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Analysing Microbial Biofilm Formation at a Molecular Level: Role of Fourier Transform Infrared and Raman Spectroscopy

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Analytical Methodologies for Biofilm Research

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Abstract

Microorganisms adhering to biotic or abiotic surfaces depend on each other for their survival in extreme environmental stress conditions such as the lack of nutrient supply, presence of antimicrobial agents, alterations in temperature and pH of the surroundings, etc. These adherent cells known to form biofilms are enclosed within a matrix of extracellular polymeric substance (EPS) comprising of polysaccharides, nucleic acids, proteins, and lipids that furnishes a suitable environment for the survival and exchange of genetic material among neighbouring cells. EPS is also the first line of defence against various antimicrobial substances as it prevents the diffusion of these components into the indwelling cells. Thus, understanding the mode of biofilm formation and survival strategy of sessile microbial species is needed for developing new therapeutic agents against these pathogenic strains. So far traditional morphological and biochemical methods are being used to identify the genotypic and phenotypic features of the microbes. However, these methods are time consuming and require expensive reagents to perform. Thus, vibrational spectroscopic techniques such as Raman and Fourier Transform Infrared (FTIR) spectroscopy have been used as an alternate method to unravel the mysteries of biofilm formation and spread of pathogenesis. They provide a rapid and accurate identification of microbial species by providing “whole organism fingerprinting” through display of spectral features characteristic to the biochemical constituents of bacterial cell. Altogether, improvement in screening efficiency mainly in clinical microbiology would greatly help in identifying the source and cause of an infection.

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References

  1. Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995) Microbial biofilms. Annu Rev Microbiol 49:711–745

    Article  CAS  PubMed  Google Scholar 

  2. Ahimou F, Semmens MJ, Haugstad G, Novak J (2007) Effect of protein, polysaccharide, and oxygen concentration profiles on biofilm cohesiveness. Appl Environ Microbiol 73:2905–2910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Costerton J, Irvin R, Cheng K (1981) The bacterial Glycocalyx in nature and disease. Annu Rev Microbiol 35:299–324

    Article  CAS  PubMed  Google Scholar 

  4. Cui L, Yang K, Zhou GW, Huang WE et al (2017) Surface-enhanced Raman spectroscopy combined with stable isotope probing to monitor nitrogen assimilation at both bulk and single-cell level. Anal Chem 89(11):5794–5801

    Article  CAS  Google Scholar 

  5. Elias S, Banin E (2012) Multi-species biofilms: living with friendly neighbors. FEMS Microbiol Rev 36(5):990–1004

    Article  CAS  PubMed  Google Scholar 

  6. Chiyangi H, Muma JB, Malama S, Manyahi J et al (2017) Identification and antimicrobial resistance patterns of bacterial enteropathogens from children aged 0–59 months at the University Teaching Hospital, Lusaka, Zambia: a prospective cross-sectional study. BMC Infect Dis 17:117

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Ellis DI, Dunn WB, Griffin JL, Allwood JW et al (2007) Metabolic fingerprinting as a diagnostic tool. Pharmacogenomics 8(9):1243–1266

    Article  CAS  PubMed  Google Scholar 

  8. Velusamy V, Arshak K, Korostynska O, Oliwa K et al (2010) An overview of foodborne pathogen detection: in the perspective of biosensors. Biotechnol Adv 28(2):232–254

    Article  CAS  PubMed  Google Scholar 

  9. Muhamadali H, Subaihi A, Mohammadtaheri M, Xu Y et al (2016) Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting. Analyst 141(17):5127–5136

    Article  CAS  PubMed  Google Scholar 

  10. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Rinke C, Schwientek P, Sczyrba A, Ivanova NN et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459):431–437

    Article  CAS  PubMed  Google Scholar 

  12. Ellis DI, Muhamadali H, Allen DP, Elliott CT et al (2016) A flavour of omics approaches for the detection of food fraud. Curr Opin Food Sci 10:7–15

    Article  Google Scholar 

  13. Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics 2(3):155–168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Nadkarni MA, Martin FE, Jacques NA, Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148(Pt. 1):257–266

    Article  CAS  PubMed  Google Scholar 

  15. Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22(5):245–252

    Article  CAS  PubMed  Google Scholar 

  16. Chisanga M, Muhamadali H, Ellis DI, Goodacre R (2018) Surface-enhanced Raman scattering (SERS) in microbiology: illumination and enhancement of the microbial world. Appl Spectrosc 72(7):987–1000

    Article  CAS  PubMed  Google Scholar 

  17. Denkhaus E, Meisen S, Telgheder U, Wingender J (2007) Chemical and physical methods for characterisation of biofilms. Microchim Acta 158:1–27

    Article  CAS  Google Scholar 

  18. Gieroba B, Krysa M, Wojtowicz K, Wiater A, Pleszczy’nska M, Tomczyk M, Sroka-BArtnicka A (2020) The FT-IR and Raman spectroscopies as tools for biofilm characterization created by cariogenic streptococci. Int J Mol Sci 21:3811

    Article  CAS  PubMed Central  Google Scholar 

  19. Xiaonan L, Hamzah M, Al-Qadiri ML, Barbara AR (2011) Application of mid-infrared and Raman spectroscopy to the study of bacteria. Food Bioprocess Technol 4:919–935

    Article  Google Scholar 

  20. Christensen GD, Simpson W, Younger J, Baddour L, Barrett F, Melton D, Beachey E (1985) Adherence of coagulase-negative staphylococci to plastic tissue culture plates: a quantitative model for the adherence of staphylococci to medical devices. J Clin Microbiol 22:996

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ruzicka F, Hola V, Votava M, Tejkalova R, Horvat R, Heroldova M, Woznicova V (2004) Folia Microbiol 49:596–600

    Article  CAS  Google Scholar 

  22. Arciola CR, Campoccia D, Gamberini S, Cervellati M, Donati E, Montanaro L (2002) Detection of slime production by means of an optimised Congo red agar plate test based on a colourimetric scale in Staphylococcus epidermidis clinical isolates genotyped for ica locus. Biomaterials 23:4233–4239

    Article  CAS  PubMed  Google Scholar 

  23. Mack D, Horstkotte MA, Rohde H, Knobloch JKM (2006) Biofilms, infection, and antimicrobial therapy. CRC Press, Boca Raton, pp 109–153

    Google Scholar 

  24. Samek O, Al-Marashi JFM, TelleLaser HH (2010) The potential of Raman spectroscopy for the identification of biofilm formation by Staphylococcus epidermidis. Phys Lett 7(5):378–383

    CAS  Google Scholar 

  25. Bumbrah GS, Sharma RM (2016) Raman spectroscopy – basic principle, instrumentation and selected applications for the characterization of drugs of abuse. Egypt J Forensic Sci 6(3):209–215

    Article  Google Scholar 

  26. Ivleva NP, Wagner M, Horn H, Niessner R, Haisch C (2009) Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy. Anal Bioanal Chem 393(1):197–206

    Article  CAS  PubMed  Google Scholar 

  27. Schwartz T, Jungfer C, Heissler S, Friedrich F, Faubel W, Obst U (2009) Combined use of molecular biology taxonomy, Raman spectrometry, and ESEM imaging to study natural biofilms grown on filter materials at waterworks. Chemosphere 77(2):249–257

    Article  CAS  PubMed  Google Scholar 

  28. Chao Y, Zhang T (2012) Surface-enhanced Raman scattering (SERS) revealing chemical variation during biofilm formation: from initial attachment to mature biofilm. Anal Bioanal Chem 404(5):1465–1475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Virdis B, Millo D, Donose BC, Batstone DJ (2014) Real-time measurements of the redox states of c-type cytochromes in electroactive biofilms: a confocal resonance Raman Microscopy study. PLoS ONE 9(2):e89918

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Virdis B, Harnisch F, Batstone DJ, Rabaey K, Donose BC (2012) Non-invasive characterization of electrochemically active microbial biofilms using confocal Raman microscopy. Energy Environ Sci 5(5):7017–7024

    Article  CAS  Google Scholar 

  31. Gyeong BJ, Seong WN, Samjin C, Lee G-J, Park H-K (2014) Evaluation of antibiotic effects on Pseudomonas aeruginosa biofilm using Raman spectroscopy and multivariate analysis. Biomed Opt Express 5(9):3238–3251

    Article  CAS  Google Scholar 

  32. Pavlicek RL, Crane NJ, Ghebremedhin M, Cilwa KE, Elster EA (2017) Diagnostic bacteriology: methods and protocols, methods in molecular biology. Springer, Cham, p 1616

    Google Scholar 

  33. Tatiana RM, Claudia DP, Fernando TM, Grettel VB (2019) Raman spectroscopic characterization of endodontic biofilm matrices. J Spectrosc 2019:1307397

    Google Scholar 

  34. Natalia PI, Michael W, Harald H, Reinhard N, Christoph H (2008) Surface-enhanced Raman scattering analysis of biofilm. Anal Chem 80:8538–8544

    Article  CAS  Google Scholar 

  35. Rasmussen TB, Skindersoe ME, Bjarnsholt T, Phipps RK, Christensen KB, Jensen PO, Andersen JB, Koch B, Larsen TO, Hentzer M, Eberl L, Hoiby N, Givskov M (2005) Identity and effects of quorum-sensing inhibitors produced by Penicillium species. Microbiology 151(Pt 5):1325–1340

    Article  CAS  PubMed  Google Scholar 

  36. Suci PA, Geesey GG, Tyler BJ (2001) Integration of Raman microscopy, differential interference contrast microscopy, and attenuated total reflection Fourier transform infrared spectroscopy to investigate chlorhexidine spatial and temporal distribution in Candida albicans biofilms. J Microbiol Methods 46:193–208

    Article  CAS  PubMed  Google Scholar 

  37. Marcotte L, Barbeau J, Lafleur M (2004) Characterization of the diffusion of polyethylene glycol in Streptococcus mutans biofilms by Raman microspectroscopy. Appl Spectrosc 58:1295–1301

    Article  CAS  PubMed  Google Scholar 

  38. Gyeong BJ, Seong WN, Samjin C, Lee G-J (2014) Park evaluation of antibiotic effects on Pseudomonas aeruginosa biofilm using Raman spectroscopy and multivariate analysis. Biomed Opt Express 5(9):3238–3251

    Article  CAS  Google Scholar 

  39. Bae K, Zheng W, Ma Y, Huang Z (2019) Real-time monitoring of pharmacokinetics of antibiotics in biofilms with Raman-tagged hyperspectral stimulated Raman scattering microscopy. Theranostics 9(5):1348–1357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Consuelo E, Catherine LW, Lorna A, Felicity C, Goodacre R (2005) Monitoring the mode of action of antibiotics using Raman spectroscopy: investigating subinhibitory effects of amikacin on Pseudomonas aeruginosa. Anal Chem 77(9):2901–2906

    Article  CAS  Google Scholar 

  41. Moritz TJ, Taylor DS, Polage CR, Krol DM, Lane SM, Chan JW (2010) Effect of cefazolin treatment on the nonresonant Raman signatures of the metabolic state of individual Escherichia coli cells. Anal Chem 82(7):2703–2710

    Article  CAS  PubMed  Google Scholar 

  42. Walter A, Reinicke M, Bocklitz T, Schumacher W, Rösch P, Kothe E, Popp J (2011) Raman spectroscopic detection of physiology changes in plasmid-bearing Escherichia coli with and without antibiotic treatment. Anal Bioanal Chem 400(9):2763–2773

    Article  CAS  PubMed  Google Scholar 

  43. Lu X, Samuelson DR, Rasco BA, Konkel ME (2012) Antimicrobial effect of diallyl sulphide on Campylobacter jejuni biofilms. J Antimicrob Chemother 67(8):1915–1926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Moritz T, Taylor DS, Polage CR et al (2010) Effect of cefazolin treatment on the nonresonant Raman signatures of the metabolic state of individual Escherichia coli cells. Anal Chem 82:2703–2710

    Article  CAS  PubMed  Google Scholar 

  45. Moritz TJ, Polage CR, Taylor DS (2010) Evaluation of Escherichia coli cell response to antibiotic treatment by use of Raman spectroscopy with laser tweezers. J Clin Microbiol 48:4287–4290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Neugebauer U, Schmid U, Baumann K (2007) The influence of fluoroquinolone drugs on the bacterial growth of S. epidermidis utilizing the unique potential of vibrational spectroscopy. J Phys Chem A 111:2898–2906

    Article  CAS  PubMed  Google Scholar 

  47. Walter A, Reinicke M, Bocklitz T (2011) Raman spectroscopic detection of physiology changes in plasmid-bearing Escherichia coli with and without antibiotic treatment. Anal Bioanal Chem 400:2763–2773

    Article  CAS  PubMed  Google Scholar 

  48. Lu X, Rasco BA, Jabal JM (2011) Investigating antibacterial mechanisms of garlic (Allium sativum) concentrate and garlic-derived organosulfur compounds on Campylobacter jejuni using FT-IR spectroscopy, Raman spectroscopy and electron microscope. Appl Environ Microbiol 77:5257–5269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Lu X, Rasco BA, Kang DH (2011) Infrared and Raman spectroscopic studies of the antimicrobial effects of garlic concentrated and diallyl constituents on foodborne pathogens. Anal Chem 83:4137–4146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Notingher I, Verrier S, Haque S, Polak JM, Hench LL (2003) Spectroscopic study of human lung epithelial cells (A549) in culture: living cells versus dead cells. Biopolymers 72(4):230–240

    Article  CAS  PubMed  Google Scholar 

  51. Jung GB, Lee YJ, Lee GH, Park HK (2013) A simple and rapid detection of tissue adhesive-induced biochemical changes in cells and DNA using Raman spectroscopy. Biomed Opt Express 4(11):2673–2682

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Bhosale P (2004) Environmental and cultural stimulants in the production of carotenoids from microorganisms. Appl Microbiol Biotechnol 63(4):351–361

    Article  CAS  PubMed  Google Scholar 

  53. Costerton JW, Stewart PS (1999) Bacterial biofilms: a common cause of persistent infections. Science 284(5418):1318–1322

    Article  CAS  PubMed  Google Scholar 

  54. Shapiro JA (1998) Bacteria as multicellular organisms. Sci Am 256:82–89

    Google Scholar 

  55. Shapiro JA (1992) Pattern and control in bacterial colony development. Sci Prog 76:399–424

    CAS  PubMed  Google Scholar 

  56. Choo-Smith LP, Maquelin K, Van Vreeswijk T, Bruining H, Puppels G, Thi NN, Kirschner C, Naumann D, Ami D, Villa A (2001) Investigating microbial (micro) colony heterogeneity by vibrational spectroscopy. Appl Environ Microbiol 67:1461–1469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Liu H, Xu Q, Huo L, Wei X, Ling J (2014) Chemical composition of Enterococcus faecalis in biofilm cells initiated from different physiologic states. Folia Microbiol 59:447–453

    Article  CAS  Google Scholar 

  58. Sandt C, Smith-Palmer T, Pink J, Brennan L, Pink D (2007) Confocal Raman microspectroscopy as a tool for studying the chemical heterogeneities of biofilms in situ. J Appl Microbiol 103:1808–1820

    Article  CAS  PubMed  Google Scholar 

  59. Sandt C, Smith-Palmer T, Comeau J, Pink D (2009) Quantification of water and biomass in small colony variant PAO1 biofilms by confocal Raman microspectroscopy. Appl Microbiol Biotechnol 83:1171–1182

    Article  CAS  PubMed  Google Scholar 

  60. Flemming HC, Wingender J (2010) The biofilm matrix. Nat Rev Microbiol 8:623–633

    Article  CAS  PubMed  Google Scholar 

  61. Chen YP, Zhang P, Guo JS, Fang F, Gao X, Li C (2013) Functional groups characteristics of EPS in biofilm growing on different carriers. Chemosphere 92:633–638

    Article  CAS  PubMed  Google Scholar 

  62. Chen P, Cui L, Zhang K (2015) Surface-enhanced Raman spectroscopy monitoring the development of dual-species biofouling on membrane surfaces. J Membr Sci 473:36–44

    Article  CAS  Google Scholar 

  63. Huang WE, Ude S, Spiers AJ (2007) Pseudomonas fluorescens SBW25 biofilm and planktonic cells have differentiable Raman spectral profiles. Microb Ecol 53:471–474

    Article  CAS  PubMed  Google Scholar 

  64. Sharma G, Prakash A (2014) Combined use of Fourier transform infrared and Raman spectroscopy to study planktonic and biofilm cells of Cronobacter sakazakii. J Microbiol Biotechnol Food Sci 3:310

    Google Scholar 

  65. Kusic D, Kampe B, Ramoji A, Neugebauer U, Rösch P, Popp J (2015) Raman spectroscopic differentiation of planktonic bacteria and biofilms. Anal Bioanal Chem 407:6803–6813

    Article  CAS  PubMed  Google Scholar 

  66. Kusic D, Rösch P, Popp J (2016) Fast label-free detection of legionella spp. In biofilms by applying immunomagnetic beads and Raman spectroscopy. Syst Appl Microbiol 39:132–140

    Article  CAS  PubMed  Google Scholar 

  67. Stewart PS, Costerton JW (2001) Antibiotic resistance of bacteria in biofilms. Lancet 358(9276):135–138

    Article  CAS  PubMed  Google Scholar 

  68. Stewart PS (1996) Theoretical aspects of antibiotic diffusion into microbial biofilms. Antimicrob Agents Chemother 40(11):2517–2522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Movasaghi Z, Rehman S, Rehman IU (2007) Raman spectroscopy of biological tissues. Appl Spectrosc Rev 42:493–541

    Article  CAS  Google Scholar 

  70. Naumann D (2001) FT-infrared and FT-Raman spectroscopy in biomedical research. Appl Spectrosc Rev 36:239–298

    Article  CAS  Google Scholar 

  71. Papenfort K, Bassler BL (2016) Quorum sensing signal–response systems in gram-negative bacteria. Nat Rev Microbiol 14:576–588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Steindler L, Venturi V (2007) Detection of quorum-sensing N-acylnhomoserine lactone signal molecules by bacterial biosensors. FEMS Microbiol Lett 266:1–9

    Article  CAS  PubMed  Google Scholar 

  73. Singh PK, Schaefer AL, Parsek MR, Moninger TO, Welsh MJ, Greenberg EP (2000) Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms. Nature 407:762–764

    Article  CAS  PubMed  Google Scholar 

  74. Wang J, Quan C, Wang X, Zhao P, Fan S (2011) Extraction, purification and identification of bacterial signal molecules based on N-acyl homoserine lactones. Microb Biotechnol 4:479–490

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Pearman WF, Lawrence-Snyder M, Angel SM, Decho AW (2007) Surface-enhanced Raman spectroscopy for in situ measurements of signaling molecules (autoinducers) relevant to bacteria quorum sensing. Appl Spectrosc 61:1295–1300

    Article  CAS  PubMed  Google Scholar 

  76. Czajkowski R, Jafra S (2009) Quenching of acyl-homoserine lactone-dependent quorum sensing by enzymatic disruption of signal molecules. Acta Biochim Pol 56(1):1–16

    Article  CAS  PubMed  Google Scholar 

  77. Culhane K, Jiang K, Neumann A, Pinchuk AO (2017) Laser-fabricated plasmonic nanostructures for surface-enhanced RAMAN spectroscopy of bacteria quorum sensing molecules. MRS Adv 2(42):2287–2294

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Claussen A, Abdali SW, Berg R, Givskov M, Sams T (2013) Detection of the quorum sensing signal molecule N-Dodecanoyl- DLHomoserine lactone below 1 nanomolar concentrations using surface enhanced Raman spectroscopy. Curr Phys Chem 3:199–210

    Article  CAS  Google Scholar 

  79. Wu X, Chen J, Li X, Zhao Y, Zughaier SM (2014) Culture-free diagnostics of Pseudomonas aeruginosa infection by silver nanorod array based SERS from clinical sputum samples. Nanomed Nanotechnol Biol Med 10:1863–1870

    Article  CAS  Google Scholar 

  80. Hall S, McDermott C, Anoopkumar-Dukie S, McFarland A, Forbes A, Perkins A (2016) Cellular effects of pyocyanin, a secreted virulence factor of Pseudomonas aeruginosa. Toxins 8:236

    Article  PubMed Central  CAS  Google Scholar 

  81. Nguyen CQ, Thrift WJ, Bhattacharjee A, Ranjbar S, Gallagher T, Varcheie MD, Sanderson RN, Capolino F, Whiteson K, Baldi P, Hochbaum AI, Ragan R (2018) Longitudinal monitoring of biofilm formation via robust SERS quantification of pseudomonas aeruginosa-produced metabolite. ACS Appl Mater Interfaces 10(15):12364–12373

    Article  CAS  PubMed  Google Scholar 

  82. Bodelón G, Montes-García V, Costas C, Pérez-Juste I, Pérez-Juste J, Pastoriza-Santos I (2017) Imaging bacterial interspecies chemical interactions by surface-enhanced Raman scattering. ACS Nano 11:4631–4640

    Article  PubMed  CAS  Google Scholar 

  83. Lee J, Zhang L (2014) The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell 6:26–41

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  84. McClean KH, Winson MK, Fish L, Taylor A, Chhabra SR, Camara M (1997) Quorum sensing and Chromobacterium violaceum: exploitation of violacein production and inhibition for the detection of N-acylhomoserine lactones. Microbiology 143:3703–3711

    Article  CAS  PubMed  Google Scholar 

  85. Rossolini GM, Mantengoli E (2005) Treatment and control of severe infections caused by multi resistant Pseudomonas aeruginosa. Clin Microbiol Infect 11:17–32

    Article  CAS  PubMed  Google Scholar 

  86. Bauer KA, Perez KK, Forrest GN, Goff DA (2014) Review of rapid diagnostic tests used by antimicrobial stewardship programs. Clin Infect Dis 59(Suppl 3):S134–S145

    Article  CAS  PubMed  Google Scholar 

  87. Cookson WOCM, Cox MJ, Moffatt MF (2017) New opportunities for managing acute and chronic lung infections. Nat Rev Microbiol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  88. Bodelón G, Montes-García V, Pérez-Juste J, Pastoriza-Santos I (2018) Surface-enhanced Raman scattering spectroscopy for label-free analysis of P. aeruginosa quorum sensing. Front Cell Infect Microbiol 8:143

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  89. Costerton JW, Stewart PS, Greenberg EP (1999) Bacterial biofilms: a common cause of persistent infections. Science 284:1318–1322

    Article  CAS  PubMed  Google Scholar 

  90. Efeoglu E, Culha M (2013) In situ-monitoring of biofilm formation by using surface-enhanced Raman scattering. Appl Spectrosc 67:498–505

    Article  CAS  PubMed  Google Scholar 

  91. Ramya S, George R, Rao RS, Dayal R (2010) Detection of algae and bacterial biofilms formed on titanium surfaces using micro-Raman analysis. Appl Surf Sci 256:5108–5115

    Article  CAS  Google Scholar 

  92. Kelestemur S, Çulha M (2017) Understanding and discrimination of biofilms of clinically relevant microorganisms using surface-enhanced Raman scattering. Appl Spectrosc 71:1180–1188

    Article  CAS  PubMed  Google Scholar 

  93. Almarashi JFM, Kapel N, Wilkinson TS, Telle HH (2012) Raman spectroscopy of bacterial species and strains cultivated under reproducible conditions. Spectrosc Int J 27:361–365

    Article  CAS  Google Scholar 

  94. Pahlow S et al (2015) Isolation and identification of bacteria by means of Raman spectroscopy. Adv Drug Deliv Rev 89:105–120

    Article  CAS  PubMed  Google Scholar 

  95. Rebrošová K, Šiler M, Samek O (2017) Rapid identification of staphylococci by Raman spectroscopy. Sci Rep 7:14846

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  96. Tien NI (2016) Diagnosis of bacterial pathogens in the dialysate of peritoneal dialysis patients with peritonitis using surface-enhanced Raman spectroscopy. Clin Chim Acta 461:69–75

    Article  CAS  PubMed  Google Scholar 

  97. Kotanen CN, Martinez L, Alvarez J, Simecek JW (2016) Surface enhanced Raman scattering spectroscopy for detection and identification of microbial pathogens isolated from human serum. Sens Biosens Res 8:20–26

    Google Scholar 

  98. Rebrosova K, Siler M, Samek O, Ruzicka F, Bernatova S, Jezek J, Zemanek P, Hola V (2019) Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy. Future Microbiol 14(6):509–518

    Article  CAS  PubMed  Google Scholar 

  99. Mora TR, Perez CD, Mendez FT, Valle G (2019) Raman spectroscopic characterization of endodontic biofilm matrices. Bourrouet J Spectrosc 2019:7

    Google Scholar 

  100. Ivleva NP, Wagner M, Horn H, Niessner R, Haisch C (2008) In situ surface-enhanced Raman scattering analysis of biofilm. Anal Chem 80:8538–8544

    Article  CAS  PubMed  Google Scholar 

  101. Rebrosova K, Siler M, Samek O, Ruzicka F, Bernatova S, Jezek J, Zemanek P, Hola V (2017) Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy. Future Microbiol 12(10):881–890

    Article  CAS  PubMed  Google Scholar 

  102. Beier BD, Quivey RG, Berger AJ (2012) Raman microspectroscopy for species identification and mapping within bacterial biofilms. AMB Express 2(35):2–6

    Google Scholar 

  103. Schmitt J, Flemming HC (1998) FTIR spectroscopy in microbial and material analysis. Int Biodeterior Biodegrad 41:1–11

    Article  CAS  Google Scholar 

  104. Suci PA, Vrany JD, Mittelman MW (1998) Investigation of interactions between antimicrobial agents and bacterial biofilms using attenuated total reflection Fourier transform infrared spectroscopy. Biomaterials 19:327–339

    Article  CAS  PubMed  Google Scholar 

  105. Ojeda JJ, Dittrich M (2012) Fourier transform infrared spectroscopy for molecular analysis of microbial cells. Methods Mol Biol 881:187–211

    Article  CAS  PubMed  Google Scholar 

  106. Naumann D, Helm D, Labischinski H (1991) Microbiological characterization by FTIR spectroscopy. Nature 351:81–82

    Article  CAS  PubMed  Google Scholar 

  107. Nivens DE, Chambers JQ, Anderson TR, Tunlid A, Smit J, White DC (1993) Monitoring microbial adhesion and biofilm formation by attenuated total reflection/Fourier transform infrared spectroscopy. J Microbiol Methods 17:199–213

    Article  Google Scholar 

  108. Neidhardt FC, Ingraham JL, Schaechter M (1992) Physiology of the bacterial cell, a molecular approach. Sinauer Associates, Sunderland, p 4

    Google Scholar 

  109. Zhao D, Liu G, Song D, Liu J, Zhou Y, Ou J, Sun S (2006) Fourier transform infrared spectroscopic study of truffles. Proc SPIE 6026:60260H-1

    Google Scholar 

  110. Suresh AK (2012) Metallic nanocrystallites and their interaction with microbial systems. Springer, New York

    Book  Google Scholar 

  111. Erukhimovitch V, Tsror L, Hazanovsky M, Talyshinsky M, Mukmanov I, Souprun Y, Huleihel M (2005) Identification of fungal phyto-pathogens by Fourier-transform infrared (FTIR) microscopy. J Agric Sci Technol 1:145–152

    Google Scholar 

  112. Muyonga JH, Cole CGB, Duodu KG (2004) Fourier transform infrared (FTIR) spectroscopic study of acid soluble collagen and gelatin from skins and bones of young and adult Nile perch (Latesniloticus). Food Chem 86:325–332

    Article  CAS  Google Scholar 

  113. Naumann D, Barnickel G, Bradaczek H, Labischinski H, Giesbrecht P (1982) Infrared spectroscopy, a tool for probing bacterial peptidoglycan potentialities of infrared spectroscopy for cell wall analytical studies and rejection of models based on crystalline chitin. Eur J Biochem 125:505–515

    Article  CAS  PubMed  Google Scholar 

  114. Nivens DE, Chambers JQ, Anderson TR (1993) Monitoring microbial adhesion and biofilm formation by attenuated total reflection/Fourier transform infrared spectroscopy. J Microbiol Methods 17:199–213

    Article  Google Scholar 

  115. Bosch A, Serra D, Prieto C, Schmitt J, Naumann D, Yantorno O (2006) Characterization of Bordetella pertussis growing as biofilm by chemical analysis and FT-IR spectroscopy. Appl Microbiol Biotechnol 71:736–747

    Article  CAS  PubMed  Google Scholar 

  116. Singhalage ID, Seneviratne G, Madawala HMSP, Manawasinghe IS (2018) Characterization of structural properties of fungal-bacterial biofilms by Fourier Transform Infrared Spectroscopy. Ceylon J Sci 47(1):77–83

    Article  Google Scholar 

  117. Quilès F, Humbert F¸o, Delille A (2010) Analysis of changes in attenuated total reflection FTIR fingerprints of Pseudomonas fluorescens from planktonic state to nascent biofilm state. Spectrochim Acta A 75:610–616

    Article  CAS  Google Scholar 

  118. Suci PA, Mittelman MW, Yu FP, Geesey GG (1994) Investigation of ciprofloxacin penetration into Pseudomonas aeruginosa biofilms. Antimicrob Agents Chemother 38:2125–2133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Faghihzadeh F, Anaya NM, Schifman LA, Oyanedel-Craver V (2016) Fourier transform infrared spectroscopy to assess molecular-level changes in microorganisms exposed to nanoparticles. Nanotechnol Environ Eng 1:1

    Article  Google Scholar 

  120. Vrany JD, Stewart PS, Suci PA (1997) Comparison of recalcitrance to ciprofloxacin and levofloxacin exhibited by Pseudomonas aeruginosa biofilms displaying rapid-transport characteristics. Antimicrob Agents Chemother 41:1352–1358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Nguyen TK, Selvanayagam R, Ho KKK, Chen R, Kutty SK, Rice SA, Kumar N, Barraud N, Duong HTT, Boyer C (2016) Co-delivery of nitric oxide and antibiotic using polymeric nanoparticles. Chem Sci 7:1016–1027

    Article  CAS  PubMed  Google Scholar 

  122. Barapatre A, Aadil KR, Jha H (2016) Synergistic antibacterial and antibiofilm activity of silver nanoparticles biosynthesized by lignin-degrading fungus. Bioprocess Bioresour 3:8

    Article  Google Scholar 

  123. Quilès F, Saadi S, Francius G, Bacharouche J, Humbert F (2016) In situ and real time investigation of the evolution of a Pseudomonas fluorescens nascent biofilm in the presence of an antimicrobial peptide. Biochim Biophys Acta 1858(1):75–84

    Article  PubMed  CAS  Google Scholar 

  124. Siddique MH, Aslam B, Imran M, Ashraf A, Nadeem H, Hayat S, Khurshid M, Afzal M, Malik IR, Shahzad M, Qureshi U, Ul Haq Khan Z (2020) Effect of silver nanoparticles on biofilm formation and EPS production of multidrug-resistant klebsiella pneumonia. Biomed Res Int 2020:6398165

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  125. Bruinsma GM, van der Mei HC, Busscher HJ (2001) Bacterial adhesion to surface hydrophilic and hydrophobic contact lenses. Biomaterials 22:3217–3224

    Article  CAS  PubMed  Google Scholar 

  126. Carlos C, Maretto DA, Poppi RJ et al (2011) Fourier transform infrared microspectroscopy as a bacterial source tracking tool to discriminate fecal E. coli strains. Microchem J 99:15–19

    Article  CAS  Google Scholar 

  127. Jiang W, Yang K, Vachet RW, Xing B (2010) Interaction between oxide nanoparticles and biomolecules of the bacterial cell envelope as examined by infrared spectroscopy. Langmuir 26:18071–18077

    Article  CAS  PubMed  Google Scholar 

  128. Riding MJ, Martin FL, Trevisan J (2012) Concentration-dependent effects of carbon nanoparticles in gram-negative bacteria determined by infrared spectroscopy with multivariate analysis. Environ Pollut 163:226–234

    Article  CAS  PubMed  Google Scholar 

  129. Wang W (2011) Photocatalytic degradation of E. coli membrane cell in the presence of ZnO nanowires. J Wuhan Univ Technol Mater Sci Ed 26:222–225

    Article  CAS  Google Scholar 

  130. Hu C, Guo J, Qu J, Hu X (2007) Photocatalytic degradation of pathogenic bacteria with AgI/TiO2 under visible light irradiation. Langmuir 23:4982–4987

    Article  CAS  PubMed  Google Scholar 

  131. Landa AS, van der Mei HC, Busscher HJ (1997) Detachment of linking film bacteria from enamel surfaces by oral rinses and penetration of sodium lauryl sulphate through an artificial oral biofilm. Adv Dent Res 11:528–538

    Article  CAS  PubMed  Google Scholar 

  132. Ojeda JJ, Romero-Gonzalez ME, Pouran HM, Banwart SA (2008) In situ monitoring of the biofilm formation of Pseudomonas putida on hematite using flow-cell ATR-FTIR spectroscopy to investigate the formation of innersphere bonds between the bacteria and the mineral. Mineral Mag 72:101–106

    Article  CAS  Google Scholar 

  133. Delille A, Quiles F, Humbert F (2007) In situ monitoring of the nascent Pseudomonas fluorescens biofilm response to variations in the dissolved organic carbon level in low-nutrient water by attenuated total reflectance-Fourier transform infrared spectroscopy. Appl Environ Microbiol 73:5782–5788

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Biotechnology, University of Engineering & Management, Kolkata, India

    Moupriya Nag, Dibyajit Lahiri, Ritwik Banerjee, Abarna Chatterjee, Anushka Ghosh & Prateek Banerjee

  2. Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India

    Rina Rani Ray

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  1. Moupriya Nag
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  1. Department of Biotechnology, University of Engineering & Management, Kolkata, West Bengal, India

    Moupriya Nag

  2. Department of Biotechnology, University of Engineering & Management, Kolkata, West Bengal, India

    Dibyajit Lahiri

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Nag, M. et al. (2021). Analysing Microbial Biofilm Formation at a Molecular Level: Role of Fourier Transform Infrared and Raman Spectroscopy. In: Nag, M., Lahiri, D. (eds) Analytical Methodologies for Biofilm Research. Springer Protocols Handbooks. Springer, New York, NY. https://doi.org/10.1007/978-1-0716-1378-8_3

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  • DOI: https://doi.org/10.1007/978-1-0716-1378-8_3

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