2018 Applied Molecular Microbiology summer school report

2018 was the seventh John Innes/Rudjer Bošković Summer School in Applied Molecular Microbiology.

The first in this series of summer schools was held in 2007 at the Mediterranean Institute for Life Sciences (MedILS) in Split and the following five (in 2008, 2010, 2012, 2014 and 2016) were at the Inter-University Centre (IUC) in Dubrovnik.

The 2018 course was again at the IUC. The co-directors of the course were Mervyn Bibb and Barrie Wilkinson from the John Innes Centre, Greg Challis from the University of Warwick and Duška Vujaklija of the Rudjer Bošković Institute. Duška was also the local organiser. Maureen Bibb and Alison Foster handled local administrative matters.

Course content, participants and faculty

These summer schools were founded to recognise the development of interest in microbial metabolites that has resulted from the explosive development of sequencing technology, bioinformatics and chemical analysis, coupled with the need for new antibiotics resulting from the rise in antibiotic resistant pathogens.

A particular aim is to make connections between the roles of small molecules in microbial communities, including cell-to-cell signalling and interactions between microbes and other inhabitants of their ecological niches and the exploitation of the metabolites as drugs and other pharmaceuticals.

The titles of the lectures and seminars this year were:

  • A brief history of antibiotics
  • Isolation, cultivation and screening of microbial producers of specialised metabolites
  • Natural product biosynthesis: an overview
  • Understanding microbiomes
  • Microbial chemical ecology
  • Introduction to the computer workshops
  • Discovery and biosynthesis of RiPPs
  • Ecology and evolution of natural product biosynthetic gene clusters
  • Practical purification and characterisation of microbial natural products
  • γ-butyrolactone signalling systems and post-translational modifications
  • Expansion of natural product chemical diversity
  • Lessons from antibiotic discovery
  • Industrial fermentation and strain improvement of producing microorganisms
  • Phylogenetic approaches to natural product discovery
  • Microbial ecology in high mountain ecosystems
  • Colour, smell and taste – the beautiful world of plants and chemistry

For 2018 we selected 45 applicants from 20 countries, representing at least 25 nationalities.

The teaching faculty consisted of Mervyn Bibb, Barrie Wilkinson and Govind Chandra from the John Innes Centre UK, Duška Vujaklija from the Rudjer Bošković Institute Croatia, Greg Challis and Emzo de los Santos from the University of Warwick UK, Julian Davies from the University of British Columbia Canada, Roberto Kolter from Harvard University USA, Flavia Marinelli from the University of Insubria Italy, Gerry Wright from McMaster University Canada and Paul Jensen from the Scripps Institution of Oceanography, USA. Alison Foster from Leamington Spa, UK and Maria Zambrano from Corporación Corpogen, Colombia gave guest seminars, as well as contributing to the small-group discussions along with the other faculty members.

Computer workshops

Emzo de los Santos, Govind Chandra and Greg Challis ran two workshops on aspects of bioinformatics relevant to the discovery and characterisation of specialised metabolites.

The first workshop focused on accessing and analysing genome sequences, genome annotation, the use of antiSmash to identify natural product gene clusters and clusterTools to search for particular types of gene clusters.

The second workshop introduced bioinformatics tools that are freely available on the internet and that are commonly used for the analysis of specialised metabolite biosynthetic gene clusters using a gene cluster encoding a cryptic modular PKS assembly line in the model actinomycete Streptomyces coelicolor A3(2) as an example. It taught how to identify putative catalytic domains within the PKS and how to decide whether they are likely to be functional. The substrate specificity of the acyltransferase domains within the PKS were predicted, as well as the stereochemical control imparted by the ketoreductase domains. This culminated in a predicted structure for the fully-assembled polyketide chain attached to the final module of the synthase and a hypothesis for the mechanism of chain release from the PKS.

Classes

In addition, this year we introduced two focused classes, providing an opportunity for more detailed interactive discussions between faculty and students which were well-received by the student cohort:

  • Mechanisms of Polyketide Biosynthesis
  • Microbial Communities

Small-group discussions

After lunch on three of the working days the attendees divided into smaller groups together with one or two faculty to discuss topics of interest in a relaxed, informal atmosphere.

The topics varied from specific aspects of science to general subjects related to career development and publishing. They were generally regarded as a very useful component of the summer school.

Ad-hoc discussions

In addition to the formal programme, the atrium of the IUC, with its associated coffee bar, proved to be a great place for discussions with faculty and between participants at mid-morning breaks and in any other spare moments.

Debate and pizza party

On the penultimate evening we met in the atrium of the IUC for a pizza party followed by a debate on a topic chosen by the students and conducted by them which proved both stimulating and enjoyable, and provided the students with an opportunity to practice their debating skills in a friendly environment.

Poster sessions

As in previous summer schools, every participant brought a poster and the poster sessions led to much fruitful exchange between students and with the faculty.

Posters were displayed throughout the period of the summer school and discussions were often to be seen around posters at different times of the day as well as during the two lively poster sessions.

The full content of nearly all the posters was made available digitally to all participants, helping to catalyse lasting collaborations on topics of mutual interest.

Relaxation

Each working day included a significant period of free time. Swimming from a pebble beach or from rocks just a few minutes away from the IUC was a very popular activity. Many also enjoyed wandering around atmospheric old Dubrovnik and climbing the hill above to obtain spectacular views of the city and the Adriatic beyond.

On the middle day of the summer school we embarked from the old harbour of Dubrovnik for an all-day excursion, first to Cavtat on the coast south of Dubrovnik and then to the small island of Supetar for a barbeque, swimming and relaxation.

2019

The eighth summer school in the series will again be at the IUC, titled; ‘Microbial Specialised Metabolites: Discovery, Biosynthesis and Evolution’. The dates will be 5-12 September 2020