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Biofouling
The Journal of Bioadhesion and Biofilm Research
Volume 37, 2021 - Issue 1
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Research Article

Databases for the study of biofilms: current status and potential applications

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Pages 96-108 | Received 04 Nov 2020, Accepted 11 Jan 2021, Published online: 28 Jan 2021

References

  • Almeida Fd, Vargas ELG, Carneiro DG, Pinto UM, Vanetti MCD. 2018. Virtual screening of plant compounds and nonsteroidal anti-inflammatory drugs for inhibition of quorum sensing and biofilm formation in Salmonella. Microb Pathog. 121:369–388. doi:10.1016/j.micpath.2018.05.014
  • Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, et al. 2017. Critical review on biofilm methods. Crit Rev Microbiol. 43:313–351. doi:10.1080/1040841X.2016.1208146
  • Bamford NC, Le Mauff F, Van Loon JC, Ostapska H, Snarr BD, Zhang Y, Kitova EN, Klassen JS, Codée JDC, Sheppard DC, et al. 2020. Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation. Nat Commun. 11:2020. doi:10.1038/s41467-020-16144-5
  • Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, et al. 2002. The protein data bank. Acta Crystallogr D Biol Crystallogr. 58:899–907. doi:10.1107/s0907444902003451
  • Boudarel H, Mathias JD, Blaysat B, Grédiac M. 2018. Towards standardized mechanical characterization of microbial biofilms: analysis and critical review. Npj Biofilms Microbiomes. 4:4. doi:10.1038/s41522-018-0062-5
  • Buetti-Dinh A, Galli V, Bellenberg S, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, et al. 2019. Deep neural networks outperform human expert’s capacity in characterizing bioleaching bacterial biofilm composition. Biotechnol Rep. 22:e00321. doi:10.1016/j.btre.2019.e00321
  • Cattò C, Cappitelli F. 2019. Testing anti-biofilm polymeric surfaces: where to start? Int J Mol Sci. 20:3794. doi:10.3390/ijms20153794. [doi Link]
  • Cho KH, Tryon RG, Kim JH. 2020. Screening for diguanylate cyclase (DGC) inhibitors mitigating bacterial biofilm formation. Front Chem. 8:2020. doi:10.3389/fchem.2020.00264 [doi Link]
  • Coenye T, Kjellerup B, Stoodley P, Bjarnsholt T, 2019 Biofilm Bash Participants. 2020. The future of biofilm research – report on the ‘2019 Biofilm Bash. Biofilm. 2:100012. doi:10.1016/j.bioflm.2019.100012
  • Cui Y, Schmid BV, Cao H, Dai X, Du Z, Ryan Easterday W, Fang H, Guo C, Huang S, Liu W, et al. 2020. Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment. Nat Commun. 11:2020. doi:10.1038/s41467-019-14099-w
  • da Silva Rocha SFL, Olanda CG, Fokoue HH, Sant'Anna CMR. 2019. Virtual screening techniques in drug discovery: review and recent applications. Curr Top Med Chem. 19:1751–1767. doi:10.2174/1568026619666190816101948
  • Di Luca M, Maccari G, Maisetta G, Batoni G. 2015. BaAMPs: the database of biofilm-active antimicrobial peptides. Biofouling. 31:193–199. doi:10.1080/08927014.2015.1021340
  • Flemming HC. 2020. Biofouling and me: my Stockholm syndrome with biofilms. Water Res. 173:115576. doi:10.1016/j.watres.2020.115576
  • Flemming HC, Wingender J. 2010. The biofilm matrix. Nat Rev Microbiol. 8:623–633. doi:10.1038/nrmicro2415
  • Fuqua C, Parsek MR, Greenberg EP. 2001. Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet. 35:439–468. doi:10.1146/annurev.genet.35.102401.090913
  • Galperin MY. 2005. The molecular biology database collection: 2005 update. Nucleic Acids Res. 33:D5–D24. doi:10.1093/nar/gki139. [doi Link]
  • Ganesan A, Coote ML, Barakat K. 2017. Molecular dynamics-driven drug discovery: leaping forward with confidence. Drug Discov Today. 22:249–269. doi:10.1016/j.drudis.2016.11.001
  • Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, et al. 2012. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 40:1100–1107. doi:10.1093/nar/gkr777 [doi Link]
  • Gericke B, Schecker N, Amiri M, Naim HY. 2017. Structure-function analysis of human sucrase-isomaltase identifies key residues required for catalytic activity. J Biol Chem. 292(26):11070–11078. doi:10.1074/jbc.M117.791939 [doi Link]
  • Gilson MK, Liu T, Baitaluk M, Nicola G, Hwang L, Chong J. 2016. BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 44:D1045–D1053. doi:10.1093/nar/gkv1072
  • Gimeno A, Ojeda-Montes MJ, Tomás-Hernández S, Cereto-Massagué A, Beltrán-Debón R, Mulero M, Pujadas G, Garcia-Vallvé S. 2019. The light and dark sides of virtual screening: what is there to know? Int J Mol Sci. 20:1375. doi:10.3390/ijms20061375 [doi Link]
  • Grinter SZ, Zou X. 2014. Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design. Molecules. 19:10150–10176. doi:10.3390/molecules190710150
  • Grudlewska-Buda K, Skowron K, Gospodarek-Komkowska E. 2020. Comparison of the intensity of biofilm formation by Listeria monocytogenes using classical culture-based method and digital droplet PCR. AMB Expr. 10:2020. doi:10.1186/s13568-020-01007-5
  • Gupta S, Sharma AK, Jaiswal SK, Sharma VK. 2016. Prediction of biofilm inhibiting peptides: an in silico approach. Front Microbiol. 7:1–11. doi:10.3389/fmicb.2016.00949 [doi link]
  • Hall CW, Mah TF. 2017. Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria. FEMS Microbiol Rev. 41:276–301. doi:10.1093/femsre/fux010
  • Hancock REW, Sahl HG. 2006. Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat Biotechnol. 24:1551–1557. doi:10.1038/nbt1267
  • Hollingsworth SA, Dror RO. 2018. Molecular dynamics simulation for all. Neuron. 99:1129–1143. doi:10.1016/j.neuron.2018.08.011
  • Jamal M, Ahmad W, Andleeb S, Jalil F, Imran M, Nawaz MA, Hussain T, Ali M, Rafiq M, Kamil MA. 2018. Bacterial biofilm and associated infections. J Chin Med Assoc. 81:7–11. doi:10.1016/j.jcma.2017.07.012
  • Jeon DM, An JS, Lim BS, Ahn SJ. 2020. Orthodontic bonding procedures significantly influence biofilm composition. Prog Orthod. 21:2020. doi:10.1186/s40510-020-00314-8
  • Kaur A, Capalash N, Sharma P. 2018. Quorum sensing in thermophiles: prevalence of autoinducer-2 system. BMC Microbiol. 18:1–16. doi:10.1186/s12866-018-1204-x
  • Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, et al. 2019. PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 47:D1102–D1109. doi:10.1093/nar/gky1033
  • Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, et al. 2016. PubChem substance and compound databases. Nucleic Acids Res. 44:D1202–D1213. doi:10.1093/nar/gkv951
  • Koo H, Allan RN, Howlin RP, Stoodley P, Hall-Stoodley L. 2017. Targeting microbial biofilms: current and prospective therapeutic strategies. Nat Rev Microbiol. 15:740–755. doi:10.1038/nrmicro.2017.99
  • Leoni G, De Poli A, Mardirossian M, Gambato S, Florian F, Venier P, Wilson DN, Tossi A, Pallavicini A, Gerdol M. 2017. Myticalins: a novel multigenic family of linear, cationic antimicrobial peptides from marine mussels (Mytilus spp). Mar Drugs. 15:1–23. doi:10.3390/md15080261 [doi link]
  • Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. 2007. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 35:198–201. doi:10.1093/nar/gkl999 [doi link]
  • Lourenço A, Coenye T, Goeres DM, Donelli G, Azevedo AS, Ceri H, Coelho FL, Flemming HC, Juhna T, Lopes SP, et al. 2014. Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces. Pathog Dis. 70:250–256. doi:10.1111/2049-632X.12146
  • Lourenço A, Ferreira A, Veiga N, Machado I, Pereira MO, Azevedo NF. 2012. Biofomics: a web platform for the systematic and standardized collection of high-throughput biofilm data. PLoS One. 7:e39960. doi:10.1371/journal.pone.0039960
  • Machineni L. 2020. Effects of biotic and abiotic factors on biofilm growth dynamics and their heterogeneous response to antibiotic challenge. J Biosci. 45:2020. doi:10.1007/s12038-020-9990-3
  • Magalhães RP, Vieira TF, Fernandes HS, Melo A, Simões M, Sousa SF. 2020. The biofilms structural database. Trends Biotechnol. 38:937–940.doi:10.1016/j.tibtech.2020.04.002 [doi link]
  • Marimuthu SK, Nagarajan K, Perumal SK, Palanisamy S, Subbiah L. 2020. In silico alpha-helical structural recognition of temporin antimicrobial peptides and its interactions with Middle East respiratory syndrome-coronavirus. Int J Pept Res Ther. 26:1473–1483. doi:10.1007/s10989-019-09951-y
  • Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, Magariños MP, Mosquera JF, Mutowo P, Nowotka M, et al. 2019. ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res. 47:D930–D940. doi:10.1093/nar/gky1075
  • Moussa DG, Fok A, Aparicio C. 2019. Hydrophobic and antimicrobial dentin: a peptide-based 2-tier protective system for dental resin composite restorations. Acta Biomater. 88:251–265. doi:10.1016/j.actbio.2019.02.007
  • Muratov EN, Bajorath J, Sheridan RP, Tetko IV, Filimonov D, Poroikov V, Oprea TI, Baskin II, Varnek A, Roitberg A, et al. 2020. QSAR without borders. Chem Soc Rev. 49:3525–3564. doi:10.1039/d0cs00098a
  • Nelson KS, Baltar F, Lamare MD, Morales SE. 2020. Ocean acidification affects microbial community and invertebrate settlement on biofilms. Sci Rep. 10:2020. doi:10.1038/s41598-020-60023-4
  • Neves RPP, Sousa SF, Ribeiro AJM, Coimbra JTS, Martins SA, Moorthy NSHN, Fernandes PA, Ramos MJ. 2013. Protein-ligand docking in the new millennium-a retrospective of 10 years in the field . Curr Med Chem. 20:2296–2314. doi:10.2174/0929867311320180002
  • Pang X, Liu C, Lyu P, Zhang S, Liu L, Lu J, Ma C, Lv J. 2016. Identification of quorum sensing signal molecule of Lactobacillus delbrueckii subsp. bulgaricus. J Agric Food Chem. 64:9421–9427. doi:10.1021/acs.jafc.6b04016
  • Pedroza-Dávila U, Uribe-Alvarez C, Morales-García L, Espinoza-Simón E, Méndez-Romero O, Muhlia-Almazán A, Chiquete-Félix N, Uribe-Carvajal S. 2020. Metabolism, ATP production and biofilm generation by Staphylococcus epidermidis in either respiratory or fermentative conditions. AMB Expr. 10:2020. doi:10.1186/s13568-020-00966-z
  • Peng LH, Liang X, Xu JK, Dobretsov S, Yang JL. 2020. Monospecific biofilms of Pseudoalteromonas promote larval settlement and metamorphosis of Mytilus coruscus. Sci Rep. 10:2020. doi:10.1038/s41598-020-59506-1
  • Rajput A, Gupta AK, Kumar M. 2015. Prediction and analysis of quorum sensing peptides based on sequence features. PLoS One. 10:e0120066–16. doi:10.1371/journal.pone.0120066
  • Rajput A, Kumar M. 2017. In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria. Sci Rep. 7:1–13. doi:10.1038/s41598-017-07241-5
  • Rajput A, Thakur A, Sharma S, Kumar M. 2018. ABiofilm: a resource of anti-biofilm agents and their potential implications in targeting antibiotic drug resistance. Nucleic Acids Res. 46:D894–D900. doi:10.1093/nar/gkx1157
  • Rigden DJ, Fernández XM. 2020. The 27th annual Nucleic Acids Research database issue and molecular biology database collection. Nucleic Acids Res. 48:D1–D8. doi:10.1093/nar/gkz1161
  • Roilides E, Simitsopoulou M, Katragkou A, Walsh TJ. 2015. How biofilms evade host defenses. Microbiol Spectr. 3:1–10. doi:10.1128/microbiolspec.MB-0012-2014 [doi link]
  • Schomburg I, Hofmann O, Baensch C, Chang A, Schomburg D. 2000. Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine. Gene Funct Dis. 1:109–118. doi:10.1002/1438-826X(200010)1:3/4<109::AID-GNFD109>3.0.CO;2-O
  • Schomburg I, Jeske L, Ulbrich M, Placzek S, Chang A, Schomburg D. 2017. The BRENDA enzyme information system – from a database to an expert system. J Biotechnol. 261:194–206. doi:10.1016/j.jbiotec.2017.04.020
  • Sharma A, Gupta P, Kumar R, Bhardwaj A. 2016. DPABBs: a novel in silico approach for predicting and designing anti-biofilm peptides. Sci Rep. 6:21839–21813. doi:10.1038/srep21839
  • Sousa SF, Cerqueira NMFSA, Fernandes PA, Joao Ramos M. 2010. Virtual screening in drug design and development. Comb Chem High Throughput Screen. 13:442–453. doi:10.2174/138620710791293001
  • Sousa SF, Fernandes PA, Ramos MJ. 2006. Protein-ligand docking: current status and future challenges. Proteins Struct Funct Genet. 65:15–26. doi:10.1002/prot.21082
  • Sun YZ, Zhang DH, Cai SB, Ming Z, Li JQ, Chen X. 2018. MDAD: a special resource for microbe-drug associations. Front Cell Infect Microbiol. 8:424. doi:10.3389/fcimb.2018.00424
  • Thöming JG, Tomasch J, Preusse M, Koska M, Grahl N, Pohl S, Willger SD, Kaever V, Müsken M, Häussler S. 2020. Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. NPJ Biofilms Microbiomes. 6:2. doi:10.1038/s41522-019-0113-6
  • Tiwari V, Meena K, Tiwari M. 2018. Differential anti-microbial secondary metabolites in different ESKAPE pathogens explain their adaptation in the hospital setup. Infect Genet Evol. 66:57–65. doi:10.1016/j.meegid.2018.09.010
  • Tobal IE, Roncero AM, Moro RF, Díez D, Marcos IS. 2020. Antibacterial natural halimanes: potential source of novel antibiofilm agents. Molecules. 25:1707. doi:10.3390/molecules25071707
  • Toropov AA, Toropova AP. 2020. QSPR/QSAR: state-of-art, weirdness, the future. Molecules. 25:1292. doi:10.3390/molecules25061292
  • Vergis J, Malik SS, Pathak R, Kumar M, Ramanjaneya S, Kurkure NV, Barbuddhe SB, Rawool DB. 2019. Antimicrobial efficacy of indolicidin against multi-drug resistant enteroaggregative Escherichia coli in a Galleria mellonella model. Front Microbiol. 10:2723. doi:10.3389/fmicb.2019.02723
  • Vert M, Doi Y, Hellwich K-H, Hess M, Hodge P, Kubisa P, Rinaudo M, Schué F. 2012. Terminology for biorelated polymers and applications (IUPAC recommendations 2012). Pure Appl Chem. 84:377–410. doi:10.1351/PAC-REC-10-12-04
  • Vieira TF, Sousa SF. 2019. Comparing AutoDock and Vina in ligand/decoy discrimination for virtual screening. Appl Sci. 9:4538. doi:10.3390/app9214538. [doi Link]
  • Vyas N, Wang QX, Manmi KA, Sammons RL, Kuehne SA, Walmsley AD. 2020. How does ultrasonic cavitation remove dental bacterial biofilm? Ultrason Sonochem. 67:105112. doi:10.1016/j.ultsonch.2020.105112
  • Waszkowycz B, Clark DE, Gancia E. 2011. Outstanding challenges in protein-ligand docking and structure-based virtual screening. WIREs Comput Mol Sci. 1:229–259. doi:10.1002/wcms.18
  • Wen B, Liu J-H, Zhang Y, Zhang H-R, Gao J-Z, Chen Z-Z. 2020. Community structure and functional diversity of the plastisphere in aquaculture waters: does plastic color matter? Sci Total Environ. 740:140082. doi:10.1016/j.scitotenv.2020.140082
  • Worthington RJ, Richards JJ, Melander C. 2012. Small molecule control of bacterial biofilms. Org Biomol Chem. 10:7457–7474. doi:10.1039/c2ob25835h
  • Wynendaele E, Bronselaer A, Nielandt J, D’Hondt M, Stalmans S, Bracke N, Verbeke F, Van De Wiele C, De Tré G, De Spiegeleer B. 2013. Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides. Nucleic Acids Res. 41:655–659. doi:10.1093/nar/gks1137 [doi link]
  • Zhao F, Yang H, Bi D, Khaledi A, Qiao M. 2020. A systematic review and meta-analysis of antibiotic resistance patterns, and the correlation between biofilm formation with virulence factors in uropathogenic E. coli isolated from urinary tract infections. Microb Pathog. 144:2020. doi:10.1016/j.micpath.2020.104196 [doi link]

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