Back to soil: awakening the production of cryptic antibiotics in Streptomyces strains

Lead Research Organisation: Edge Hill University
Department Name: Biology


The increasing incidence of antibiotic-resistant bacterial pathogens has resulted in an urgent need for new, clinically useful antibiotics. Most of the antibiotics used in medicine are produced by actinomycetes, and particularly a genus of harmless bacteria called Streptomyces, which is abundant in all soil environments.

Based on their genome sequences, each Streptomyces species has the potential to produce on average around 10-15 antibacterial agents of natural product origin. However, when these species are grown under laboratory conditions, only one or two antimicrobial compounds are usually detected. This is because most of these antibiotic gene clusters appear dormant (i.e. are not expressed) under laboratory conditions. The fact Streptomyces species maintain these intact antibiotic gene clusters in their genomes suggest the products are useful in nature, probably to attack competitor microorganisms in the harsh soil environment. These dormant or cryptic antibiotic gene clusters represent an untapped resource in terms of novel chemistry which could lead to the discovery of new antimicrobial compounds that could be very useful in the clinic.

Preliminary work leading to this research proposal has allowed us to grow two of these Streptomyces species, for the first time, in ecologically relevant environments including sterile and non-sterile soils. This project aims to understand when previously uncharacterised antibiotic gene clusters encoded within the genomes of these Streptomyces species are expressed and produced in more natural environments. The data generated will provide us with key information which will allow us to generate genetically modified strains with the ability to produce detectable amounts of these compounds under laboratory and industrial fermentation conditions.

The aims of this research are:

1. To identify how these cryptic antibiotics are made by Streptomyces species in soil.
2. To detect which cryptic antibiotics are produced under ecologically relevant conditions.
3. To use the information obtained in objectives 1 and 2 in order to generate genetically modified Streptomyces variants with the ability to produce detectable amounts of these new antibiotics under laboratory and fermentation conditions.

To accomplish these aims we will use RNA sequencing, a technique used to identify which genes are being expressed under a particular growth condition. This will allow us to relate genes that are co-expressed and will provide the information required to identify global and specific regulators of cryptic antibiotic clusters, as well as key metabolic pathways leading to the production of these compounds. We will use chromatography and mass spectrometry to identify new antibiotics produced by the bacterial cells when grown in both sterile and non-sterile soils. We will combine the above information in order to select gene candidates involved in the production of particular cryptic antibiotics. We will then genetically manipulate these candidate genes from the bacterial genome one at a time. In some cases, we will insert extra copies of these candidate genes and in others we will delete these genes from the original genome. After each experiment, the production of that particular antibiotic will be analysed to see if these genetic changes increase production of the compound or if any new compounds are produced. This will allow us to generate variants of these Streptomyces species able to produce detectable levels of new antibiotics under laboratory conditions.

The results from this work will have particular significance in the field of antimicrobial resistance (AMR) as it aims to increase the number of novel natural products available to test and therefore provide many more lead candidates to take forward in order to produce much needed new clinically relevant antimicrobial compounds.

Technical Summary

Although there is plenty of transcriptomic data for most industrially relevant Streptomyces strains grown under laboratory conditions, there is no data regarding their growth in more ecologically relevant environments.

Understanding the conditions for expression of cryptic clusters and the regulatory pathways that lead to the production of antimicrobial compounds in industrially useful strains will allow us to generate knowledge to improve strains for the production of natural products. By conducting RNA sequencing combined with an unbiased metabolomics approach on wild-type and antibiotic overproducing mutant variants of these Streptomyces strains, we will identify regulators and metabolic pathways which can then be manipulated to increase production of these compounds under fermentation conditions.

This research project will add value to natural product research and industry in two ways: by providing information about the regulation and expression of current cryptic clusters in ecologically relevant environments we will be able to generate strains which have the ability to express previously untapped cryptic pathways for further exploitation. Moreover, the data generated in this study will allow the community, particularly industrial partners, to understand the regulation of production of antimicrobials already known. This should lead to an increase of yield of these compounds, thus increasing the chances of promising natural products to undergo clinical trials.

Proposed Research Plan:

1. Identification of global transcriptional patterns leading to the activation of cryptic clusters when S. venezuelae and S. rimosus are grown in an ecologically relevant environment using RNA sequencing.
2. Metabolomic analyses of S. venezuelae and S. rimosus when the strains are grown in ecologically relevant conditions using UPLC/HRMS.
3. Generation of genetically modified industrial Streptomyces strains based on the RNA sequencing and metabolomic data.

Planned Impact

We believe that our research has the potential for long term far-reaching health, societal, economic and academic impacts - not just through the results generated, but through associated AMR related outreach and engagement activities.

The discovery of new antimicrobial compounds with novel chemistry and therefore possible new modes of action would be of value to the pharmaceutical industry. Streptomyces species account for over two thirds of clinically used antimicrobial compounds and are also an abundant source of other types of bioactive molecules including anticancer agents and immunosuppressants, currently accounting for billions of annual revenues generated worldwide by the pharmaceutical industry.

It is estimated that 700,000 people die of AMR infections every year (O'Neill report on AMR, May 2016). The World Bank predicts that if action is not taken, by 2030 AMR could cost the world economy $1 trillion every year. The current financial burden of antimicrobial resistant pathogens alone in the UK is considerable. In 2018, multiple drug resistant E. coli infections have cost the NHS £2.3 billion. A more effective treatment could reduce this cost substantially.

In addition, introduction of new classes of antibiotics to the clinic would mean that antibiotics of last resort, which are increasingly being used more frequently to treat MRSA and other multiple drug resistant infections, could once again be retained for emergency cases thus prolonging their efficacy.

Apart from the evident long term health, societal and economic impacts associated with the development of a successful new antibiotic we believe that the AMR specific outreach and public engagement associated with our research will contribute to raise awareness and understanding of the problems associated with misuse and over use of antibiotics by the general public. This should lead to a shift in behaviour and attitudes towards more responsible and informed use of antibiotics.

Dr. Fernandez-Martinez has a strong track record in engagement with primary and secondary school children through science festivals and national and international outreach activities and she plans to continue this throughout the project. Dr. Fernandez-Martinez will train and encourage both the RA and PDRA to engage in such activities. We believe that raising awareness in the next generation of antibiotic consumers will not only have a positive impact in their attitudes towards the use of antibiotics but will also inspire the next generation of natural product scientists through our outreach and engagement activities.
Description By growing Streptomyces strains that are important in industry in soil, we have been able to identify new ways of activating the production of much needed antibiotics
Exploitation Route We will need to continue working on trying to understand how antibiotics are made in nature and future funding applications derived from the data generated during this research project will be placed in the near future
Sectors Agriculture

Food and Drink



including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology

Description ActinoBase site editor. ActinoBase is an actinomycete community research resource that promotes best practice sharing and networking amongst researchers worldwide
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact By collating protocols and best practice resources ActinoBase is promoting good quality research in developing regions such as South America and Africa. ActinoBase organised a series of research online presentations throughout the summer 2020, during the pandemic, and provided remote training to early career researchers, particularly those from countries with fewer resources, prior to their presentation. Presenting to this international audience has provided training and new research ideas to those participating.
Description Infection Programme Leadership group member for Liverpool's Health Partners'
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Membership of a guideline committee
Description Microbiology Society "A sustainable future" case study on antimicrobial resistance
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
Title Culturing Streptomyces in soil 
Description This funded project has allowed us to optimise a novel way of growing Streptomyces strains in soil 
Type Of Material Technology assay or reagent 
Year Produced 2022 
Provided To Others? Yes  
Impact This method has lead to research collaborations and has the potential to impact on our understanding of microbial communities in agricultural settings 
Description John Innes Centre 
Organisation Norwich Research Park
Country United Kingdom 
Sector Private 
PI Contribution Intellectual input and experimental data provided
Collaborator Contribution Training of the researc assistant Lina Pintor Escobar as well as running of metabolomic experiment to try to identify the antibiotics made by the strains used for this funded project
Impact We hope to be able to continue researching possible novel antibiotics as part of this collaboration. The data generated at the John Innes Centre will prove very valuable for future studies funded by Edge Hill University.
Start Year 2018
Description University of Florida (USA) 
Organisation University of Florida
Country United States 
Sector Academic/University 
PI Contribution The Streptomyces soil growth system established in this project has led to a collaboration with Dr Marc Chevrette to study microbial soil interactions
Collaborator Contribution Providing soil microorganisms to be tested in our newly developed system
Impact Joint funding application to be written in summer 2023
Start Year 2022
Description Actinomycetes as nature's pharmacists outreach article in Microbiology Today 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Outreach article in the November 2019 issue of microbiology today, the Microbiology Society magazine

Although the article was published in November 2019, prior to the start of this award, I was invited to write about the research that the award will fund, and therefore I believe this output can be rightly attributed to this award
Year(s) Of Engagement Activity 2019
Description Actinomycetes genomic tools international LatinAmerican workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact International LatinAmerican workshop to train promising LatinAmerican early career researchers in the latest developments in Actinomycetes research
Year(s) Of Engagement Activity 2022
Description Edge Hill Outreach day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Outreach activity to discuss current research to visiting school visitors
Year(s) Of Engagement Activity 2022
Description Microbiology Today podcast: Natural Products and Drug Discovery 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Microbiology Today podcast: Natural Products and Drug Discovery podcast describing my research and how it is helping to combat antimicrobial resistance.

Although the podcast was recorded in November 2019, prior to the start of this award, I was invited to discuss the research that the award will fund, and therefore I believe this output can be rightly attributed to this award
Year(s) Of Engagement Activity 2019
Description School outreach event 
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 Workshop with primary school children to teach them about the importance of antimicrobial resistance
Year(s) Of Engagement Activity 2022
Description Science me a story 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Wrote a short story for the Spanish Researchers in the UK society about the work conducted in this BBSRC funded grant which was selected as one of the finalist stories
Year(s) Of Engagement Activity 2020