Summer Schools in Applied Molecular Microbiology

John Innes/Rudjer Bošković
Summer Schools in Applied Molecular Microbiology

Sixth 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 four (in 2008, 2010, 2012 and 2014 were at the Inter-University Centre (IUC) in Dubrovnik. An account of the origin of the series and of the first five courses can be found here:

The 2016 course was again at the IUC ( The co-directors of the course were David Hopwood and Mervyn Bibb from the John Innes Centre, Julian Davies of the University of British Columbia and Duška Vujaklija of the Rudjer Bošković Institute. Duška was also the faculty organiser. Joyce Hopwood and Maureen Bibb 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 of how microbes make molecules. Microbial chemical ecology.  Introduction to the computer workshops. Manipulating natural product biosynthesis - discovery and engineering of new chemical entities. Regulation of specialised metabolism (and morphological differentiation) and its analysis. Practical purification and characterisation of microbial natural products. Industrial fermentation and strain improvement of producing microorganisms. Expansion of specialized metabolite
chemical diversity: lessons from antibiotic discovery, using resistance to advantage.
Reversible protein phosphorylation is a regulatory mechanism for diverse cellular processes. Antibiotics, antibiotic resistance and the meaning of life.  Metabolic pathway discovery by genomics and activation of cryptic pathways for drug discovery. Microbial communities and diversity. Colour, smell and taste – the beautiful world of plants and chemistry.

This year we selected 44 applicants from 21 countries, representing 28 nationalities, facilitated by a grant from the Federation of European Microbiological Societies (FEMS) through the Croatian Microbiological Society to contribute to the costs for 10 European applicants. The IUC generously covered the costs of the Croatian participant. Thirty-three of the group were PhD students, ten were post-docs and one was a junior university faculty member. The teaching faculty consisted of Mervyn and Maureen Bibb, Govind Chandra and David Hopwood from the John Innes Centre in Norwich, Duška Vujaklija from the Rudjer Bošković Institute in Zagreb, Greg Challis from the University of Warwick, Roberto Kolter from Harvard, Flavia Marinelli from the University of Insubria, Varese, Gerry Wright from McMaster University and Brad Moore from the Scripps Institution of Oceanography in San Diego. Alison Foster from the Royal University Botanic Garden in London and Maria Zambrano from Corporación Corpogen, Bogotá, Colombia gave guest seminars, as well as contributing to the small-group discussions along with the other faculty members.

Computer Workshops

Govind Chandra, Greg Challis and Mervyn Bibb ran two workshops on aspects of bioinformatics relevant to the discovery and characterisation of specialised metabolites. The first workshop (written by Juan Pablo Gomez-Escribano, John Innes Centre, Norwich) dealt with the steps involved in deriving a high quality genome sequence using a combination of PacBio and Illumina sequencing technologies. This involved aligning Illumina MiSeq reads onto a PacBio genome scaffold, the use of Artemis (GC Frame Plot) to identify likely errors in the PacBio sequence and their correction using Artemis.  AntiSmash was also used to examine the complement of biosynthetic gene clusters contained in the genome sequence. 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.

Ad-hoc discussions

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.

Small-group discussions

After lunch on each working day 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.

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 entirely conducted by them. The proposal was: “All scientists should be obliged to take part in outreach to the public”. Before the first speeches a secret ballot was taken and compared with the result of a show of hands at the end of a lively debate. Interestingly, the motion was lost by a three-fifths majority compared with an even split before the arguments were presented. There was virtual unanimity that outreach was essential but the majority felt that best interests would not be served by forcing it on unwilling exponents.

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 has been made available digitally to all participants, helping to catalyse lasting collaborations on topics of mutual interest.


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.

The next summer school

The seventh summer school in the series will again be at the IUC, with the title to be announced. The dates will be 8-16 September 2018. Please watch the web site at for developments and draw the website to the attention of anyone who might be interested in applying in due course. Applications will be invited in autumn 2017, with a deadline in spring 2018.