Halophilic & halotolerant prokaryotes in humans

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References

• 1 Lagier J-C, Khelaifia S, Alou MT et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat. Microbiol. 1, 16203 (2016). •• Culturomics studies allowed isolating nearly 40 halophilic prokaryotes from human gut.
  Medline CASGoogle Scholar
• 2 Rampelotto PH. Biotechnology of Extremophiles: Advances and Challenges (1st Ed.). Springer, Basel, Switzerland (2016).
  Google Scholar
• 3 Oren A. Salinibacter: an extremely halophilic bacterium with archaeal properties. FEMS Microbiol. Lett. 342(1), 1–9 (2013).
  Medline CASGoogle Scholar
• 4 Adamiak J, Otlewska A, Gutarowska B, Pietrzak A. Halophilic microorganisms in deteriorated historic buildings: insights into their characteristics. Acta Biochim. Pol. 63(2), 335–341 (2016).
  Medline CASGoogle Scholar
• 5 Hugon P, Dufour J-C, Colson P, Fournier P-E, Sallah K, Raoult D. A comprehensive repertoire of prokaryotic species identified in human beings. Lancet Infect. Dis. 15(10), 1211–1219 (2015). •• A methodology inspiring to establish the repertoire of bacteria already isolated in humans and their pathogenicity.
  MedlineGoogle Scholar
• 6 Dridi B. Laboratory tools for detection of archaea in humans. Clin. Microbiol. Infect. 18(9), 825–833 (2012).
  Medline CASGoogle Scholar
• 7 DasSarma S, DasSarma P. Halophiles. In: eLS. John Wiley & Sons, Ltd, Chichester, UK, 1 (2012).
  Google Scholar
• 8 Oren PA. Life at high salt concentrations. In: The Prokaryotes. Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (Eds). Springer, Berlin, Germany, 421–440 (2013).
  Google Scholar
• 9 Oren A. Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes. Front. Microbiol. 4, 315 (2013).
  MedlineGoogle Scholar
• 10 Oren A. Halophilic microbial communities and their environments. Curr. Opin. Biotechnol. 33, 119–124 (2015). • Explains the physiology of halophilic prokaryotes and returned to the environments in which they grow.
  Medline CASGoogle Scholar
• 11 Oren A. Taxonomy of halophilic archaea: current status and future challenges. Extremophiles 18(5), 825–834 (2014).
  MedlineGoogle Scholar
• 12 Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT. Microbial diversity of hypersaline environments: a metagenomic approach. Curr. Opin. Microbiol. 25(Suppl. C), 80–87 (2015).
  Medline CASGoogle Scholar
• 13 Andrei A-Ş, Banciu HL, Oren A. Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems. FEMS Microbiol. Lett. 330(1), 1–9 (2012).
  Medline CASGoogle Scholar
• 14 Edbeib MF, Wahab RA, Huyop F. Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J. Microbiol. Biotechnol. 32(8), 135 (2016).
  MedlineGoogle Scholar
• 15 Reed CJ, Lewis H, Trejo E, Winston V, Evilia C. Protein adaptations in archaeal extremophiles. Archaea Vanc. BC. 2013, 373275 (2013).
  Google Scholar
• 16 Dalmaso GZL, Ferreira D, Vermelho AB. Marine extremophiles: a source of hydrolases for biotechnological applications. Mar. Drugs. 13(4), 1925–1965 (2015).
  Medline CASGoogle Scholar
• 17 Graziano G, Merlino A. Molecular bases of protein halotolerance. Biochim. Biophys. Acta BBA 1844(4), 850–858 (2014).
  Medline CASGoogle Scholar
• 18 Hamedi J, Mohammadipanah F, Ventosa A. Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes. Extremophiles 17(1), 1–13 (2013).
  Medline CASGoogle Scholar
• 19 Kim J-S, Makama M, Petito J, Park N-H, Cohan FM, Dungan RS. Diversity of bacteria and archaea in hypersaline sediment from Death Valley National Park, California: diversity of bacteria and archaea in hypersaline sediment. MicrobiologyOpen 1(2), 135–148 (2012).
  Medline CASGoogle Scholar
• 20 Gibtan A, Park K, Woo M et al. Diversity of extremely halophilic archaeal and bacterial communities from commercial salts. Front. Microbiol. 10(8), 799 (2017).
  Google Scholar
• 21 Lee H-S. Diversity of halophilic archaea in fermented foods and human intestines and their application. J. Microbiol. Biotechnol. 23(12), 1645–1653 (2013). • Molecular biology technique showing the ability of halophilic prokaryotes to live in human gut and their presence in salty foods.
  Medline CASGoogle Scholar
• 22 Diop A, Khelaifia S, Armstrong N et al. Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov. Microb. Ecol. Health Dis. 27, 32049 (2016).
  MedlineGoogle Scholar
• 23 Dridi B, Fardeau M-L, Ollivier B, Raoult D, Drancourt M. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int. J. Syst. Evol. Microbiol. 62(Pt 8), 1902–1907 (2012).
  Medline CASGoogle Scholar
• 24 Kaptein EM, Sreeramoju D, Kaptein JS, Kaptein MJ. A systematic literature search and review of sodium concentrations of body fluids. Clin. Nephrol. 86(10), 203–228 (2016).
  Medline CASGoogle Scholar
• 25 Bang C, Schmitz RA. Archaea associated with human surfaces: not to be underestimated. FEMS Microbiol. Rev. 39(5), 631–648 (2015).
  Medline CASGoogle Scholar
• 26 Dridi B, Fardeau M-L, Ollivier B, Raoult D, Drancourt M. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int. J. Syst. Evol. Microbiol. 62(8), 1902–1907 (2012).
  Medline CASGoogle Scholar
• 27 Schulze-Röbbecke R. [Mycobacteria in the environment]. Immun. Infekt. 21(5), 126–131 (1993).
  Medline CASGoogle Scholar
• 28 Lagier J-C, Armougom F, Million M et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin. Microbiol. Infect. 18(12), 1185–1193 (2012).
  Medline CASGoogle Scholar
• 29 Lagier J-C, Hugon P, Khelaifia S, Fournier P-E, La Scola B, Raoult D. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin. Microbiol. Rev. 28(1), 237–264 (2015).
  Medline CASGoogle Scholar
• 30 Seck E, Rathored J, Khelaifia S et al. Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut. New Microbes New Infect. 8, 116–126 (2015).
  Medline CASGoogle Scholar
• 31 Lagier J-C, Edouard S, Pagnier I, Mediannikov O, Drancourt M, Raoult D. Current and past strategies for bacterial culture in clinical microbiology. Clin. Microbiol. Rev. 28(1), 208–236 (2015).
  Medline CASGoogle Scholar
• 32 Robert A, Danin P-É, Quintard H et al. Seawater drowning-associated pneumonia: a 10-year descriptive cohort in intensive care unit. Ann. Intensive Care 7(1), 45 (2017). • A work pointing to bacteria implicated in the infective complications of drowning.
  MedlineGoogle Scholar
• 33 American Biological Safety Association. Risk group classification for infectious agents (2017). www.absa.org/riskgroups/.
  Google Scholar
• 34 The Dead Sea: The Lake and Its Setting. Niemi TM, Ben-Avraham Z, Gat J (Eds). Oxford University Press, NYUSA (1997).
  Google Scholar
• 35 Millero FJ, Feistel R, Wright DG, McDougall TJ. The composition of standard seawater and the definition of the reference–composition salinity scale. Deep Sea Res. Part Oceanogr. Res. Pap. 55(1), 50–72 (2008).
  Google Scholar
• 36 Ahmed W, Gyawali P, Sidhu JPS, Toze S. Relative inactivation of faecal indicator bacteria and sewage markers in freshwater and seawater microcosms. Lett. Appl. Microbiol. 59(3), 348–354 (2014).
  Medline CASGoogle Scholar
• 37 Cloutier DD, Alm EW, McLellan SL. Influence of land use, nutrients, and geography on microbial communities and fecal indicator abundance at Lake Michigan beaches. Appl. Environ. Microbiol. 81(15), 4904–4913 (2015). • A work describing the factors affecting the survival of bacteria, mainly fecal indicator.
  Medline CASGoogle Scholar
• 38 Campos CJA, Kershaw SR, Lee RJ. Environmental influences on faecal indicator organisms in coastal waters and their accumulation in bivalve shellfish. Estuaries Coasts Port Repub. 36(4), 834–853 (2013).
  CASGoogle Scholar
• 39 Sassoubre LM, Yamahara KM, Boehm AB. Temporal stability of the microbial community in sewage-polluted seawater exposed to natural sunlight cycles and marine microbiota. Appl. Environ. Microbiol. 81(6), 2107–2116 (2015).
  Medline CASGoogle Scholar
• 40 Pesciaroli C, Cupini F, Selbmann L, Barghini P, Fenice M. Temperature preferences of bacteria isolated from seawater collected in Kandalaksha Bay, White Sea, Russia. Polar Biol. 35(3), 435–445 (2012).
  Google Scholar
• 41 Podell S, Emerson JB, Jones CM et al. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 8(5), 979–990 (2014).
  Medline CASGoogle Scholar
• 42 Gin KY-H, Goh SG. Modeling the effect of light and salinity on viable but non-culturable (VBNC) Enterococcus. Water Res. 47(10), 3315–3328 (2013). • Shows the effects of solar radiation and temperature on the survival of bacteria in the sea and explains that nonmarine bacteria growth is constrained by several factors in marine waters.
  Medline CASGoogle Scholar
• 43 Daniszewski P. Determination of metals in sea water of the Baltic Sea in Międzyzdroje. Int. Lett. Chem. Phys. Astron. 13, 13–22 (2013).
  Google Scholar
• 44 Wanjugi P, Harwood VJ. The influence of predation and competition on the survival of commensal and pathogenic fecal bacteria in aquatic habitats. Environ. Microbiol. 15(2), 517–526 (2013).
  MedlineGoogle Scholar
• 45 Hansell DA, Carlson CA. Biogeochemistry of Marine Dissolved Organic Matter (2nd Ed.). Academic Press, FLUSA (2014).
  Google Scholar
• 46 Korajkic A, Wanjugi P, Harwood VJ. Indigenous microbiota and habitat influence Escherichia coli survival more than sunlight in simulated aquatic environments. Appl. Environ. Microbiol. 79(17), 5329–5337 (2013).
  Medline CASGoogle Scholar
• 47 Rashad FM, Fathy HM, El-Zayat AS, Elghonaimy AM. Isolation and characterization of multifunctional Streptomyces species with antimicrobial, nematicidal and phytohormone activities from marine environments in Egypt. Microbiol. Res. 175(Suppl. C), 34–47 (2015).
  Medline CASGoogle Scholar
• 48 Reglero P, Ciannelli L, Alvarez-Berastegui D, Balbin R, Lopez-Jurado JL, Alemany F. Geographically and environmentally driven spawning distributions of tuna species in the western Mediterranean Sea. Mar. Ecol. Prog. Ser. 463, 273–284 (2012).
  Google Scholar
• 49 Janda JM. Shewanella: a marine pathogen as an emerging cause of human disease. Clin. Microbiol. Newsl. 36(4), 25–29 (2014).
  Google Scholar
• 50 Vezzulli L, Colwell RR, Pruzzo C. Ocean warming and spread of pathogenic vibrios in the aquatic environment. Microb. Ecol. 65(4), 817–825 (2013).
  MedlineGoogle Scholar
• 51 Fewtrell L, Kay D. Recreational water and infection: a review of recent findings. Curr. Environ. Health Rep. 2(1), 85–94 (2015). •• A review revisiting infective risks associated with recreational water and discussing the risk of infection associated to marine water.
  MedlineGoogle Scholar
• 52 Fleisher JM, Jones F, Kay D, Stanwell-Smith R, Wyer MD, Morano R. Water and non-water-related risk factors for gastroenteritis among bathers exposed to sewage-contaminated marine waters. Int. J. Epidemiol. 22(4), 698–708 (1993).
  Medline CASGoogle Scholar
• 53 Byappanahalli MN, Roll BM, Fujioka RS. Evidence for occurrence, persistence, and growth potential of Escherichia coli and Enterococci in Hawaii's soil environments. Microbes Environ. 27(2), 164–170 (2012).
  MedlineGoogle Scholar
• 54 Byappanahalli MN, Nevers MB, Korajkic A, Staley ZR, Harwood VJ. Enterococci in the environment. Microbiol. Mol. Biol. Rev. 76(4), 685–706 (2012).
  Medline CASGoogle Scholar
• 55 Stocker MD, Rodriguez-Valentín JG, Pachepsky YA, Shelton DR. Spatial and temporal variation of fecal indicator organisms in two creeks in Beltsville, Maryland. Water Qual. Res. J. 51(2), 167–179 (2016).
  CASGoogle Scholar
• 56 Halliday E, Gast RJ. Bacteria in beach sands: an emerging challenge in protecting coastal water quality and bather health. Environ. Sci. Technol. 45(2), 370–379 (2011).
  Medline CASGoogle Scholar
• 57 Yamahara KM, Sassoubre LM, Goodwin KD, Boehm AB. Occurrence and persistence of bacterial pathogens and indicator organisms in beach sand along the California coast. Appl. Environ. Microbiol. 78(6), 1733–1745 (2012).
  Medline CASGoogle Scholar
• 58 Amagliani G, Brandi G, Schiavano GF. Incidence and role of Salmonella in seafood safety. Food Res. Int. 45(2), 780–788 (2012).
  Google Scholar
• 59 Ishikawa M, Yamasato K, Kodama K et al. Alkalibacterium gilvum sp. nov., slightly halophilic and alkaliphilic lactic acid bacterium isolated from soft and semi-hard cheeses. Int. J. Syst. Evol. Microbiol. 63(4), 1471–1478 (2013).
  Medline CASGoogle Scholar
• 60 Hirota K, Hanaoka Y, Nodasaka Y, Yumoto I. Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing. Int. J. Syst. Evol. Microbiol. 64(9), 3174–3180 (2014).
  Medline CASGoogle Scholar
• 61 Ishikawa M, Tanasupawat S, Nakajima K et al. Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., slightly halophilic and alkaliphilic marine lactic acid bacteria isolated from marine organisms and salted foods collected in Japan and Thailand. Int. J. Syst. Evol. Microbiol. 59(5), 1215–1226 (2009).
  Medline CASGoogle Scholar
• 62 Ntougias S, Russell NJ. Alkalibacterium olivoapovliticus gen. nov., sp. nov., a new obligately alkaliphilic bacterium isolated from edible-olive wash-waters. Int. J. Syst. Evol. Microbiol. 51(3), 1161–1170 (2001).
  Medline CASGoogle Scholar
• 63 Hong SW, Kwon S-W, Kim S-J et al. Bacillus oryzaecorticis sp. nov., a moderately halophilic bacterium isolated from rice husks. Int. J. Syst. Evol. Microbiol. 64(Pt 8), 2786–2791 (2014).
  Medline CASGoogle Scholar
• 64 Choi EJ, Lee SH, Jung JY, Jeon CO. Brevibacterium jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int. J. Syst. Evol. Microbiol. 63(Pt 9), 3430–3436 (2013).
  Medline CASGoogle Scholar
• 65 Lo N, Lee SH, Jin HM, Jung JY, Schumann P, Jeon CO. Garicola koreensis gen. nov., sp. nov., isolated from saeu-jeot, traditional Korean fermented shrimp. Int. J. Syst. Evol. Microbiol. 65(Pt 3), 1015–1021 (2015).
  Medline CASGoogle Scholar
• 66 Tamang JP, Watanabe K, Holzapfel WH. Review: diversity of microorganisms in global fermented foods and beverages. Front. Microbiol. 7, 377 (2016).
  MedlineGoogle Scholar
• 67 Koo OK, Lee SJ, Chung KR, Jang DJ, Yang HJ, Kwon DY. Korean traditional fermented fish products: jeotgal. J. Ethn. Foods 3(2), 107–116 (2016).
  Google Scholar
• 68 Shimoshige H, Yamada T, Minegishi H et al. Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt. Int. J. Syst. Evol. Microbiol. 63(Pt 3), 861–866 (2013).
  Medline CASGoogle Scholar
• 69 Nagaoka S, Minegishi H, Echigo A, Shimane Y, Kamekura M, Usami R. Halostagnicola alkaliphila sp. nov., an alkaliphilic haloarchaeon from commercial rock salt. Int. J. Syst. Evol. Microbiol. 61(Pt 5), 1149–1152 (2011).
  Medline CASGoogle Scholar
• 70 Kuda T, Izawa Y, Yoshida S, Koyanagi T, Takahashi H, Kimura B. Rapid identification of Tetragenococcus halophilus and Tetragenococcus muriaticus, important species in the production of salted and fermented foods, by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Food Control. 35(1), 419–425 (2014).
  CASGoogle Scholar
• 71 Cadenas MB, Maggi RG, Diniz PPVP, Breitschwerdt KT, Sontakke S, Breithschwerdt EB. Identification of bacteria from clinical samples using Bartonella α-Proteobacteria growth medium. J. Microbiol. Methods 71(2), 147–155 (2007).
  Medline CASGoogle Scholar
• 72 Senghor B, Seck EH, Khelaifia S et al. Description of ‘Bacillus dakarensis’ sp. nov., ‘Bacillus sinesaloumensis’ sp. nov., ‘Gracilibacillus timonensis’ sp. nov., ‘Halobacillus massiliensis’ sp. nov., ‘Lentibacillus massiliensis’ sp. nov., ‘Oceanobacillus senegalensis’ sp. nov., ‘Oceanobacillus timonensis’ sp. nov., ‘Virgibacillus dakarensis’ sp. nov. and ‘Virgibacillus marseillensis’ sp. nov., nine halophilic new species isolated from human stool. New Microbes New Infect. 17, 45–51 (2017).
  Medline CASGoogle Scholar
• 73 Khelaifia S, Raoult D. Haloferax massiliensis sp. nov., the first human-associated halophilic archaea. New Microbes New Infect. 12, 96–98 (2016).
  Medline CASGoogle Scholar
• 74 Yeo SH, Kwak JH, Kim YU et al. Peritoneal dialysis-related peritonitis due to Halomonas hamiltonii. Medicine (Baltimore). 95(47), e5424 (2016).
  MedlineGoogle Scholar
• 75 Seck EH, Fournier P-E, Raoult D, Khelaifia S. ‘Halomonas massiliensis’ sp. nov., a new halotolerant bacterium isolated from the human gut. New Microbes New Infect. 14, 19–20 (2016).
  Medline CASGoogle Scholar
• 76 Kim KK, Lee J-S, Stevens DA. Microbiology and epidemiology of Halomonas species. Future Microbiol. 8(12), 1559–1573 (2013).
  CASGoogle Scholar
• 77 Brändle G, L'Huillier AG, Wagner N, Gervaix A, Wildhaber BE, Lacroix L. First report of Kocuria marina spontaneous peritonitis in a child. BMC Infect. Dis. 14, 719 (2014).
  MedlineGoogle Scholar
• 78 Wareham D, Phee L, Hornsey M. P317 Isolation and characterisation of a novel Nesterenkonia species from a human bloodstream infection. Int. J. Antimicrob. Agents 2(Suppl. 42), S141–S142 (2013).
  Google Scholar
• 79 Zhang Y-J, Tang S-K, Shi R et al. Salinisphaera halophila sp. nov., a moderately halophilic bacterium isolated from brine of a salt well. Int. J. Syst. Evol. Microbiol. 62(Pt 9), 2174–2179 (2012).
  Medline CASGoogle Scholar
• 80 Sinha M, Shivaprakash MR, Chakrabarti A, Shafiulla M, Babu KG, Jayshree RS. Bacteraemia caused by Sciscionella marina in a lymphoma patient: phenotypically mimicking Nocardia. J. Med. Microbiol. 62(Pt 6), 929–931 (2013).
  Medline CASGoogle Scholar
• 81 Kalinowski J, Ahrens B, Al-Dilaimi A et al. Isolation and whole genome analysis of endospore-forming bacteria from heroin. Forensic Sci. Int. Genet. 32(Suppl. C), 1–6 (2018).
  Medline CASGoogle Scholar
• 82 Khelaifia S, Croce O, Lagier J-C et al. Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut. New Microbes New Infect. 8, 78–88 (2015).
  Medline CASGoogle Scholar
• 83 Chan K-S, Cheng K-C, Lee M-F, Yu W-L. A fish-stunning wound infection with acute cardiac injury. Am. J. Emerg. Med. 32(3), 289.e1–289.e2 (2014).
  Google Scholar
• 84 Fewtrell L, Kay D. Recreational water and infection: a review of recent findings. Curr. Environ. Health Rep. 2(1), 85–94 (2015).
  MedlineGoogle Scholar
• 85 Hugon P, Dufour J-C, Colson P, Fournier P-E, Sallah K, Raoult D. A comprehensive repertoire of prokaryotic species identified in human beings. Lancet Infect. Dis. 15(10), 1211–1219 (2015).
  MedlineGoogle Scholar
• 86 Mengel MA, Delrieu I, Heyerdahl L, Gessner BD. Cholera outbreaks in Africa. In: Cholera Outbreaks. Springer, Berlin, Germany, 117–144 (2014) [cited 2017 Oct 16].
  Google Scholar
• 87 Odeyemi OA. Incidence and prevalence of Vibrio parahaemolyticus in seafood: a systematic review and meta-analysis. SpringerPlus 5, 464 (2016).
  MedlineGoogle Scholar
• 88 Tadié JM, Heming N, Serve E et al. Drowning associated pneumonia: a descriptive cohort. Resuscitation 83(3), 399–401 (2012).
  Medline CASGoogle Scholar
• 89 Vignier N, Barreau M, Olive C et al. Human infection with Shewanella putrefaciens and S. algae: report of 16 cases in Martinique and review of the literature. Am. J. Trop. Med. Hyg. 89(1), 151–156 (2013).
  MedlineGoogle Scholar
• 90 Yamahara KM, Sassoubre LM, Goodwin KD, Boehm AB. Occurrence and persistence of bacterial pathogens and indicator organisms in beach sand along the California coast. Appl. Environ. Microbiol. 78(6), 1733–1745 (2012).
  Medline CASGoogle Scholar