How to build a biofilm

Lead Research Organisation: University of Dundee
Department Name: College of Life Sciences

Abstract

A house is made from basic components that include bricks, roof tiles and mortar. Each part is essential to allow the building to be constructed. In addition the component parts need to be assembled in the correct order, and with the correct spatial arrangement, for the house to be strong and secure. Following this analogy, biofilms are communities of microbes (where the cells can be considered the bricks and roof tiles) that are surrounded by an extracellular matrix (the mortar) that provides structure. When living in the biofilm the microbes benefit and become resistant to antibiotics and other antimicrobial agents. This can result in the formation of chronic antibiotic resistant infections. We are interested in how a biofilm is built. The main component parts that are needed have been identified and in this proposal we aim to understand how they are assembled. Understanding how they are assembled will allow the development of novel strategies to block assembly in the natural environment and therefore guide future development of novel antimicrobial compounds for chronic debilitating biofilm infections.

Technical Summary

It is accepted across the medical and scientific community that there is an urgent need to uncover new targets to fight difficult-to-treat Gram-positive and Gram-negative chronic bacterial infections. Such infections are predominantly the result of microbial biofilms; structured complex communities of microbial cells that are enclosed in a self-produced extracellular matrix. There have been significant recent advances in our understanding of the regulatory pathways and key building blocks required for the nucleation and growth of biofilms for many species of bacteria. However it is still not understood how the extracellular and cell wall components physically interact to allow a three dimensional biofilm to develop. Bacillus subtilis is a very suitable model for biofilm formation in Gram-positive bacteria. It forms biofilms that contain differentiated cells that display a complex three-dimensional architecture. We have recently shown that a small protein called YuaB is essential for biofilm formation and that it acts in a synergistic manner with the TasA amyloid fibres and the exopolysaccharide found in the extracellular matrix to allow biofilm development. Therefore our system is ideally suited to allow us to generate a detailed understanding of how the biofilm is constructed. We aim to determine when YuaB is needed to allow biofilm formation, how the extracellular polymers interact with each other, and to elucidate the structure and function of YuaB. We will accomplish this using a collaborative interdisciplinary approach with techniques that cross the boundaries of biology and chemistry. We will utilise a combination of classical molecular genetic techniques, in association with state-of-the-art chemical and structural analyses.

Planned Impact

A. i) Smaller Biotech companies such as Novacta, Biotica, and Aquapharm. ii) These companies have active anti-infective research programmes. They will benefit from the proposed research programme that will generate novel and exciting knowledge on a target relevant to the development of novel antibiofilm agents. iii) It is currently too early in the project to identify industrial partners specifically. The lead institution will act to protect any intellectual property and to maximise opportunities for collaborative research or licensing. The Dundee research and innovation team have a wealth of industrial contacts and close links to Scottish Enterprise, and will help maximise the impact of all findings of commercial value. As and when appropriate, results will be peer-reviewed and published. B. i) Members of the wider academic community. ii) Biofilms are responsible for the majority of chronic infections and also the majority of beneficial remediation and biocontrol processes. This work will increase our understanding of the role and mechanisms of the extracellular matrix of the biofilm thus facilitating future study and exploitation for therapeutic purposes. iii) The PDRA and PIs will attend and contribute to a variety of conferences and the PIs will present results through invited research talks, both nationally and internationally. As appropriate, results will be peer-reviewed and published. Strains and other resources will be made available as appropriate. C. i) PDRA and PIs. ii) The University of Dundee takes training of early career researchers (including PIs) very seriously, thereby ensuring a successful contribution to the knowledge-led economy of UK Plc. The appointed PDRA will be encouraged to be innovative in their work. There will be opportunities for them to train undergraduate, postgraduate and visiting scientists. They will be given multiple opportunities to present their findings at major research conferences, facilitating their career development through the acquisition and refining of key presentational and networking skills. iii) The appointed PDRA will have access to training in transferable/generic skills through the professional development schemes. In line with the Concordat 2009, the PDRA will be actively encouraged to undertake at least 5 days training in generic skills per annum. In addition, both institutes have an annual appraisal scheme to actively facilitate the career development of staff, including PDRAs and PIs. The PDRA will also be encouraged to design and supervise undergraduate projects and to become involved in science communication. D. i) The general public. ii) It is important that members of the general public are aware and supportive of how tax payers' money is spent on scientific research. Therefore as part of our work on this project, we will engage with local communities, through face-to-face discussion of our work and family focussed scientific event days. iii) The applicants are experienced, energetic and ardent science communicators. For example, the University of Dundee partners have teamed up with the Dundee Science Centre to organize a 2-day event in May 2010 entitled 'Magnificent Microbes'. This event attracted teachers, children, the general public and the local media to learn about the research going on in the Division of Molecular Microbiology and educated, inspired and entertained the public about microbiology research. Approximately 400 people visited the event and we now intend to repeat it in 2012, which would be during the course of the project.

Publications

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Arnaouteli S (2016) Just in case it rains: building a hydrophobic biofilm the Bacillus subtilis way. in Current opinion in microbiology

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Brandani GB (2015) The Bacterial Hydrophobin BslA is a Switchable Ellipsoidal Janus Nanocolloid. in Langmuir : the ACS journal of surfaces and colloids

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Bromley KM (2015) Interfacial self-assembly of a bacterial hydrophobin. in Proceedings of the National Academy of Sciences of the United States of America

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Hobley L (2013) BslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilm. in Proceedings of the National Academy of Sciences of the United States of America

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Marlow VL (2013) Blast a biofilm: a hands-on activity for school children and members of the public. in Journal of microbiology & biology education

 
Title Animation - raincoat 
Description Animation about scientific research 
Type Of Art Film/Video/Animation 
Year Produced 2015 
Impact Been used widely for both scientific and public presentations. Has been widely viewed by members of the public. Has been used in art exhibitions. 
URL https://www.youtube.com/watch?v=TME-V7D2saY
 
Description The majority of bacteria are capable of protecting themselves by making a community or structure that is called a biofilm. It contained many millions of cells that are embedded in a self-produced stick matrix. We were interested in how the biofilm is built. We wanted to know what materials the bacteria used to build the community and also how these materials functioned. We uncovered that a common bacterium found in the soil, called Bacillus subtilis, uses a protein called BslA not only to allow the bacteria to structure their local environment but also to make it hydrophobic. This means that water and other liquids cannot easily get inside. The bacteria are effectively making a raincoat to protect the residents. What was particularly exciting was that we solved the crystal structure of BslA, which let us learn how the protein works in exquisite detail. The way the protein works is really novel. We also found out that the protein has a lot of uses in biotechnology and therefore we explored how it might work to stabilise formulations. This became the focus of future work that was funded to explore commercial development of the protein.
Exploitation Route Working out how BslA works at the protein level turned out to be very important. The impact was felt not only in the area of biofilm formation but also in industrial sectors. We have seen multiple industries express an interest in using BslA in their formulations. This means that potentially there could be new or improved products generated.
Sectors Agriculture, Food and Drink,Chemicals,Education,Manufacturing, including Industrial Biotechology

 
Description The finding that the protein made by Bacillus subtilis, called BslA, has industrial uses led us to protect the innovation through a patent application. The patent has been published and has stimulated industrial interest in the application of BslA. The fact that the bacteria form an obviously hydrophobic layer has also been an excellent tool to talk with members of the public about how and why bacteria living in biofilms can become tolerant to antibiotics. Seeing water droplets sitting on top of the cells is a very visual way to explain the protective mechanisms that are employed by bacteria in biofilms to ensure their survival.
First Year Of Impact 2011
Sector Education,Manufacturing, including Industrial Biotechology
Impact Types Cultural,Economic

 
Description Vacation Scholarship 2010
Amount £1,880 (GBP)
Organisation Society of General Microbiology 
Sector Charity/Non Profit
Country European Union (EU)
Start 06/2010 
End 08/2010
 
Description Biophysics 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution We contribute biological knowledge and expertise. This included intellectual input and also training for staff.
Collaborator Contribution Partner contributes biophysical knowledge and expertise. This included intellectual input and also training for staff.
Impact PMID: 26685107 PMID: 26378478 PMID: 25907113 PMID: 25870300 PMID: 23904481
Start Year 2012
 
Description Continued professional development Primary School Teachers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Primary school CPD on the topic of microbiology. Raising awareness of experiments that can be done with microbes and increasing confidence.
Year(s) Of Engagement Activity 2016
 
Description Magnificent Microbes 2014 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Outreach event Dundee Science Centre March 2014.

Two days - one for school children and the other for members of the public.
"Magnificent Microbes" is organised and run by Dr. Nicola Stanley-Wall.

The activity involves many members of the division of Molecular Microbiology from technical staff, PhD students, postdoctoral scientists to academic staff.

Magnificent Microbes is an innovative outreach event designed to educate, inspire and entertain large numbers of school children and family groups about microbes, the roles that they play in shaping our environment, and how they influence the food, health, and green energy sectors of our economy.



The activity involved many members of the division of Molecular Microbiology from technical staff, PhD students,postdoctoral scientists to academic staff.

Teachers reported increased confidence to undertake microbiology related activities in the classroom.
Year(s) Of Engagement Activity 2013,2014
URL http://blog.wellcome.ac.uk/2014/06/05/how-to-get-researchers-involved-in-public-engagement/
 
Description Outreach event (London) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact talking with members of the public sparked interest and curiosoty in BBSRC funded research

After the event approx 7000 people had been engaged and stimulated by British bioscience.
Year(s) Of Engagement Activity 2014
URL http://www.bbsrc.ac.uk/engagement/exhibitions/gb-bioscience-festival/
 
Description Plant Science (Tayport) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact We initiated a citizen science project with a local community garden organisation. We had multiple interactions with the volunteers at PLANT and we also ran two events where members of the public were encouraged to bring soil and isolate spore forming bacteria called Bacillus subtilis. We have used these strains in our research.
Year(s) Of Engagement Activity 2017
 
Description Talk- John Innes Centre 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Participants in your research and patient groups
Results and Impact Talk invited outreach and research Talk at IFR outreach event organised by PhD students. The goal was to spark interest in outreach activities and get scientists thinking about what is possible.

The views of the scientists were positively impacted by the event.
Contacted by school teacher for help with in school activities.
Year(s) Of Engagement Activity 2013
 
Description continuted professioal development (teachers) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Talks sparked interest and discussions

The teachers have gained confidence and have increased the partical activities they undertake in the classroom in topic relating to microbiology
Year(s) Of Engagement Activity 2015
 
Description media interest (uses of novel biologic) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We released a press statment about on going work with the goal of stimulating business interest

The work was covered by many media outlets and also several small adn multinational businesses have made contact and we are currently in disucssions with them.
Year(s) Of Engagement Activity 2015
URL http://www.dundee.ac.uk/news/2015/slower-melting-ice-cream-in-pipeline-thanks-to-new-ingredient.php
 
Description schools visit (Dundee) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact talks sparked thinking about how science is reported in the media

Children reported thinking about the "headlines" in newspaers and online media in different ways. School gained confience to enter a competition.
Year(s) Of Engagement Activity 2015
 
Description schools visit (carnoustie) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact talk sparked interest and many many questions from the children.

After the event the children in the class undertook further experiments and reported the findings back to us.
Year(s) Of Engagement Activity 2015