Trends in Biotechnology
Volume 38, Issue 9, September 2020, Pages 937-940
Journal home page for Trends in Biotechnology

Scientific Life
The Biofilms Structural Database

https://doi.org/10.1016/j.tibtech.2020.04.002Get rights and content

The Biofilms Structural Database (BSD) is a collection of structural, mutagenesis, kinetics, and inhibition data to understand the processes involved in biofilm formation. Presently, it includes curated information on 425 structures of proteins and enzymes involved in biofilm formation and development for 42 different bacteria. It is available at www.biofilms.biosim.pt.

Section snippets

Biofilms in Health

Biofilms are heterogeneous and complex structures of microorganisms, typically adhered to a surface and presenting sophisticated singular and collective behaviors. Bacteria in biofilms are embedded in a self-produced matrix of extracellular polymeric substances (EPS) composed of (glyco)proteins, (glyco)lipids, mono- or poly-saccharides, extracellular DNA, minerals, and water [1]. This protected mode of growth allows bacteria to survive in hostile environments. In the health context, some

Strategies for Inhibiting Biofilm Formation

Antibacterial strategies focusing on inhibiting cellular growth often induce antimicrobial resistance by imposing a strong selective pressure on bacteria. By contrast, alternatives that target the processes associated with biofilm formation and development, which include bacterial motility, cell adhesion, biofilm dispersion, the synthesis of EPS, and also cell-to-cell communication or quorum sensing (QS), can be more efficient [5,6], as these processes are less amenable to induce antimicrobial

The Shift from the Cellular to the Molecular Level

Over the past few years, there has been an immense increase in the number of 3D structures (particularly X-ray) of proteins and enzymes associated with biofilm formation and development. The data associated with these structures, together with the vast body of work dispersed throughout the scientific literature – including kinetic and mutagenesis data, amino acid sequences, and inhibitory activity of known molecules – offers new opportunities to understand biofilms at a structural and atomic

Data Selection

The main focus of the BSD is at the molecular level. However, biofilm research integrates several different scales. Therefore, the database was designed to create a comprehensive repository of structural data on biofilm research that could integrate with the information available in other databases, beyond the molecular level, to link different fields. An intensive literature search was performed to extract the relevant structural information about the proteins and enzymes involved in biofilm

Organization of the Database

The BSD is organized in a simple and intuitive manner. Each entry in the database corresponds to one atomic structure with a unique PDB code. A total of 425 PDB entries are currently included, corresponding to a total of 133 unique proteins (Figure 1A). Each entry is identified through the PDB code associated with the corresponding structure in the PDB and by the name of the protein. Entries are classified by protein category and mechanism. The term ‘category’ refers to the general and main

Concluding Remarks

The BSD is a free-access catalogue containing the structures of all known proteins and enzymes involved in biofilm formation. This database is a tool that helps to visualize, explore, and understand biofilm targets to design and develop new and effective antibiofilm drugs and to understand the structure and activity of proteins and enzymes involved in biofilm development. The interface is easy to use and accessible to anyone wishing to start their work in this field.

Acknowledgments

This work was supported by national funds from Fundação para a Ciência e a Tecnologia (grant numbers: SFRH/BD/137844/2018, SFRH/BD/115396/2016, IF/00052/2014, UID/Multi/04378/2019, UIDB/04378/2020, PTDC/QUI-QIN/30649/2017, UID/QUI/50006/2019, and NORTE-01-0145-FEDER-000011) and the Interreg SUDOE NanoDesk (SOE1/P1/E0215; UP). This work was also financially supported by: Base Funding – UIDB/00511/2020 of LEPABE, funded by national funds through the FCT/MCTES (PIDDAC), projects

References (15)

  • M. Jamal

    Bacterial biofilm and associated infections

    J. Chinese Med. Assoc.

    (2018)
  • M. Simões

    A review of current and emergent biofilm control strategies

    LWT Food Sci. Technol.

    (2010)
  • H.-C. Flemming et al.

    The biofilm matrix

    Nat. Rev. Microbiol.

    (2010)
  • R. Roy

    Strategies for combating bacterial biofilms: a focus on anti-biofilm agents and their mechanisms of action

    Virulence

    (2018)
  • H. Koo

    Targeting microbial biofilms: current and prospective therapeutic strategies

    Nat. Rev. Microbiol.

    (2017)
  • N.F. Kamaruzzaman

    Targeting the bacterial protective armour; challenges and novel strategies in the treatment of microbial biofilm

    Materials (Basel)

    (2018)
  • C. Guilhen

    Biofilm dispersal: multiple elaborate strategies for dissemination of bacteria with unique properties

    Mol. Microbiol.

    (2017)
There are more references available in the full text version of this article.

Cited by (0)

4

These authors contributed equally to this work.

View full text