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Applications and challenges for single-bacteria analysis by flow cytometry

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  • SPECIAL TOPIC · Fluorescent Chemical/Biological Sensors and Imaging
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Abstract

Flow cytometry (FCM) is a powerful technique for single-bacteria analysis via simultaneous light-scattering and fluorescence measurements. By offering high-throughput, quantitative, and multiparameter analysis at the single-cell level, FCM has gained an increased popularity in microbiological research, food safety monitoring, water quality control, and clinical diagnosis. Here we will review the recent applications of flow cytometry in areas such as (1) total bacterial cell count, (2) bacterial viability analysis, (3) specific bacterial detection and identification, (4) characterization of physiological changes under environmental perturbations, and (5) biological function studies. Nevertheless, despite these widespread applications, challenges still remain for the detection of small sizes of bacteria and biochemical features that cannot be brightly stained via fluorescence. Recent improvement in FCM instrumentation will be discussed, and particularly the development of high sensitivity flow cytometry for advanced analysis of single bacterial cells will be highlighted.

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References

  1. Trouillon R, Passarelli MK, Wang J, Kurczy ME, Ewing AG. Anal Chem, 2013, 85: 522–542

    Article  CAS  Google Scholar 

  2. Stratz S, Eyer K, Kurth F, Dittrich PS. Anal Chem, 2014, 86: 12375–12381

    Article  CAS  Google Scholar 

  3. Grote J, Krysciak D, Streit WR. Appl Environ Microb, 2015: 5280–5289

    Google Scholar 

  4. Manina G, Dhar N, McKinney JD. Cell Host Microbe, 2015, 17: 32–46

    Article  CAS  Google Scholar 

  5. Deris JB, Kim M, Zhang Z, Okano H, Hermsen R, Groisman A, Hwa T. Science, 2013, 342: 1237435

    Article  CAS  Google Scholar 

  6. Gefen O, Balaban NQ. FEMS Microbiol Rev, 2009, 33: 704–717

    Article  CAS  Google Scholar 

  7. Sanchez-Romero MA, Casadesus J. Proc Natl Acad Sci USA, 2014, 111: 355–360

    Article  CAS  Google Scholar 

  8. Morrissey I, Oggioni MR, Knight D, Curiao T, Coque T, Kalkanci A, Martinez JL, Consortium B. PLoS One, 2014, 9: e86669

    Article  CAS  Google Scholar 

  9. Gullo M, Verzelloni E, Canonico M. Process Biochem, 2014, 49: 1571–1579

    Article  CAS  Google Scholar 

  10. Ravyts F, De Vuyst L, Leroy F. Eng Life Sci, 2012, 12: 356–367

    Article  CAS  Google Scholar 

  11. Diaz M, Herrero M, Garcia LA, Quiros C. Biochem Eng J, 2010, 48: 385–407

    Article  CAS  Google Scholar 

  12. Davey ME, O’toole GA. Microbiol Mol Biol R, 2000, 64: 847–867

    Article  CAS  Google Scholar 

  13. Subashchandrabose S, Hazen TH, Brumbaugh AR, Himpsl SD, Smith SN, Ernst RD, Rasko DA, Mobley HL. Proc Natl Acad Sci USA, 2014, 111: 18327–18332

    Article  CAS  Google Scholar 

  14. Blainey PC. FEMS Microbiol Rev, 2013, 37: 407–427

    Article  CAS  Google Scholar 

  15. Rohde A, Hammerl JA, Appel B, Dieckmann R, Al Dahouk S. Food Microbiol, 2015, 46: 395–407

    Article  CAS  Google Scholar 

  16. Cecala C, Sweedler JV. Analyst, 2012, 137: 2922–2929

    Article  CAS  Google Scholar 

  17. Arnfinnsdottir NB, Ottesen V, Lale R, Sletmoen M. PLoS One, 2015, 10: e0128162

    Article  Google Scholar 

  18. Vora GJ, Meador CE, Bird MM, Bopp CA, Andreadis JD, Stenger DA. Proc Natl Acad Sci USA, 2005, 102: 19109–19114

    Article  CAS  Google Scholar 

  19. Czechowska K, Johnson DR, van der Meer JR. Curr Opin Microbiol, 2008, 11: 205–212

    Article  CAS  Google Scholar 

  20. Ambriz-Avina V, Contreras-Garduno JA, Pedraza-Reyes M. Biomed Res Int, 2014, 2014: 461941

    Article  CAS  Google Scholar 

  21. Chapman GV. J Immunol Methods, 2000, 243: 3–12

    Article  CAS  Google Scholar 

  22. Cram LS. Flow cytometry, an overview. In: Sobti RC, Krishan A, Eds. Advanced Flow Cytometry: Applications in Biological Research. Netherlands: Springer, 2002. 24: 1–9

    Google Scholar 

  23. Shapiro HM, Nebe-von-Caron G. Multiparameter flow cytometry of bacteria. In: Hawley TS, Hawley RG, Eds. Flow Cytometry Protocols. Volume 263 of the Series Methods in Molecular Biology. Humana Press, 2004. 263: 33–44

    Chapter  Google Scholar 

  24. Bailey JE, Fazel-Makjlessi J, McQuitty DN, Lee YN, Allred JC, Oro JA. Science, 1977, 198: 1175–1176

    Article  CAS  Google Scholar 

  25. Paau AS, Cowles JR, Oro J. Can J Microbiol, 1977, 23: 1165–1169

    Article  CAS  Google Scholar 

  26. Vives-Rego J, Lebaron P, Nebe-von Caron G. FEMS Microbiol Rev, 2000, 24: 429–448

    Article  CAS  Google Scholar 

  27. Hammes F, Egli T. Anal Bioanal Chem, 2010, 397: 1083–1095

    Article  CAS  Google Scholar 

  28. Liu G, van der Mark EJ, Verberk JQJC, van Dijk JC. Biomed Res Int, 2013: 595872

    Google Scholar 

  29. Forster S, Snape JR, Lappin-Scott HM, Porter J. Appl Environ Microb, 2002, 68: 4772–4779

    Article  CAS  Google Scholar 

  30. Van Nevel S, Koetzsch S, Weilenmann HU, Boon N, Hammes F. J Microbiol Meth, 2013, 94: 73–76

    Article  Google Scholar 

  31. Robertson KL, Vora GJ. Appl Environ Microb, 2012, 78: 14–20

    Article  CAS  Google Scholar 

  32. Joyce E, Al-Hashimi A, Mason TJ. J Appl Microbiol, 2011, 110: 862–870

    Article  CAS  Google Scholar 

  33. Gandhi A, Shah NP. Food Microbiol, 2015, 49: 197–202

    Article  CAS  Google Scholar 

  34. Chen WW, Li QZ, Zheng WS, Hu F, Zhang GX, Wang Z, Zhang DQ, Jiang XY. Angew Chem Int Ed, 2014, 53: 13734–13739

    Article  CAS  Google Scholar 

  35. Yang LL, Zhu SB, Hang W, Wu L, Yan XM. Anal Chem, 2009, 81: 2555–2563

    Article  CAS  Google Scholar 

  36. Zhu SB, Ma L, Wang S, Chen CX, Zhang WQ, Yang LL, Hang W, Nolan JP, Wu LN, Yan XM. ACS Nano, 2014, 8: 10998–11006

    Article  CAS  Google Scholar 

  37. Wang YY, Hammes F, De Roy K, Verstraete W, Boon N. Trends Biotechnol, 2010, 28: 416–424

    Article  CAS  Google Scholar 

  38. Hammes F, Berney M, Wang YY, Vital M, Koster O, Egli T. Water Res, 2008, 42: 269–277

    Article  CAS  Google Scholar 

  39. Bressan M, Gattin IT, Desaire S, Castel L, Gangneux C, Laval K. Appl Soil Ecol, 2015, 88: 60–68

    Article  Google Scholar 

  40. Falcioni T, Manti A, Boi P, Canonico B, Balsamo M, Papal S. Cytom Part B-Clin Cy, 2006, 70B: 149–153

    Article  Google Scholar 

  41. Foladori P, Laura B, Gianni A, Giuliano Z. Water Res, 2007, 41: 235–243

    Article  CAS  Google Scholar 

  42. Schellenberg J, Blake Ball T, Lane M, Cheang M, Plummer F. J Microbiol Meth, 2008, 73: 216–226

    Article  CAS  Google Scholar 

  43. Gunasekera TS, Attfield PV, Veal DA. Appl Environ Microb, 2000, 66: 1228–1232

    Article  CAS  Google Scholar 

  44. Bensch G, Ruger M, Wassermann M, Weinholz S, Reichl U, Cordes C. Appl Microbiol Biot, 2014, 98: 4897–4909

    Article  CAS  Google Scholar 

  45. Muller JA, Stanton C, Sybesma W, Fitzgerald GF, Ross RP. J Appl Microbiol, 2010, 108: 1369–1379

    Article  CAS  Google Scholar 

  46. Novo DJ, Perlmutter NG, Hunt RH, Shapiro HM. Antimicrob Agents Ch, 2000, 44: 827–834

    Article  CAS  Google Scholar 

  47. Berney M, Hammes F, Bosshard F, Weilenmann HU, Egli T. Appl Environ Microb, 2007, 73: 3283–3290

    Article  CAS  Google Scholar 

  48. Delcaru C, Chifiriuc MC, Olguta D, Iordache C, Limban C, Nitulescu GM, Vasile MA, Chirita IC, Badiceanu C, Bleotu C, Sakizlian R, Israil AM. Afr J Pharm Pharmaco, 2012, 6: 1631–1638

    Google Scholar 

  49. Suller MT, Lloyd D. Cytometry, 1999, 35: 235–241

    Article  CAS  Google Scholar 

  50. Krause M, Rosch P, Radt B, Popp J. Anal Chem, 2008, 80: 8568–8575

    Article  CAS  Google Scholar 

  51. Mustapha P, Epalle T, Allegra S, Girardot F, Garraud O, Riffard S. Res Microbiol, 2015, 166: 215–219

    Article  CAS  Google Scholar 

  52. Raymond Y, Champagne CP. Food Microbiol, 2015, 46: 176–183

    Article  Google Scholar 

  53. Manoil D, Filieri A, Gameiro C, Lange N, Schrenzel J, Wataha JC, Bouillaguet S. Photodiagn Photodyn, 2014, 11: 372–379

    Article  Google Scholar 

  54. Doherty SB, Wang L, Ross RP, Stanton C, Fitzgerald GF, Brodkorb A. J Microbiol Meth, 2010, 82: 301–310

    Article  CAS  Google Scholar 

  55. Boi P, Manti A, Pianetti A, Sabatini L, Sisti D, Rocchi MB, Bruscolini F, Galluzzi L, Papa S. Cytom Part B-Clin Cy, 2015, 88: 149–153

    Article  CAS  Google Scholar 

  56. Antolinos V, Esteban MD, Ros-Chumillas M, Huertas JP, Periago PM, Palop A, Fernandez PS. Food Res Int, 2014, 66: 306–312

    Article  CAS  Google Scholar 

  57. Rüger M, Ackermann M, Reichl U. BMC Microbiol, 2014, 14: 56

    Article  Google Scholar 

  58. Fuchslin HP, Kotzsch S, Keserue HA, Egli T. Cytom Part A, 2010, 77: 264–274

    Google Scholar 

  59. Smartt AE, Xu T, Jegier P, Carswell JJ, Blount SA, Sayler GS, Ripp S. Anal Bioanal Chem, 2012, 402: 3127–3146

    Article  CAS  Google Scholar 

  60. Awais R, Fukudomi H, Miyanaga K, Unno H, Tanji Y. Biotechnol Progr, 2006, 22: 853–859

    Article  CAS  Google Scholar 

  61. Namura M, Hijikata T, Miyanaga K, Tanji Y. Biotechnol Progr, 2008, 24: 481–486

    Article  CAS  Google Scholar 

  62. Schofield DA, Molineux IJ, Westwater C. J Clin Microbiol, 2009, 47: 3887–3894

    Article  CAS  Google Scholar 

  63. Derda R, Lockett MR, Tang SKY, Fuller RC, Maxwell EJ, Breiten B, Cuddemi CA, Ozdogan A, Whitesides GM. Anal Chem, 2013, 85: 7213–7220

    Article  CAS  Google Scholar 

  64. Edgar R, McKinstry M, Hwang J, Oppenheim AB, Fekete RA, Giulian G, Merril C, Nagashima K, Adhya S. Proc Natl Acad Sci USA, 2006, 103: 4841–4845

    Article  CAS  Google Scholar 

  65. Yim PB, Clarke ML, McKinstry M, De Paoli Lacerda SH, Pease LF III, Dobrovolskaia MA, Kang H, Read TD, Sozhamannan S, Hwang J. Biotechnol Bioeng, 2009, 104: 1059–1067

    Article  CAS  Google Scholar 

  66. Wu LN, Huang TT, Yang LL, Pan JB, Zhu SB, Yan XM. Angew Chem Int Ed, 2011, 50: 5873–5877

    Article  CAS  Google Scholar 

  67. Wu LN, Luan T, Yang XT, Wang S, Zheng Y, Huang TX, Zhu SB, Yan XM. Anal Chem, 2014, 86: 907–912

    Article  CAS  Google Scholar 

  68. Piddock LJ. Nat Rev Microbiol, 2006, 4: 629–636

    Article  CAS  Google Scholar 

  69. Nikaido H, Pages JM. FEMS Microbiol Rev, 2012, 36: 340–363

    Article  CAS  Google Scholar 

  70. Yamasaki S, Nikaido E, Nakashima R, Sakurai K, Fujiwara D, Fujii I, Nishino K. Nat Commun, 2013, 4: 2078

    Article  CAS  Google Scholar 

  71. Paixao L, Rodrigues L, Couto I, Martins M, Fernandes P, de Carvalho CC, Monteiro GA, Sansonetty F, Amaral L, Viveiros M. J Biol Eng, 2009, 3: 18

    Article  CAS  Google Scholar 

  72. Bosshard F, Berney M, Scheifele M, Weilenmann HU, Egli T. Microbiol-SGM, 2009, 155: 1310–1317

    Article  CAS  Google Scholar 

  73. Heinemann JA, Ankenbauer RG, Amabile-Cuevas CF. Drug Discov Today, 2000, 5: 195–204

    Article  CAS  Google Scholar 

  74. Spellberg B, Guidos R, Gilbert D, Bradley J, Boucher HW, Scheld WM, Bartlett JG, Edwards J, Amer IDS. Clin Infect Dis, 2008, 46: 155–164

    Article  Google Scholar 

  75. Negi PS, Jayaprakasha GK, Jena BS. LWT-Food Sci Technol, 2008, 41: 1857–1861

    Article  CAS  Google Scholar 

  76. Huang TH, Ning XH, Wang XJ, Murthy N, Tzeng YL, Dickson RM. Anal Chem, 2015, 87: 1941–1949

    Article  CAS  Google Scholar 

  77. Soejima T, Minami J, Iwatsuki K. BBA-Gen Subjects, 2012, 1820: 1980–1986

    Article  CAS  Google Scholar 

  78. Cronin UP, Wilkinson MG. J Food Prot, 2008, 71: 2168–2176

    CAS  Google Scholar 

  79. Mols M, Abee T. Environ Microbiol, 2011, 13: 2835–2843

    Article  CAS  Google Scholar 

  80. Mols M, van Kranenburg R, van Melis CC, Moezelaar R, Abee T. Environ Microbiol, 2010, 12: 873–885

    Article  CAS  Google Scholar 

  81. Cronin UP, Wilkinson MG. J Rapid Meth Aut Mic, 2008, 16: 164–184

    Article  Google Scholar 

  82. Cronin UP, Wilkinson MG. Food Microbiol, 2008, 25: 235–243

    Article  CAS  Google Scholar 

  83. Paparella A, Taccogna L, Aguzzi I, Chaves-Lopez C, Serio A, Marsilio F, Suzzi G. Food Control, 2008, 19: 1174–1182

    Article  CAS  Google Scholar 

  84. Patterson GH, Lippincott-Schwartz J. Science, 2002, 297: 1873–1877

    Article  CAS  Google Scholar 

  85. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. Science, 1994, 263: 802–805

    Article  CAS  Google Scholar 

  86. Southward CM, Surette MG. Mol Microbiol, 2002, 45: 1191–1195

    Article  CAS  Google Scholar 

  87. Vromman F, Laverriere M, Perrinet S, Dufour A, Subtil A. PLoS One, 2014, 9: e99197

    Article  CAS  Google Scholar 

  88. Silva-Rocha R, de Lorenzo V. PLoS One, 2012, 7: e34675

    Article  CAS  Google Scholar 

  89. Burmølle M, Hansen LH, Sorensen SJ. Microb Ecol, 2005, 50: 221–229

    Article  CAS  Google Scholar 

  90. Norman A, Hansen LH, Sorensen SJ. Appl Environ Microb, 2005, 71: 2338–2346

    Article  CAS  Google Scholar 

  91. Casavant NC, Thompson D, Beattie GA, Phillips GJ, Halverson LJ. Environ Microbiol, 2003, 5: 238–249

    Article  CAS  Google Scholar 

  92. Balestrino D, Hamon MA, Dortet L, Nahori MA, Pizarro-Cerda J, Alignani D, Dussurget O, Cossart P, Toledo-Arana A. Appl Environ Microb, 2010, 76: 3625–3636

    Article  CAS  Google Scholar 

  93. Tabor JJ, Bayer TS, Simpson ZB, Levy M, Ellington AD. Mol Biosyst, 2008, 4: 754–761

    Article  CAS  Google Scholar 

  94. Tracy BP, Gaida SM, Papoutsakis ET. Curr Opin Biotech, 2010, 21: 85–99

    Article  CAS  Google Scholar 

  95. Geng J, Beloin C, Ghigo JM, Henry N. PLoS One, 2014, 9: e102049

    Article  CAS  Google Scholar 

  96. Schenk M, Raffellini S, Guerrero S, Blanco GA, Alzamora SM. LWT-Food Sci Technol, 2011, 44: 191–198

    Article  CAS  Google Scholar 

  97. Cronin UP, Wilkinson MG. J Ind Microbiol Biot, 2008, 35: 1695–1703

    Article  CAS  Google Scholar 

  98. Aharoni A, Amitai G, Bernath K, Magdassi S, Tawfik DS. Chem Biol, 2005, 12: 1281–1289

    Article  CAS  Google Scholar 

  99. Foladori P, Quaranta A, Ziglio G. Water Res, 2008, 42: 3757–3766

    Article  CAS  Google Scholar 

  100. Balaev AE, Dvoretski KN, Doubrovski VA. Proc Soc Photo-Opt Ins, 2002, 5068: 375–380

    Google Scholar 

  101. Müller S, Nebe-von-Caron G. FEMS Microbiol Rev, 2010, 34: 554–587

    Article  CAS  Google Scholar 

  102. Gunther S, Geyer W, Harms H, Müller S. J Microbiol Meth, 2007, 70: 272–283

    Article  CAS  Google Scholar 

  103. Rajwa B, Venkatapathi M, Ragheb K, Banada PP, Hirleman ED, Lary T, Robinson JP. Cytom Part A, 2008, 73A: 369–379

    Article  Google Scholar 

  104. Ultra-flexible high performance system. http://www.xitogen.com/us/, 2015-09-18

  105. http://www.bdbiosciences.com/us/instruments/research/cell-sorters/bd-influx/m/744777?cc=US, 2015-09-18

  106. http://www.apogeeflow.com/products.php, 2015-09-18

  107. Keller RA, Ambrose WP, Goodwin PM, Jett JH, Martin JC, Wu M. Appl Spectrosc, 1996, 50: A12–A32

    Article  Google Scholar 

  108. Ambrose WP, Goodwin PM, Jett JH, Van Orden A, Werner JH, Keller RA. Chem Rev, 1999, 99: 2929–2956

    Article  CAS  Google Scholar 

  109. Zhu SB, Yang LL, Long Y, Gao M, Huang TX, Hang W, Yan XM. J Am Chem Soc, 2010, 132: 12176–12178

    Article  CAS  Google Scholar 

  110. Yang LL, Zhu SB, Hang W, Yan XM. Chem J Chinese U, 2008, 29: 1549–1551

    CAS  Google Scholar 

  111. Yang LL, Wu LN, Zhu SB, Long Y, Hang W, Yan XM. Anal Chem, 2010, 82: 1109–1116

    Article  CAS  Google Scholar 

  112. Zhu SB, Wang S, Yang LL, Huang TX, Yan XM. Sci China Chem, 2011, 54: 1244–1253

    Article  CAS  Google Scholar 

  113. Yang LL, Zhou YX, Zhu SB, Huang TX, Wu LN, Yan XM. Anal Chem, 2012, 84: 1526–1532

    Article  CAS  Google Scholar 

  114. Zhang SY, Zhu SB, Yang LL, Zheng Y, Gao M, Wang S, Zeng JZ, Yan XM. Anal Chem, 2012, 84: 6421–6428

    Article  CAS  Google Scholar 

  115. Yang LL, Huang TX, Zhu SB, Zhou YX, Jiang YB, Wang S, Chen YQ, Wu LN, Yan XM. Biosens Bioelectron, 2013, 48: 49–55

    Article  CAS  Google Scholar 

  116. Yu MX, Wu LN, Huang TX, Wang S, Yan XM. Anal Methods, 2015, 7: 3072–3079

    Article  CAS  Google Scholar 

  117. Zhang X, Zhang SY, Zhu SB, Chen S, Han JY, Gao KM, Zeng JZ, Yan XM. Anal Chem, 2014, 86: 5232–5237

    Article  CAS  Google Scholar 

  118. Shao Q, Zheng Y, Dong XM, Tang K, Yan XM, Xing BG. Chem-Eur J, 2013, 19: 10903–10910

    Article  CAS  Google Scholar 

  119. Chen CX, Zhang X, Zhang SY, Zhu SB, Xu JY, Zheng Y, Han JY, Zeng JZ, Yan XM. Biosens Bioelectron, 2015, 74: 476–482

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Key Laboratory of Spectrochemical Analysis & Instrumentation, Ministry of Education, Xiamen, 361005, China

    Lina Wu, Shuo Wang, Yiyi Song, Xu Wang & Xiaomei Yan

  2. Key Laboratory for Chemical Biology of Fujian Province, Xiamen, 361005, China

    Lina Wu, Shuo Wang, Yiyi Song, Xu Wang & Xiaomei Yan

  3. Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China

    Lina Wu, Shuo Wang, Yiyi Song, Xu Wang & Xiaomei Yan

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  1. Lina Wu
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  2. Shuo Wang
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  4. Xu Wang
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Correspondence to Xiaomei Yan.

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Wu, L., Wang, S., Song, Y. et al. Applications and challenges for single-bacteria analysis by flow cytometry. Sci. China Chem. 59, 30–39 (2016). https://doi.org/10.1007/s11426-015-5518-3

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