriophages. II. The serological classification of coli – dysentery phages. J Pathol Bacteriol 36:307–318. https://doi.org/10.1002/path.1700360212
Burnet FM (1933b) The classification of dysentery-Coli bacteriophages. III. A correlation of the serological classification with certain biochemical tests. J Pathol Bacteriol 37:179–184. https://doi.org/10.1002/path.1700370203
Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278–288. https://doi.org/10.1128/AEM.01177-06
Chibeu A (2013) Bacteriophages in food safety. In: Méndez-Vilas A (ed) Microbial pathogens and strategies for combating them: science, technology and education. Formatex Research Center, Badajoz, pp 1041–1052
Chibeu A, Agius L, Gao A, Sabour PM, Kropinski AM, Balamurugan S (2013) Efficacy of bacteriophage LISTEX™P100 combined with chemical antimicrobials in reducing Listeria monocytogenes in cooked turkey and roast beef. Int J Food Microbiol 167:208–214. https://doi.org/10.1016/j.ijfoodmicro.2013.08.018
Christensen H, Kuhnert P, Olsen JE, Bisgaard M (2004) Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol 54:1601–1609. https://doi.org/10.1099/ijs.0.03018-0
Clarridge JE (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17:840–862. https://doi.org/10.1128/CMR.17.4.840-862.2004
Cockell CS, Jones HL (2009) Advancing the case for microbial conservation. Oryx 43:520–526
Colwell RR (1997) Microbial diversity: the importance of exploration and conservation. J Ind Microbiol Biotechnol 18:302–307. https://doi.org/10.1038/sj.jim.2900390
Cox CS, Harris WJ, Lee J (1974) Viability and electron microscope studies of phages T3 and T7 subjected to freeze-drying, freeze-thawing and aerosolization. J Gen Microbiol 81(1):207–215. https://doi.org/10.1099/00221287-81-1-207
d’Hérelle F (1918) Technique de la recherche du microbe filtrant bactériophage (Bacteriophagum intestinale). C R Soc Biol 81:1160–1162
d’Hérelle F (1917) Sur un microbe invisible antagoniste des bacilles dysentériques. C R Acad Sci 165:373–375
Doore SM, Fane BA (2016) The Microviridae: diversity, assembly, and experimental evolution. Virology 491:45–55. https://doi.org/10.1016/j.virol.2016.01.020
EFSA Panel on Biological Hazards (BIOHAZ) (2011) Scientific opinion on Campylobacter in broiler meat production: control options and performance objectives and/or targets at different stages of the food chain. EFSA J9:2105. https://doi.org/10.2903/j.efsa.2011.2105
Eisenstark A (1967) Bacteriophage techniques. In: Maramorosch K, Koprowski H (eds) Methods in virology, vol 1. Academic, New York, pp 449–525
Farber JM, Peterkin PI (1991) Listeria monocytogenes, a foodborne pathogen. Microbiol Rev 55:476–511
Fenton M, Keary R, McAuliffe O et al (2013) Bacteriophage-derived peptidase CHAP(K) eliminates and prevents staphylococcal biofilms. Int J Microbiol 2013:625341. https://doi.org/10.1155/2013/625341
Fischetti VA (2005) Bacteriophage lytic enzymes: novel anti-infectives. Trends Microbiol 13(10):491–496. https://doi.org/10.1016/j.tim.2005.08.007
Fokine A, Rossmann MG (2014) Molecular architecture of tailed double-stranded DNA phages. Bacteriophage 4:e28281. https://doi.org/10.4161/bact.28281
Glaeser SP, Kämpfer P (2015) Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 38(4):237–245. https://doi.org/10.1016/j.syapm.2015.03.007
Golec P, Dąbrowski K, Hejnowicz MS et al (2011) A reliable method for storage of tailed phages. J Microbiol Methods 84:486–489. https://doi.org/10.1016/j.mimet.2011.01.007
Goodfellow M (2000) Microbial systematics: background and uses. In: Priest FG, Goodfellow M (eds) Applied microbial systematics. Springer, Dordrecht, pp 1–18. https://doi.org/10.1007/978-94-011-4020-1_1
Guenther S, Herzig O, Fieseler L et al (2012) Biocontrol of Salmonella Typhimurium in RTE foods with the virulent bacteriophage FO1-E2. Int J Food Microbiol 154:66–72. https://doi.org/10.1016/j.ijfoodmicro.2011.12.023
Guglielmotti DM, Reinheimer JA, Binetti AG, Giraffa G, Carminati D, Quiberoni A (2006) Characterization of spontaneous phage-resistant derivatives of Lactobacillus delbrueckii commercial strains. Int J Food Microbiol 111:126–133. https://doi.org/10.1016/j.ijfoodmicro.2006.04.035
Gürtler V, Stanisich VA (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142(Pt 1):3–16. https://doi.org/10.1099/13500872-142-1-3
Hagens S, Habel A, von Ahsen U, von Gabain A, Bläsi U (2004) Therapy of experimental Pseudomonas infections with a nonreplicating genetically modified phage. Antimicrob Agents Chemother 48:3817–3822. https://doi.org/10.1128/AAC.48.10.3817-3822.2004
Hamana K, Matsuzaki S (1992) Polyamines as a chemotaxonomic marker in bacterial systematics. Crit Rev Microbiol 18:261–283. https://doi.org/10.3109/10408419209113518
Hankin EH (1896) L’action bactericide des eaux de la Jumna et du Gange sur le vibrion du cholera. Ann Inst Pasteur (Paris) 10:511–523
Hansen DS, Skov R, Benedí JV, Sperling V, Kolmos HJ (2002) Klebsiella typing: pulsed-field gel electrophoresis (PFGE) in comparison with O:K-serotyping. Clin Microbiol Infect 8:397–404. https://doi.org/10.1046/j.1469-0691.2002.00411.x
Häring M, Rachel R, Peng X, Garrett RA, Prangishvili D (2005) Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus, Acidianus bottle-shaped virus, from a new family, the Ampullaviridae. J Virol 79:9904–9911. https://doi.org/10.1128/JVI.79.15.9904-9911.2005
Hatfull GF (2008) Bacteriophage genomics. Curr Opin Microbiol 11:447–453. https://doi.org/10.1016/j.mib.2008.09.004
Hatfull GF, Hendrix RW (2011) Bacteriophages and their genomes. Curr Opin Virol 1:298–303. https://doi.org/10.1016/j.coviro.2011.06.009
He Y, Xie Y, Reed S (2014) Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates. Methods Mol Biol 1085:103–111. https://doi.org/10.1007/978-1-62703-664-1_6
Holmes FO (1948) Order Virales. In: Breed RS, Murray EGD, Hitchens AP (eds) Bergey’s manual of determinative bacteriology, 6th edn. Williams & Wilkins, Baltimore, pp 1126–1286
Huang S, Vignolles ML, Chen XD, Le Loir Y, Jan G, Schuck P, Jeantet R (2017) Spray drying of probiotics and other food-grade bacteria: a review. Trends Food Sci Technol. 63:1–17. https://doi.org/10.1016/j.tifs.2017.02.007
Hubálek Z (2003) Protectants used in the cryopreservation of microorganisms. Cryobiology 46:205–229. https://doi.org/10.1016/S0011-2240(03)00046-4
Hudson JA, Billington C, Cornelius AJ et al (2013) Use of a bacteriophage to inactivate Escherichia coli O157:H7 on beef. Food Microbiol 36:14–21. https://doi.org/10.1016/j.fm.2013.03.006
Hulton CS, Higgins CF, Sharp PM (1991) ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 5(4):825–834. https://doi.org/10.1111/j.1365-2958.1991.tb00755.x
Iacobellis NS, DeVay JE (1986) Long-term storage of plant-pathogenic bacteria in sterile distilled water. Appl Environ Microbiol 52:388–389
ICTV (2011) ICTV ninth report; 2009 Taxonomy Release. https://talk.ictvonline.org/ictv-reports/ictv_9th_report/dsdna-viruses-2011/w/dsdna_viruses/103/bicaudaviridae. Accessed 31 May 2017
ICTV (2016) Virus taxonomy: 2016 release. https://talk.ictvonline.org/taxonomy/. Accessed 31 May 2017
Inoue-Nagata AK, Albuquerque LC, Rocha WB et al (2004) A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. J Virol Methods 116:209–211. https://doi.org/10.1016/j.jviromet.2003.11.015
Jackman J (2012) The microbe: the basics of structure, morphology, and physiology as they relate to microbial characterization and attribution. In: Cliff JB, Kreuzer HW, Ehrhardt CJ, Wunschel DS (eds) Chemical and physical signatures for microbial forensics. Springer, New York, pp 13–34. https://doi.org/10.1007/978-1-60327-219-3_2
Janda JM, Abbott SL (2007) 16S rRNA Gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clinl Microbiol 45(9):2761–2764. https://doi.org/10.1128/JCM.01228-07
Janež N, Loc-Carrillo C (2013) Use of phages to control Campylobacter spp. J Microbiol Methods 95:68–75. https://doi.org/10.1016/j.mimet.2013.06.024
Jay JM, Loessner MJ, Golden DA (2006) Modern food microbiology. Springer, New York. https://doi.org/10.1007/b100840
Karigar CS, Rao SS (2011) Role of microbial enzymes in the bioremediation of pollutants: a review. Enzyme Res 2011:11. https://doi.org/10.4061/2011/805187
Kaur S, Harjai K, Chhibber S (2014) Bacteriophage-aided intracellular killing of engulfed methicillin-resistant Staphylococcus aureus (MRSA) by murine macrophages. Appl Microbiol Biotechnol 98:4653–4661. https://doi.org/10.1007/s00253-014-5643-5
Kenzaka T, Utrarachkij F, Suthienkul O, Nasu M (2006) Rapid monitoring of Escherichia coli in Southeast Asian urban canals by fluorescent-bacteriophage assay. J Health Sci 52:666–671. https://doi.org/10.1248/jhs.52.666
KEYENCE (2017) Microscope types & principles. http://www.keyence.com/ss/products/microscope/bz-x700/study/principle/002/index.jsp. Accessed 31 May 2017
Klovins J, Overbeek GP, van den Worm SH, Ackermann HW, van Duin J (2002) Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages. J Gen Virol 83:1523–1533. https://doi.org/10.1099/0022-1317-83-6-1523
Klumpp J, Fouts DE, Sozhamannan S (2012) Next generation sequencing technologies and the changing landscape of phage genomics. Bacteriophage 2:190–199. https://doi.org/10.4161/bact.22111
Knirel YA, Valvano MA (eds) (2011) Bacterial lipopolysaccharides. Structure, chemical synthesis, biogenesis and interaction with host cells. Springer, Wien. https://doi.org/10.1007/978-3-7091-0733-1
Kotsonis SE, Powell IB, Pillidge CJ, Limsowtin GKY, Hillier AJ, Davidson BE (2008) Characterization and genomic analysis of phage asccφ28, a phage of the family Podoviridae infecting Lactococcus lactis. Appl Environ Microbiol 74:3453–3460. https://doi.org/10.1128/AEM.02379-07
Krawczyk B, Samet A, Leibner J, Sledzińska A, Kur J (2006) Evaluation of a PCR melting profile technique for bacterial strain differentiation. J Clin Microbiol 44:2327–2332. https://doi.org/10.1128/JCM.00052-06
Krawczyk B, Leibner-Ciszak J, Mielech A, Nowak M, Kur J (2009) PCR melting profile (PCR MP) – a new tool for differentiation of Candida albicans strains. BMC Infect Dis 9:177. https://doi.org/10.1186/1471-2334-9-177
Krishnamurthy KV (2003) Textbook of biodiversity. Science
Krupovic M, Bamford DH (2007) Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria. BMC Genomics 8:236. https://doi.org/10.1186/1471-2164-8-236
Krupovic M, Prangishvili D, Hendrix RW, Bamford DH (2011) Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 75:610–635. https://doi.org/10.1128/MMBR.00011-11
Kwarcinski W, Lazarkiewicz B, Weber-Dabrowska B, Rudnicki J, Kamiński K, Sciebura M (1994) Bacteriophage therapy in the treatment of recurrent subphrenic and subhepatic abscess with jejunal fistula after stomach resection. Pol Tyg Lek 49:535
Lee JH, Shin H, Son B, Heu S, Ryu S (2013) Characterization and complete genome sequence of a virulent bacteriophage B4 infecting food-borne pathogenic Bacillus cereus. Arch Virol 158:2101–2108. https://doi.org/10.1007/s00705-013-1719-2
Liao CH, Shollenberger LM (2003) Survivability and long-term preservation of bacteria in water and in phosphate-buffered saline. Lett Appl Microbiol 37:45–50. https://doi.org/10.1046/j.1472-765X.2003.01345.x
Lin T, Lin L, Zhang F (2014) Review on molecular typing methods of pathogens. Open J Med Microbiol 4:147–152. https://doi.org/10.4236/ojmm.2014.43017
Loc-Carrillo C, Abedon ST (2011) Pros and cons of phage therapy. Bacteriophage 1(2):111–114. https://doi.org/10.4161/bact.1.2.14590
Loeffler JM, Nelson D, Fischetti VA (2001) Rapid killing of Streptococcus pneumoniae with a bacteriophage cell wall hydrolase. Science 294(5549):2170–2172. https://doi.org/10.1126/science.1066869
LPSN (2018) Classification of domains and phyla – hierarchical classification of prokaryotes (bacteria). http://www.bacterio.net/-classifphyla.html#bacteria. Accessed 30 July 2018
Lunder M, Bratkovic T, Kreft S, Štrukelj B (2005) Peptide inhibitor of pancreatic lipase selected by phage display using different elution strategies. J Lipid Res 46:1512–1516. https://doi.org/10.1194/jlr.M500048-JLR200
Lwoff A, Horne RW, Tournier P (1962) A system of viruses. Cold Spring Harb Symp Quant Biol 27:51–55
Mahilum-Tapy L (2009) The importance of microbial culture collection and gene banks in biotechnology. In: Doelle HW, Rokem JS, Berovic M (eds) Biotechnology, vol I: Fundamentals in biotechnology. EOLSS, Oxford
Matinkhoo S, Lynch KH, Dennis JJ, Finlay WH, Vehring R (2011) Spray-dried respirable powders containing bacteriophages for the treatment of pulmonary infections. J Pharm Sci 100:5197–5205. https://doi.org/10.1002/jps.22715
Meladze GD, Mebuke MG, Chkhetia NS, Kiknadze NI, Koguashvili GG (1982) The efficacy of staphylococcal bacteriophage in treatment of purulent diseases of lungs and pleura. Grudn Khir 1:53–56
Mendell JE, Clements KD, Choat JH, Angert ER (2008) Extreme polyploidy in a large bacterium. Proc Natl Acad Sci USA 105:6730–6734. https://doi.org/10.1073/pnas.0707522105
Merabishvili M, Vervaet C, Pirnay JP, De Vos D, Verbeken G, Mast J, Chanishvili N, Vaneechoutte M (2013) Stability of Staphylococcus aureus phage ISP after freeze-drying (lyophilization). PLoS One 8:e68797. https://doi.org/10.1371/journal.pone.0068797
Mishra M, Chauhan P (2016) Applications of microscopy in bacteriology. Microscopy Res 4:1–9. https://doi.org/10.4236/mr.2016.41001
Mochizuki T, Yoshida T, Tanaka R, Forterre P, Sako Y, Prangishvili D (2010) Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1, APBV1, the first representative of the family Clavaviridae. Virology 402:347–354. https://doi.org/10.1016/j.virol.2010.03.046
Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D (2012) Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome. Proc Natl Acad Sci USA 109:13386–13391. https://doi.org/10.1073/pnas.1203668109
Mohan SV, Reddy MV, Chandra R, Subhash GV, Devi MP, Srikanth S (2013) Bacteria for bioenergy: a sustainable approach towards renewability. In: Gaspard S, Ncbi MC (eds) Biomass for sustainable applications: pollution, remediation and energy. RSC, London, pp 251–289. https://doi.org/10.1039/9781849737142-00251
Muller JA, Ross RP, Fitzgerald GF, Stanton C (2009) Manufacture of probiotic bacteria. In: Charalampopoulos D, Rastall RA (eds) Prebiotics and probiotics science and technology. Springer, New York, pp 725–759. https://doi.org/10.1007/978-0-387-79058-9_18
Murthy K, Engelhardt R (2008) Encapsulated bacteriophage formulation. US Patent US 13/528,215
NCBI (2017) Viruses – complete genomes. https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239&opt=Virus. Accessed 31 May 2017
Novik GI (1998) Structure-functional organization of bifidobacteria. Mikrobiologiia 67:376–383
Novik G, Savich V (2015) Bacteriophages of Pseudomonas bacteria: application in medicine and agriculture. In: Méndez-Vilas A (ed) The battle against microbial pathogens: basic science, technological advances and educational programs, vol 1. Formatex Research Center, Badajoz, pp 295–304
Novik GI, Vysotskiĭ VV (1995) Architectonics of Bifidobacteria populations: submicroscopic aspect of cell cohesion in Bifidobacterium adolescentis and Bifidobacterium bifidum. Mikrobiologiia 64(2):222–227
Novik GI, Vysotskiĭ VV, Bogdanovskaia ZN (1994) Cellular ultrastructure of various species of the genus Bifidobacterium. Mikrobiologiia 63:515–522
Novik GI, Astapovich NI, Samartsev AA (2001) Study of the physiological and biochemical characteristics of bifidobacteria at the late stages of population development. Mikrobiologiia 70:495–502
Novik GI, Astapovich NI, Kubler J, Gamian A (2002) Characterization of the cell-bound polysaccharides of Bifidobacterium adolescentis 94 BIM. Mikrobiologiia 71:205–210. https://doi.org/10.1023/A:1015194020327
Novik GI, Astapovich NI, Grzegorzewicz A, Gamian A (2005a) Isolation and comparative analysis of glycolipid fractions in bifidobacteria. Mikrobiologiia 74:772–780. https://doi.org/10.1007/s11021-005-0122-8
Novik GI, Astapovich NI, Pasciak M, Gamian A (2005b) Biological activity of polar lipids from bifidobacteria. Mikrobiologiia 74:781–787. https://doi.org/10.1007/s11021-005-0123-7
Novik GI, Astapovich NI, Grzhegorzhevich A, Gamian A (2006a) Analysis of phospholipids in bifidobacteria. Mikrobiologiia 75:40–45. https://doi.org/10.1134/S0026261706010061
Novik G, Gamian A, Francisco Jda C, Dey ES (2006b) A novel procedure for the isolation of glycolipids from Bifidobacterium adolescentis 94 BIM using supercritical carbon dioxide. J Biotechnol 121:555–562. https://doi.org/10.1016/j.jbiotec.2005.08.018
Ogilvie LA, Jones BV (2015) The human gut virome: a multifaceted majority. Front Microbiol 6:918. https://doi.org/10.3389/fmicb.2015.00918
Oksanen HM, ICTV Report Consortium (2017) ICTV virus taxonomy profiles: corticoviridae. J Gen Virol 98:888–889. https://doi.org/10.1099/jgv.0.000795
Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669
Oliveira M, Viñas I, Colàs P, Anguera M, Usall J, Abadias M (2014) Effectiveness of a bacteriophage in reducing Listeria monocytogenes on fresh-cut fruits and fruit juices. Food Microbiol 38:137–142. https://doi.org/10.1016/j.fm.2013.08.018
OPS Diagnostics (2017) Bacteria lyophilization overview. http://opsdiagnostics.com/notes/ranpri/bacteria_lyophilization_overview.htm. Accessed 31 May 2017
Patel JB (2001) 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol Diagn 6:313–321. https://doi.org/10.1054/modi.2001.29158
Pawlowski A, Rissanen I, Bamford JK, Krupovic M, Jalasvuori M (2014) Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae. Arch Virol 159:1541–1554. https://doi.org/10.1007/s00705-013-1970-6
Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM, Pei Z (2009) Diversity of 23S rRNA genes within individual prokaryotic genomes. PLoS One 4:e5437. https://doi.org/10.1371/journal.pone.0005437
Perry SF (1995) Freeze-drying and cryopreservation of bacteria. Methods Mol Biol 38:21–30. https://doi.org/10.1385/0-89603-296-5:21
Pfankuch E, Kausche GA (1940) Isolierung und übermikroskopische Abbildung eines Bakteriophagen. Naturwissenschaften 28:46. https://doi.org/10.1007/BF01486932
Pietilä MK, Demina TA, Atanasova NS, Oksanen HM, Bamford DH (2014) Archaeal viruses and bacteriophages: comparisons and contrasts. Trends Microbiol 22:334–344. https://doi.org/10.1016/j.tim.2014.02.007
Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM (2016) Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes. Arch Virol 161:249–256. https://doi.org/10.1007/s00705-015-2613-x
Pina M, Bize A, Forterre P, Prangishvili D (2011) The archeoviruses. FEMS Microbiol Rev 35:1035–1054. https://doi.org/10.1111/j.1574-6976.2011.00280.x
Quiberoni A, Reinheimer JA, Suárez VB (1998) Performance of Lactobacillus helveticus spontaneous phage-resistant mutants in hard cheese production. Int Dairy J 8:941–949. https://doi.org/10.1016/S0958-6946(98)00126-5
Rakhuba DV, Kolomiets EI, Dey ES, Novik GI (2010) Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol J Microbiol 59:145–155. https://doi.org/10.1016/j.micres.2015.01.008.1.94
Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C (2014) Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide. New Microbiol 37:1–15
Razin S, Cosenza BJ (1966) Growth phases of Mycoplasma in liquid media observed with phase-contrast microscope. J Bacteriol 91:858–869
Rohwer F, Edwards R (2002) The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184:4529–4535. https://doi.org/10.1128/JB.184.16.4529-4535.2002
Rokyta DR, Burch CL, Caudle SB, Wichman HA (2006) Horizontal gene transfer and the evolution of microvirid coliphage genomes. J Bacteriol 188:1134–1142. https://doi.org/10.1128/JB.188.3.1134-1142.2006
Romero P, López R, García E (2004) Genomic organization and molecular analysis of the inducible prophage EJ-1, a mosaic myovirus from an atypical pneumococcus. Virology 322(2):239–252. https://doi.org/10.1016/j.virol.2004.01.029
Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) (2013) The prokaryotes. Springer, Berlin. https://doi.org/10.1007/978-3-642-31331-8
Roux S, Krupovic M, Poulet A, Debroas D, Enault F (2012) Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLoS One 7:e40418. https://doi.org/10.1371/journal.pone.0040418
Ruska H (1940) Über die Sichtbarmachung der bakteriophagen Lyse im Übermikroskop. Naturwissenschaften 28:45–46. https://doi.org/10.1007/BF01486931
Ruska H (1943a) Versuch zu einer Ordnung der Virusarten. Archiv für die gesamte Virusforschung 2:480–498. https://doi.org/10.1007/BF01244584
Ruska H (1943b) Ergebnisse der Bakteriophagenforschung und ihre Deutung nach morphologischen Befunden. Ergeb Hyg Bakteriol Immunforsch Exp Ther 25:437–498
Ryberg A, Olsson C, Ahrné S, Monstein HJ (2011) Comparison of (GTG)5-oligonucleotide and ribosomal intergenic transcribed spacer (ITS)-PCR for molecular typing of Klebsiella isolates. J Microbiol Methods 84:183–188. https://doi.org/10.1016/j.mimet.2010.11.019
Samson JE, Magadán AH, Sabri M, Moineau S (2013) Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol 11:675–687. https://doi.org/10.1038/nrmicro3096
Schleifer KH (2009) Classification of bacteria and archaea: past, present and future. Syst Appl Microbiol 32:533–542. https://doi.org/10.1016/j.syapm.2009.09.002
Schuch R, Nelson D, Fischetti VA (2002) A bacteriolytic agent that detects and kills Bacillus anthracis. Nature 418:884–889. https://doi.org/10.1038/nature01026
Schulz HN, Jorgensen BB (2001) Big bacteria. Annu Rev Microbiol 55:105–137. https://doi.org/10.1146/annurev.micro.55.1.105
Sentausa E, Fournier PE (2013) Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect 19:790–795. https://doi.org/10.1111/1469-0691.12181
Sharma M, Patel JR, Conway WS, Ferguson S, Sulakvelidze A (2009) Effectiveness of bacteriophages in reducing Escherichia coli O157:H7 on fresh-cut cantaloupes and lettuce. J Food Prot 72:1481–1485. https://doi.org/10.4315/0362-028X-72.7.1481
Sharma SK, Gupta AK, Shukla AK, Ahmad E, Sharma MP, Ramesh A (2016) Microbial conservation strategies and methodologies: status and challenges. Indian J Plant Genet Resour 29:340–342. https://doi.org/10.5958/0976-1926.2016.00062.0
Sharples GJ, Lloyd RG (1990) A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res 18:6503–6508
Shivaswamy VC, Kalasuramath SB, Sadanand CK, Basavaraju AK, Ginnavaram V, Bille S, Ukken SS, Pushparaj UN (2015) Ability of bacteriophage in resolving wound infection caused by multidrug-resistant Acinetobacter baumannii in uncontrolled diabetic rats. Microb Drug Resist 21:171–177. https://doi.org/10.1089/mdr.2014.0120
Sidorenko AV, Novik GI, Akimov VN (2008) Application of the methods of molecular systematics to classification and identification of bacteria of the genus Bifidobacterium. Mikrobiologiia 77:293–302. https://doi.org/10.1134/S0026261708030016
Sinclair JB, Dhingra OD (1995) Basic plant pathology methods. CRC Press, Boca Raton
Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–1317. https://doi.org/10.1126/science.4001944
Sneath PHA, Brenner DJ (1992) “Official” nomenclature lists. ASM News 58:175
Soni KA, Nannapaneni R (2010) Bacteriophage significantly reduces Listeria monocytogenes on raw salmon fillet tissue. J Food Prot 73(1):32–38
Soni KA, Desai M, Oladunjoye A, Skrobot F, Nannapaneni R (2012) Reduction of Listeria monocytogenes in queso fresco cheese by a combination of listericidal and listeriostatic GRAS antimicrobials. Int J Food Microbiol 155:82–88. https://doi.org/10.1016/j.ijfoodmicro.2012.01.010
Stern MJ, Ames GF, Smith NH et al (1984) Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37:1015-1026. doi: https://doi.org/10.1016/0092-8674(84)90436-7
Stroj L, Weber-Dabrowska B, Partyka K, Mulczyk M, Wójcik M (1999) Successful treatment with bacteriophage in purulent cerebrospinal meningitis in a newborn. Neurol Neurochir Pol 33:693–698
Sulakvelidze A, Kutter E (2005) Bacteriophage therapy in humans. In: Kutter E, Sulakvelidze A (eds) Bacteriophages: biology and applications. CRC Press, Boca Raton, pp 382–436
Summers WC (2012) The strange history of phage therapy. Bacteriophage 2:130–133. https://doi.org/10.4161/bact.20757
Suttle CA (2005) Viruses in the sea. Nature 437(7057):356–361. https://doi.org/10.1038/nature04160
Szczepankowska AK, Górecki RK, Kołakowski P, Bardowski JK (2013) Lactic acid bacteria resistance to bacteriophage and prevention techniques to lower phage contamination in dairy fermentation. In: Marcelino Kongo J (ed) Lactic acid bacteria – R&D for food, health and livestock purposes. InTech. https://doi.org/10.5772/51541. https://www.intechopen.com/books/lactic-acid-bacteria-r-d-for-food-health-and-livestock-purposes/lactic-acid-bacteria-resistance-to-bacteriophage-and-prevention-techniques-to-lower-phage-contaminat. Accessed 31 May 2017
Thung TY, Premarathne JMKJK, San Chang W, Loo YY, Chin YZ, Kuan CH, Tan CW, Basri DF, Radzi CWJWM, Radu S (2017) Use of a lytic bacteriophage to control Salmonella Enteritidis in retail food. LWT – Food Sci Technol 78:222–225. https://doi.org/10.1016/j.lwt.2016.12.044
Tikhonenko AS (1970) Ultrastructure of bacterial viruses. Springer, New York, pp 29–32. https://doi.org/10.1007/978-1-4684-1779-1
Twort FW (1915) An investigation on the nature of ultramicroscopic viruses. Lancet 186:1241–1243. https://doi.org/10.1016/S0140-6736(01)20383-3
Valueva OA, Rakhuba D, Shashkov AS, Zdorovenko EL, Kiseleva E, Novik G, Knirel YA (2011) Structure of the major O-specific polysaccharide from the lipopolysaccharide of Pseudomonas fluorescens BIM B-582: identification of 4-deoxy-D-xylo-hexose as a component of bacterial polysaccharides. J Nat Prod 74:2161–2167. https://doi.org/10.1021/np200472p
Valueva OA, Shashkov AS, Zdorovenko EL, Chizhov AO, Kiseleva E, Novik G, Knirel YA (2013) Structures of cell-wall phosphate-containing glycopolymers of Bifidobacterium longum BIM B-476-D. Carbohydr Res 373:22–27. https://doi.org/10.1016/j.carres.2013.03.006
Ventola CL (2015) The antibiotic resistance crisis: part 1: causes and threats. P T 40:277–283
Viscardi M, Capparelli R, Di Matteo R, Carminati D, Giraffa G, Iannelli D (2003) Selection of bacteriophage-resistant mutants of Streptococcus thermophilus. J Microbiol Methods 55:109–119. https://doi.org/10.1016/S0167-7012(03)00146-5
Wan J, Johnson ML, Guntupalli R, Petrenko VA, Chin BA (2007) Detection of Bacillus anthracis spores in liquid using phage-based magnetoelastic micro-resonators. Sens Actuators B 127:559–566. https://doi.org/10.1016/j.snb.2007.05.017
Wang LT, Lee FL, Tai CJ, Kasai H (2007) Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 57:1846–1850. https://doi.org/10.1099/ijs.0.64685-0
Wang M, Cao B, Yu Q, Liu L, Gao Q, Wang L, Feng L (2008) Analysis of the 16S–23S rRNA gene internal transcribed spacer region in Klebsiella species. J Clin Microbiol 46:3555–3563. https://doi.org/10.1128/JCM.00927-08
WDCM (2018) WDCM CCINFO cover. http://www.wfcc.info/ccinfo/. Accessed 30 July 2018
Weimer BC, Blake M, Hillier AJ, Davidson BE (1993) Studies on the isolation of phage-resistant derivatives of Lactococcus lactis subsp. cremoris FG2 with phage sk1. Aust J Dairy Technol 48:59–61
Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583. https://doi.org/10.1073/pnas.95.12.6578
Wildy P (1971) Classification and nomenclature of viruses. First report of the International Committee on Nomenclature of Viruses. Karger, Basel
Willford JD, Bisha B, Bolenbaugh KE, Goodridge LD (2011) Luminescence based enzyme-labeled phage (phazyme) assays for rapid detection of Shiga toxin producing Escherichia coli serogroups. Bacteriophage 1:101–110. https://doi.org/10.4161/bact.1.2.15666
Williamson KE, Radosevich M, Wommack KE (2005) Abundance and diversity of viruses in six Delaware soils. Appl Environ Microbiol 71:3119–3125. https://doi.org/10.1128/AEM.71.6.3119-3125.2005
Winters RD, Winn WC Jr (2010) A simple effective method for bacterial culture storage: a brief technical report. J Bacteriol Virol 40:99–101. https://doi.org/10.4167/jbv.2010.40.2.99
Wommack KE, Colwell RR (2000) Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64:69–114. https://doi.org/10.1128/MMBR.64.1.69-114.2000
Yamamoto S, Harayama S (1998) Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48(Pt 3):813–819. https://doi.org/10.1099/00207713-48-3-813
Young KD (2006) The selective value of bacterial shape. Microbiol Mol Biol Rev 70:660–703. https://doi.org/10.1128/MMBR.00001-06
Zdorovenko EL, Kachala VV, Sidarenka AV, Izhik AV, Kisileva EP, Shashkov AS, Nobik GI, Knirel YA (2009) Structure of the cell wall polysaccharides of probiotic bifidobacteria Bifidobacterium bifidum BIM B-465. Carbohydr Res 344:2417–2420. https://doi.org/10.1016/j.carres.2009.08.039
Zimecki M, Artym J, Kocieba M, Weber-Dabrowska B, Borysowski J, Górski A (2009) Effects of prophylactic administration of bacteriophages to immunosuppressed mice infected with Staphylococcus aureus. BMC Microbiol 9:169. https://doi.org/10.1186/1471-2180-9-169
Zinder SH, Dworkin M (2006) Morphological and physiological diversity. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, vol 1. Springer, New York, pp 185–220. https://doi.org/10.1007/0-387-30741-9_7
Acknowledgments
We thank Prof. A. Gamian, Dr. A. Grzhegorzhevich, and Dr. M. Pasciak from the Institute of Immunology and Experimental Therapy, Polish Academy of Sciences for their extensive consultations on the identification of bacterial glycolipids and phospholipids.
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Novik, G., Savich, V., Kiseleva, E. (2018). Biodiversity Conservation of Phages and Microbial Populations. In: Sharma, S., Varma, A. (eds) Microbial Resource Conservation. Soil Biology, vol 54. Springer, Cham. https://doi.org/10.1007/978-3-319-96971-8_10
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