Metagenomic approach to study biofilm in medical context
Main Article Content
Abstract
Microbial organization in biofilms plays an important role in health and disease. This microbial lifestyle can protect its host against pathogens and contribute to the metabolism of nutrients. On the other hand, pathogenic biofilms can increase the morbidity and mortality of patients, raising the economic cost of infections. Here, we describe how biofilm is organized, its role in different scenarios in the human body and discuss how metagenomic studies has contributed to understand the microbial diversity that interact with the host. It is currently known that many biofilms in the human body may have a polymicrobial composition. In the context of infectious diseases, this composition may limit therapeutic approaches to combat biofilms even more. Thus, describing microbial diversity could help to guide therapeutic decisions.
Article Details
How to Cite
RIBEIRO, Suzana Meira; DE CASTRO, Alinne Pereira; FRANCO, Octávio Luiz.
Metagenomic approach to study biofilm in medical context.
Medical Research Archives, [S.l.], v. 5, n. 5, may 2017.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/1222>. Date accessed: 04 dec. 2024.
Keywords
Biofilm; metagenomic; polymicrobial infection
Section
Review Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
References
1. Carlet J, Collignon P, Goldmann D, Goossens H, Gyssens IC, Harbarth S, et al. Society’s failure to protect a precious resource: antibiotics. The Lancet. 2011 Jul 23;378(9788):369–71.
2. Bertelli C, Greub G. Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis. 2013 Sep;19(9):803–13.
3. Weimer KED, Juneau RA, Murrah KA, Pang B, Armbruster CE, Richardson SH, et al. Divergent mechanisms for passive pneumococcal resistance to β-lactam antibiotics in the presence of Haemophilus influenzae. J Infect Dis. 2011 Feb 15;203(4):549–55.
4. Dunne WM, Westblade LF, Ford B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis Off Publ Eur Soc Clin Microbiol. 2012 Aug;31(8):1719–26.
5. Greninger AL, Chen EC, Sittler T, Scheinerman A, Roubinian N, Yu G, et al. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PloS One. 2010 Oct 18;5(10):e13381.
6. Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ-M, Quick J, et al. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA. 2013 Apr 10;309(14):1502–10.
7. Padmanabhan R, Mishra AK, Raoult D, Fournier P-E. Genomics and metagenomics in medical microbiology. J Microbiol Methods. 2013 Dec;95(3):415–24.
8. Battin TJ, Besemer K, Bengtsson MM, Romani AM, Packmann AI. The ecology and biogeochemistry of stream biofilms. Nat Rev Microbiol. 2016 Apr;14(4):251–63.
9. Flemming H-C, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016 Sep;14(9):563–75.
10. Cook LCC, Dunny GM. The influence of biofilms in the biology of plasmids. Microbiol Spectr. 2014 Oct 10;2(5):12.
11. Kean R, Rajendran R, Haggarty J, Townsend EM, Short B, Burgess KE, et al. Candida albicans Mycofilms Support Staphylococcus aureus Colonization and Enhances Miconazole Resistance in Dual-Species Interactions. Front Microbiol. 2017;8:258.
12. Hughes G, Webber MA. Novel approaches to the treatment of bacterial biofilm infections. Br J Pharmacol. 2017 Jan 1;n/a-n/a.
13. Johnson CH, Dejea CM, Edler D, Hoang LT, Santidrian AF, Felding BH, et al. Metabolism Links Bacterial Biofilms and Colon Carcinogenesis. Cell Metab. 2015 Jun 2;21(6):891–7.
14. Macfarlane S, Bahrami B, Macfarlane GT. Mucosal biofilm communities in the human intestinal tract. Adv Appl Microbiol. 2011;75:111–43.
15. Percival SL, Emanuel C, Cutting KF, Williams DW. Microbiology of the skin and the role of biofilms in infection. Int Wound J. 2012 Feb;9(1):14–32.
16. Büttner H, Mack D, Rohde H. Structural basis of Staphylococcus epidermidis biofilm formation: mechanisms and molecular interactions. Front Cell Infect Microbiol. 2015;5:14.
17. Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, et al. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature. 2010 May 20;465(7296):346–9.
18. Vos WM de. Microbial biofilms and the human intestinal microbiome. Npj Biofilms Microbiomes. 2015 Mar 25;1:15005.
19. Hattori M, Taylor TD. The Human Intestinal Microbiome: A New Frontier of Human Biology. DNA Res Int J Rapid Publ Rep Genes Genomes. 2009 Feb;16(1):1–12.
20. Marsh PD, Zaura E. Dental biofilm: ecological interactions in health and disease. J Clin Periodontol. 2017 Mar 1;44:S12–22.
21. Guarner F, Malagelada J-R. Gut flora in health and disease. Lancet Lond Engl. 2003 Feb 8;361(9356):512–9.
22. Li S, Konstantinov SR, Smits R, Peppelenbosch MP. Bacterial Biofilms in Colorectal Cancer Initiation and Progression. Trends Mol Med. 2017 Jan;23(1):18–30.
23. Ai D, Huang R, Wen J, Li C, Zhu J, Xia LC. Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics. 2017;18(1):1041.
24. Curtis MA, Zenobia C, Darveau RP. The relationship of the oral microbiotia to periodontal health and disease. Cell Host Microbe. 2011 Oct 20;10(4):302–6.
25. Gbejuade HO, Lovering AM, Webb JC. The role of microbial biofilms in prosthetic joint infections. Acta Orthop. 2015 Mar 4;86(2):147–58.
26. Rieger UM, Mesina J, Kalbermatten DF, Haug M, Frey HP, Pico R, et al. Bacterial biofilms and capsular contracture in patients with breast implants. Br J Surg. 2013 May 1;100(6):768–74.
27. Sands KM, Wilson MJ, Lewis MAO, Wise MP, Palmer N, Hayes AJ, et al. Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation. J Crit Care. 2017 Feb;37:30–7.
28. Stickler DJ. Clinical complications of urinary catheters caused by crystalline biofilms: something needs to be done. J Intern Med. 2014 Aug 1;276(2):120–9.
29. Rather IA, Kim B-C, Bajpai VK, Park Y-H. Self-medication and antibiotic resistance: Crisis, current challenges, and prevention. Saudi J Biol Sci [Internet]. [cited 2017 Feb 20]; Available from: http://www.sciencedirect.com/science/article/pii/S1319562X17300049
30. Dickson RP, Erb-Downward JR, Huffnagle GB. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med. 2014 Mar;2(3):238–46.
31. Frank C, Werber D, Cramer JP, Askar M, Faber M, an der Heiden M, et al. Epidemic profile of Shiga-toxin-producing Escherichia coli O104:H4 outbreak in Germany. N Engl J Med. 2011 Nov 10;365(19):1771–80.
32. Kim S, Jonghe JD, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, et al. High-throughput automated microfluidic sample preparation for accurate microbial genomics. Nat Commun. 2017 Jan 27;8:13919.
33. Fischer N, Rohde H, Indenbirken D, Günther T, Reumann K, Lütgehetmann M, et al. Rapid metagenomic diagnostics for suspected outbreak of severe pneumonia. Emerg Infect Dis. 2014 Jun;20(6):1072–5.
34. Lewandowska DW, Zagordi O, Zbinden A, Schuurmans MM, Schreiber P, Geissberger F-D, et al. Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains. Diagn Microbiol Infect Dis. 2015 Oct;83(2):133–8.
35. Loman NJ, Pallen MJ. Twenty years of bacterial genome sequencing. Nat Rev Microbiol. 2015;13(12):787–94.
36. Gabrilska RA, Rumbaugh KP. Biofilm models of polymicrobial infection. Future Microbiol. 2015;10(12):1997–2015.
37. Wolcott R, Costerton JW, Raoult D, Cutler SJ. The polymicrobial nature of biofilm infection. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis. 2013 Feb;19(2):107–12.
38. Paganin P, Fiscarelli EV, Tuccio V, Chiancianesi M, Bacci G, Morelli P, et al. Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function. PloS One. 2015;10(4):e0124348.
39. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PloS One. 2012;7(6):e37919.
40. Lee KWK, Periasamy S, Mukherjee M, Xie C, Kjelleberg S, Rice SA. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. ISME J. 2014 Apr;8(4):894–907.
41. Mottola C, Mendes JJ, Cristino JM, Cavaco-Silva P, Tavares L, Oliveira M. Polymicrobial biofilms by diabetic foot clinical isolates. Folia Microbiol (Praha). 2016 Jan;61(1):35–43.
42. McLean RJC, Kakirde KS. Enhancing metagenomics investigations of microbial interactions with biofilm technology. Int J Mol Sci. 2013 Nov 11;14(11):22246–57.
2. Bertelli C, Greub G. Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis. 2013 Sep;19(9):803–13.
3. Weimer KED, Juneau RA, Murrah KA, Pang B, Armbruster CE, Richardson SH, et al. Divergent mechanisms for passive pneumococcal resistance to β-lactam antibiotics in the presence of Haemophilus influenzae. J Infect Dis. 2011 Feb 15;203(4):549–55.
4. Dunne WM, Westblade LF, Ford B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis Off Publ Eur Soc Clin Microbiol. 2012 Aug;31(8):1719–26.
5. Greninger AL, Chen EC, Sittler T, Scheinerman A, Roubinian N, Yu G, et al. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PloS One. 2010 Oct 18;5(10):e13381.
6. Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ-M, Quick J, et al. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA. 2013 Apr 10;309(14):1502–10.
7. Padmanabhan R, Mishra AK, Raoult D, Fournier P-E. Genomics and metagenomics in medical microbiology. J Microbiol Methods. 2013 Dec;95(3):415–24.
8. Battin TJ, Besemer K, Bengtsson MM, Romani AM, Packmann AI. The ecology and biogeochemistry of stream biofilms. Nat Rev Microbiol. 2016 Apr;14(4):251–63.
9. Flemming H-C, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016 Sep;14(9):563–75.
10. Cook LCC, Dunny GM. The influence of biofilms in the biology of plasmids. Microbiol Spectr. 2014 Oct 10;2(5):12.
11. Kean R, Rajendran R, Haggarty J, Townsend EM, Short B, Burgess KE, et al. Candida albicans Mycofilms Support Staphylococcus aureus Colonization and Enhances Miconazole Resistance in Dual-Species Interactions. Front Microbiol. 2017;8:258.
12. Hughes G, Webber MA. Novel approaches to the treatment of bacterial biofilm infections. Br J Pharmacol. 2017 Jan 1;n/a-n/a.
13. Johnson CH, Dejea CM, Edler D, Hoang LT, Santidrian AF, Felding BH, et al. Metabolism Links Bacterial Biofilms and Colon Carcinogenesis. Cell Metab. 2015 Jun 2;21(6):891–7.
14. Macfarlane S, Bahrami B, Macfarlane GT. Mucosal biofilm communities in the human intestinal tract. Adv Appl Microbiol. 2011;75:111–43.
15. Percival SL, Emanuel C, Cutting KF, Williams DW. Microbiology of the skin and the role of biofilms in infection. Int Wound J. 2012 Feb;9(1):14–32.
16. Büttner H, Mack D, Rohde H. Structural basis of Staphylococcus epidermidis biofilm formation: mechanisms and molecular interactions. Front Cell Infect Microbiol. 2015;5:14.
17. Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, et al. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature. 2010 May 20;465(7296):346–9.
18. Vos WM de. Microbial biofilms and the human intestinal microbiome. Npj Biofilms Microbiomes. 2015 Mar 25;1:15005.
19. Hattori M, Taylor TD. The Human Intestinal Microbiome: A New Frontier of Human Biology. DNA Res Int J Rapid Publ Rep Genes Genomes. 2009 Feb;16(1):1–12.
20. Marsh PD, Zaura E. Dental biofilm: ecological interactions in health and disease. J Clin Periodontol. 2017 Mar 1;44:S12–22.
21. Guarner F, Malagelada J-R. Gut flora in health and disease. Lancet Lond Engl. 2003 Feb 8;361(9356):512–9.
22. Li S, Konstantinov SR, Smits R, Peppelenbosch MP. Bacterial Biofilms in Colorectal Cancer Initiation and Progression. Trends Mol Med. 2017 Jan;23(1):18–30.
23. Ai D, Huang R, Wen J, Li C, Zhu J, Xia LC. Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics. 2017;18(1):1041.
24. Curtis MA, Zenobia C, Darveau RP. The relationship of the oral microbiotia to periodontal health and disease. Cell Host Microbe. 2011 Oct 20;10(4):302–6.
25. Gbejuade HO, Lovering AM, Webb JC. The role of microbial biofilms in prosthetic joint infections. Acta Orthop. 2015 Mar 4;86(2):147–58.
26. Rieger UM, Mesina J, Kalbermatten DF, Haug M, Frey HP, Pico R, et al. Bacterial biofilms and capsular contracture in patients with breast implants. Br J Surg. 2013 May 1;100(6):768–74.
27. Sands KM, Wilson MJ, Lewis MAO, Wise MP, Palmer N, Hayes AJ, et al. Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation. J Crit Care. 2017 Feb;37:30–7.
28. Stickler DJ. Clinical complications of urinary catheters caused by crystalline biofilms: something needs to be done. J Intern Med. 2014 Aug 1;276(2):120–9.
29. Rather IA, Kim B-C, Bajpai VK, Park Y-H. Self-medication and antibiotic resistance: Crisis, current challenges, and prevention. Saudi J Biol Sci [Internet]. [cited 2017 Feb 20]; Available from: http://www.sciencedirect.com/science/article/pii/S1319562X17300049
30. Dickson RP, Erb-Downward JR, Huffnagle GB. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med. 2014 Mar;2(3):238–46.
31. Frank C, Werber D, Cramer JP, Askar M, Faber M, an der Heiden M, et al. Epidemic profile of Shiga-toxin-producing Escherichia coli O104:H4 outbreak in Germany. N Engl J Med. 2011 Nov 10;365(19):1771–80.
32. Kim S, Jonghe JD, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, et al. High-throughput automated microfluidic sample preparation for accurate microbial genomics. Nat Commun. 2017 Jan 27;8:13919.
33. Fischer N, Rohde H, Indenbirken D, Günther T, Reumann K, Lütgehetmann M, et al. Rapid metagenomic diagnostics for suspected outbreak of severe pneumonia. Emerg Infect Dis. 2014 Jun;20(6):1072–5.
34. Lewandowska DW, Zagordi O, Zbinden A, Schuurmans MM, Schreiber P, Geissberger F-D, et al. Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains. Diagn Microbiol Infect Dis. 2015 Oct;83(2):133–8.
35. Loman NJ, Pallen MJ. Twenty years of bacterial genome sequencing. Nat Rev Microbiol. 2015;13(12):787–94.
36. Gabrilska RA, Rumbaugh KP. Biofilm models of polymicrobial infection. Future Microbiol. 2015;10(12):1997–2015.
37. Wolcott R, Costerton JW, Raoult D, Cutler SJ. The polymicrobial nature of biofilm infection. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis. 2013 Feb;19(2):107–12.
38. Paganin P, Fiscarelli EV, Tuccio V, Chiancianesi M, Bacci G, Morelli P, et al. Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function. PloS One. 2015;10(4):e0124348.
39. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PloS One. 2012;7(6):e37919.
40. Lee KWK, Periasamy S, Mukherjee M, Xie C, Kjelleberg S, Rice SA. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. ISME J. 2014 Apr;8(4):894–907.
41. Mottola C, Mendes JJ, Cristino JM, Cavaco-Silva P, Tavares L, Oliveira M. Polymicrobial biofilms by diabetic foot clinical isolates. Folia Microbiol (Praha). 2016 Jan;61(1):35–43.
42. McLean RJC, Kakirde KS. Enhancing metagenomics investigations of microbial interactions with biofilm technology. Int J Mol Sci. 2013 Nov 11;14(11):22246–57.