New publication: microbial mass movements

Delighted that our perspective in Science has been published.

Zhu Y-G, Gillings M, Simonet P, Stekel DJ, Banwart S and Penuelas J. Microbial mass movements. Science 357: 1099-1100.

My involvement is relatively minor: we have written a much longer piece (which we are looking to publish also) to which I have contributed a fairly substantial section on modelling – and then when Michael Gillings put together this short perspective for Science, he compressed everything I wrote into a single sentence! Maybe it is an improvement ūüôā Anyway, it is a real privelege to have coauthored which such amazing international scientists, and a delight that we have had it published in such a great journal.


For several billion years, microorganisms and the genes they carry have mainly been moved by physical forces such as air and water currents. These forces generated biogeographic patterns for microorganisms that are similar to those of animals and plants (1). In the past 100 years, humans have changed these dynamics by transporting large numbers of cells to new locations through waste disposal, tourism, and global transport and by modifying selection pressures at those locations. As a consequence, we are in the midst of a substantial alteration to microbial biogeography. This has the potential to change ecosystem services and biogeochemistry in unpredictable ways.


Medical Research Foundation funds ¬£2.8M PhD programme in antimicrobial resistance

The Medical Research Foundation has announced a ¬£2.8M PhD programme in antimicrobial resistance. Led by Matthew Avison at Bristol, this will bring 18 fully funded PhD students to support ongoing AMR projects. One of the students will be at Nottingham in association with the EVAL-FARMS project. We will be advertising three projects as part of the programme; these will be led by team members who don’t have any direct resource from the existing EVAL-FARMS funding – and are likely to be in the areas of phage-mediated spread of resistance, use of anaerobic digestion to mitigate resistance, and farm systems economic models to identify factors to best mitigate the impact of agri-AMR on human health.

Nottingham has also posted a Blog on the funding and I reproduce the text below:

New funding for Antimicrobial Resistance research

Research into new ways to tackle antimicrobial resistance has been given a boost as the University of Nottingham is one of the universities set to benefit from a £2.85m investment from the Medical Research Foundation.

New scientists will explore ways to tackle antimicrobial resistance through a new PhD training programme by the Medical Research Foundation, the charitable foundation of the Medical Research Council (MRC).

Fully funded

The first intake of the Antimicrobial Resistance PhD Training Programme will fully fund 18 students for four years, and the University of Nottingham is one of the 16 participating universities across the UK.

Dr Dov Stekel¬†is leading the University of Nottingham programme and will be looking to recruit students later this year ready to start in 2018. Dr Stekel says: ‚ÄúThis funding allows us to broaden our research with a PhD student working with team members who have not yet had access to resources from our other antimicrobial resistance research grants. Antimicrobial Resistance is a major global challenge and it will be very exciting to see the type of projects that are put forward and how they will help us progress our understanding of this problem.‚ÄĚ

Antibiotics transformed healthcare in the 20th Century and are considered one of the greatest medical achievements of the era. Today, we still rely on antibiotics to treat everything from minor cuts to life-threatening bacterial infections, and to prevent infection after surgery. These drugs have drastically improved our quality of life and increased our lifespan.

Global threat

In the 21st Century, antibiotic overuse and misuse has led to antibiotics rapidly becoming ineffective. Antimicrobial resistance, specifically antibiotic resistance, now poses a global threat to human life. We need urgent action to halt resistance and to speed up new treatments for bacterial infection. The Medical Research Foundations PhD Training Programme in AMR has been designed in response.

Working with the MRC, the Medical Research Foundation spotted a gap in funding for PhD studentships in this field of research ‚Äď currently there are few emerging researchers trained in the multidisciplinary approach required to tackle the antimicrobial resistance problem. The programme is designed to help build a strong, active network of new researchers to approach this global challenge in innovative ways.

The Medical Research Foundation‚Äôs Chair, Professor Nicholas Lemoine, said: ‚ÄúThe Medical Research Foundation is delighted to be funding the UK‚Äôs only¬†national PhD Training Programme in antimicrobial¬†resistance research. ¬†We believe¬†this will¬†help to strengthen the UK‚Äôs research capacity to respond to the¬†global health challenge of antimicrobial resistance,¬†including¬†antibiotic¬†resistance and¬†drug-resistant infections.‚ÄĚ

The Medical Research Foundation is continuing to seek funds from its supporters and other sources to fund two further cohorts of PhD students in antimicrobial resistance in the future.


Sankalp Arya will be speaking at EDAR 4

Sankalp is on a roll! More good news. His Abstract to the 4th International Symposium on the Environmental Dimension of Antibiotic Resistance has been accepted as an oral presentation. He’ll be giving a talk with title “Comparison of Different Modelling Approaches for Plasmid Transfer Dynamics” during Session 7 on Thursday 17th August. We have some interesting phage model results too so it is possible he may talk about both plasmid and phage mediated transfer.

When we submitted the abstract there was a “modelling” stream to submit to (which we dutifully did) – interestingly there is no modelling stream at the conference. There appear to be some bioinformatics talks, but it looks like Sankalp’s will be the only modelling talk. I am a bit surprised by this – there is a very clear need for models to be able to quantify spread of AMR, and make predictions about interventions. Perhaps on the other hand this is an opportunity for collaborations – we do modelling!

Congratulations again to Sankalp Arya

Congratulations again to Sankalp Arya for obtaining another scholarship. He has received a Travel Award to present his work at the 4th International Symposium on the Environmental Dimension of Antibiotic Resistance (EDAR4). EDAR3 was fantastic – and EDAR4 will no doubt be much more widely attended. This is going to be a great opportunity for Sankalp to present his work (we are not yet sure whether this will be oral or poster) and hear from the best in the field.


Now recruiting: Research Associate/Fellow in Antimicrobial Resistance Modelling

We are now recruiting the mathematical modelling post-doc for the EVAL-FARMS project. This post will work with me, Theo Kypraios in Maths, and the EVAL-FARMS team more generally, developing mathematical models for risk of emergence of AMR pathogens in agricultural waste, using all the exciting data that are being generated by the empirical researchers on the grant. Details of the advert, as well as links to it, are:

Research Associate/Fellow in Antimicrobial Resistance Modelling

Agricultural & Environmental Sciences

Location:  Sutton Bonington
Salary:  £26,052 to £38,183 per annum, depending on skills and experience (minimum £29301 with relevant PhD). Salary progression beyond this scale is subject to performance
Closing Date:  Wednesday 28 June 2017
Reference:  SCI158617

We are seeking an excellent researcher in modelling of antimicrobial resistance. The successful applicant will use mathematical and statistical models to make predictions on risk of emergence of antimicrobial resistant pathogens in a farm slurry system and slurry amended soil. The post is funded by NERC-led EVAL-FARMS project (Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries). Thus the role holder will work closely with an interdisciplinary team, including experimental researchers in microbiology and analytical chemistry, and social researchers in science and technology studies, in order to develop meaningful, data driven risk models that could inform policy and practise. The work will involve deterministic and stochastic models, Bayesian statistics, data analysis and presentation.

Applicants must have, or be very close to completing, a PhD in mathematical, computer or statistical models applied to a relevant area in the biological or environmental sciences. Research experience in applying such models in antimicrobial resistance, metagenomics, analytical chemistry and/or water quality would be desirable. Applicants must be able to demonstrate skills in Bayesian approaches, including relevant computational techniques such as MCMC, development and analysis of deterministic and stochastic models, programming in a relevant language (e.g. R, Python or Matlab) and a broader appreciation of science. Applicants must also be able to demonstrate research ambition through timely publication of research, coupled with commitment to the research project as part of their on-going career development. Excellent oral and written English language skills are essential.

The post is a joint appointment between the Schools of Biosciences and Mathematical Sciences. The post holder will normally work on the Sutton Bonington Campus, and will also have meetings on the University Park Campus with staff in the School of Mathematics and other collaborating schools.

Fixed term for 2 years from 1st September 2017

Applications can be made through the University of Nottingham web site. I am happy to receive informal enquiries.

Congratulations to Sankalp Arya: International Research Collaboration Award

Congratulations to Sankalp who has received a ¬£2300 International Research Collaboration Award from the University of Nottingham. Sankalp will spend two months (September and October) in Barth Smets’s laboratory at the Technical University of Denmark. This is a really fantastic opportunity for Sankalp to work in one of the leading environmental microbiology groups in the world. His work will focus on developing the iDynomics platform for individual based modelling of microbial interactions to model antimicrobial resistance. Well done Sankalp! And I look forward to visiting Barth’s lab too as part of the project.


Alan Perelson’s 70th Birthday Conference: Viral Dynamics: Past, Present and Future

Sankalp and I have just returned from a weekend trip to Santa Fe for the Viral Dynamics conference in honour of Alan Perelson’s 70th birthday.

The conference itself was very high quality – excellent talks throughout from some extremely eminent people in virus research. I particularly appreciated David Ho’s opening talk and Alan Perelson’s closing keynote; David’s talk on HIV dynamics reminding me just how good Alan and Avidan Neumann’s modelling contribution was: it wasn’t about developing big complex models, or doing very fancy mathematics; it was about doing the right simple model to make the most use of the data. Alan’s talk focussed on his earlier work in theoretical immunology – very many interesting examples showing how much you can learn by thinking in mathematical/computational ways.

The best part of the conference was meeting up with people – whether old friends from the short time I spent in LANL (Alan, Jack) and my PhD days (Ruy, Sebastian) – or brilliant people I hadn’t met before with whom I had some very stimulating conversations.

What was also evident was the warmth felt by so many people towards Alan. I only spent 3 months in the lab in 1994 – in between my degree and PhD – and went back for another month in the summer of 1995 – and yet when Ruy Ribeiro sent the invitation I immediately felt that this was a meeting I couldn’t miss. Many people there had collaborated with Alan for many years. And while Alan’s contribution to science is enormous, the plaque that the organizers made for him was for friendship, collaboration and mentorship, with a network graph of his collaborative research outputs. In this, Alan is a positive example for us all.

We went with a poster:


which was Sankalp’s first conference poster presentation! I thought that this would be a good opportunity for him; although Sankalp’s model is about bacteriophage in the context of AMR, while the conference focussed on human disease viruses, the conference attendees mainly worked in mathematical models of virus dynamics. This meant that Sankalp was among people who understood what he was doing and why he was doing it, speaking the same language. Sankalp was busy – he had people speaking with him for the full 2 hours of the poster session – and we received many interesting ideas and suggestions from these conversations.