Applied Molecular Microbiology

The next John Innes Centre/Rudjer Bošković Summer School in Applied Molecular Microbiology, ‘Microbial Specialised Metabolites: Discovery, Biosynthesis and Evolution’, will take place in Dubrovnik from 5-12 September 2020.

  • Applications for 2020 are now closed

The summer school is intended primarily for scientists at postgraduate and early postdoctoral level, or early career industrial scientists. However, some junior faculty may also qualify.

Applicants who are members of a FEMS Member Society may apply for a FEMS Meeting Attendance Grant. Note that the deadline for the FEMS application is 1 March 2020.

Scientists from less developed countries, and other applicants subject to financial constraints, may apply for a grant from the Summer School organisation. To apply, attach a letter to your application making a case for financial assistance.

Course contents

The summer schools recognise the recent development of interest in microbial metabolites that has resulted from the sequencing of small molecule-producing microorganisms, coupled with the explosive development of sequencing technology, bioinformatics and chemical analysis.

Ecological developments highlighting the wide range of roles for small molecules in microbial communities are also very significant and an important aim is to bring together a cadre of young scientists from diverse backgrounds, to share information that can lead to inter-disciplinary approaches to understanding and exploiting metabolite production, including:

  • Molecular microbiology
  • Chemistry
  • Microbial ecology
  • Bioinformatics

There is an urgent need for novel antibiotics precipitated by multi-drug resistance among many pathogenic microorganisms, and a special feature of the summer school will be hands-on computer workshops focused on genome mining and the analysis natural product gene clusters.

The 2020 course is likely to cover the following areas:

  • Isolation and screening of metabolite-producing microorganisms
  • Diversity of specialised metabolite producers
  • Purification and characterisation of microbial natural products
  • Natural product biosynthesis
  • Natural products in microbial communities and cell-cell interactions
  • Natural products in symbioses with higher organisms
  • Ecology and evolution of natural product biosynthetic gene clusters
  • Regulation of natural product biosynthesis, including intra- and extracellular signalling
  • Metagenomics and heterologous pathway expression
  • Genome mining for novel natural product discovery
  • Prediction and characterisation of biosynthetic pathways in silico and experimentally
  • Activation of transcriptionally silent cryptic gene clusters
  • Pathway engineering

Hands-on computer workshops will be a unique aspect of the course. Next generation sequencing of microbial genomes and communities can now be accomplished in a matter of days and is becoming increasingly affordable.

The two workshops will focus on the latest bioinformatic tools that greatly facilitate the handling, interrogation and exploitation of such sequences, including genome assembly and analysis, and the recognition of the diverse array of gene clusters for specialised metabolism. Analyses will include the identification of functional catalytic domains, and prediction of substrate specificity and stereochemical control within a large modular polyketide synthase gene cluster.

A typical working day will include lectures in the morning, computer workshops, and small-group discussions and classes in the afternoon, and student presentations and poster sessions in the evening; all participants will be asked to bring a poster. There will be free time on the working days and one day will be devoted to an all-day excursion. There will be a welcome mixer party on the day of arrival and a farewell party on the final evening before departure the next day.

The course will be limited to 40-45 participants.

Costs, venue and accommodation

The total charge for the eight days board and lodging, including the opening reception and the closing party, is  €700, with an additional registration fee of  €200 Euro. Some grants will be available to assist qualifying applicants. We hope that these measures will make the summer school accessible to a wide range of applicants.

The 2020 Summer School will be held at the Inter-University Centre (IUC) in Dubrovnik.

The Centre has bedroom accommodation (a mixture of single and twin bedrooms) on the top floor and facilities for lectures and seminars, computer teaching, poster viewing and spaces for small group discussions and relaxation. Swimming from a rocky bathing spot is a few minutes’ walk from the Centre and the Old City of Dubrovnik is also very close. A sandy beach is less than 30 minutes’ walk away. Transfers from the airport are easy: the airport bus to town stops very close to the IUC.

Participants will be accommodated in single or twin air-conditioned rooms at the IUC and all meals will be provided at a restaurant within a couple of minutes of the Centre or at other venues in the beautiful Old City of Dubrovnik.

2020 teaching faculty

  • Mervyn Bibb, John Innes Centre
  • Greg Challis, University of Warwick, UK
  • Marie Elliot, McMaster University, Hamilton, Canada
  • Alison Foster, Associate Lecturer, Centre for Biocultural Diversity, University of Kent, UK
  • Paul Jensen, Scripps Oceanographic Institution, San Diego, USA
  • Roberto Kolter Harvard Medical School, USA
  • Flavia Marinelli, University of Insubria, Varese, Italy
  • Mônica T. Pupo, University of Sao Paulo, Brasil
  • Emzo de los Santos, University of Warwick, UK
  • Andrew Truman, John Innes Centre
  • Duška Vujaklija, Rudjer Bošković Institute, Croatia
  • Barrie Wilkinson, John Innes Centre
  • Gerry Wright, McMaster University, Hamilton, Canada
  • María Mercedes Zambrano, Corporación Corpogen, Bogotá, Colombia


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 IUC.