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Edinburgh Genomics

Project contact
Cameron Chalmers
Consultancy Manager

Edinburgh Genomics helps GlaxoSmithKline study historic fungal strains used in antibiotic manufacture

Edinburgh Genomics supported a project involving Professor Louise Horsfall, Dr Matt Edmundson and GlaxoSmithKline (GSK) to investigate the genetics of historic fungal strains used for penicillin production.

Large scale production of penicillin began during the second world war, as well as subsequent work to identify bacterial strains with the highest natural production. Strain NRRL 1951 was discovered on a mouldy melon at a local market and became the ancestor of all modern production strains. Descendent strains were produced via mutagenesis with X-rays and UV light resulting in large archives of fungal mutants, some being discarded while others were further developed.

Modern strains produce 500 times the amount of penicillin of NRRL 1951 and 42,000 times that of Fleming’s original 1920s strain. Modern strains have been sequenced but it was impossible to distinguish beneficial, silent or deleterious mutations.

The project involved sequencing selected archived strains and early production strains, followed by comparison of the sequences of genes known to be involved in penicillin production.

Edinburgh Genomics supported the project with advice on genomic DNA purification and PacBio single-molecule long-read sequencing, as high molecular weight DNA and high purity are required for PacBio sequencing and specifically the removal of RNA and extraction contaminants. Genomic sequences were assembled and compared followed by a secondary bioinformatics analysis by Dr Edmundson.

Results were validated in a subsequent metabolomic screen which determined how specific genomic changes affected penicillin production. GSK were quite pleased to discover some of the secrets their strains had been hiding since the 1940s.

Edinburgh Genomics


  • Agri-tech, agri-food and plant biology
  • Food and drink
  • Healthcare and disease
  • Life sciences and industrial biotechnology
  • Pharmaceuticals and medical biotechnology

Technologies available


Advanced genomics services:

  • High-throughput next-generation sequencing (NGS) data using Illumina platforms, and long-read single-molecule sequencing data using Oxford Nanopore and PacBio sequencers.
  • Modular and flexible access to the latest genomics technologies as services or collaborations.
  • End-to-end support on projects from extracted nucleic acids to data analysis for the sequencing and analysis of genomes, transcriptomes, epigenomes, metagenomes and single cells.


Bioinformatics services ensure high-quality sequencing data generation for clients. Bespoke bioinformatics analysis use tailored tools and automatic workflows to distil the many millions of data points into biologically interpretable information. Our Bioinformatics team has considerable expertise analysing data across many applications including de novo genome assembly and annotation, variant interpretation, transcriptome profiling and annotation, epigenetics, metagenomics and metabarcoding.

Equipment available

Wide range of sequencing platforms: Illumina’s MiSeq and NovaSeq 6000 instruments, Pacific Biosciences Sequel IIe platform, MinION and PromethION sequencers from Oxford Nanopore Technologies. Bioinformatics operations are supported by a dedicated high-performance compute cluster infrastructure, 3,000 compute cores, 7PB of storage and several dedicated servers.

The combination of sequencing and computing infrastructure with the team’s expert knowledge across a broad range of applications enables us to support a diverse portfolio of sequencing projects. Bespoke bioinformatics analysis and training are also available.

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Edinburgh Genomics

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