Living with Environmental Change III

Another update on our currently running module “Living with Environmental Change” and another host of excellent guest speakers. At St. Lukes, we had the pleasure to hear Dr. Fiona Mathews talk about “The Environment and Reproductive Health”. Fiona has done some amazing work on reproductive biology, a topic of fundamental interest to evolutionary biologists (see here for example). She presented a range of her findings, including the observation that there are statistically more male than female still births, a pattern consisten across the world in countries with varying levels of income, which is not yet understood. Another topic was the detrimental effect of mobile phone usage on sperm quality and yet another amazing finding (that made headlines all over the world) is that maternal diet at conception influences the chance of having a boy or a girl. This is such a cool graph that I have bothered to copy the legend (read the paper here).


Relationship between usual maternal intakes of energy and breakfast cereal prior to pregnancy, split at approximate tertiles, and the proportion of male infants (Cs.e.m.). Comparisons of the numbers of males and females across the groups were made using c2-test for linear association. The numbers above each bar indicate the numbers of women in each category of intake. For energy, the bars represent the low (open), moderate (filled) and high (hatched) thirds of intake; c2Z5.83, pZ0.016. For breakfast cereal, the bars represent less than one bowl per week (open), two to six bowls per week (filled) and one or more bowl per day (hatched); Chi sq.=13.96, p<0.001.

At Penryn, we had a very different, but equally interesting and relevant lecture that week, namely by Professor Steve Rowland, who is at Plymouth University, but also has an honorary professorship at Exeter. Steve talked about his research on the environmental impacts of oil contamination, in particular about the tar sands in Canada. This politically controversial topic was all over the news that week because of the elections in Canada and because of Shell’s decision to shut down its operations there for the foreseeable future, again demonstrating how topical the module is. The extraction of oil from tar sands is an absolutely massive operation (tailings ponds can be seen from space) with far-ranging impacts on the environment and human populations. I really liked the format of this lecture, which consisted of a multiple choice question, followed by student discussion after which more in-depth explanation was given. Tar-sands-oil-canada-2Another session was delivered by Professor Tamara Galloway in Penryn and Professor Lorna Harries in Exeter; both spoke about their joint work on Bisphenol A (BPA). BPA is the world’s highest production volume compound with 3.2 million tonnes produced per year (earning producers £500k per hour). Originally developed as a synthetic oestrogen, it was later discovered that this molecule was great for the production of polycarbonate plastics, ubiquitously present in consumer goods. However, the problem is that BPA slowly leaches out of plastic packaging (especially when microwaved), thermal receipts and the lining of tin cans. BPA can be detected in urine in about 93% of us and there are statistically significant associations of BPA levels in humans with adverse effects on health, see for instance here:m_joc80072f1The lecture highlighted some of the ongoing work by Galloway and Harries, including a study where school children follow a diet minimizing the use of packaged (junk)food, followed by the monitoring of BPA levels in urine and gene expression of two genes where expression has been shown to vary with BPA levels. Very interesting stuff that of course led up to discussions on how to limit BPA levels in our own daily lives. More Living with Environmental Change module updates to follow!


Posted in cool science, environment and human health, teaching | Tagged , , , , , , , , | Leave a comment

Living with Environmental Change II

The Living with Environmental Change module might be one of the broadest modules taught at the University and this particularly well-illustrated by the diversity of guest lecturers featured in this post. Sean Meaden is currently finishing his PhD with collaborator Britt Koskella (who moved to Berkely this summer) on interactions between plant pathogenic bacteria, their plant hosts and their viral parasites. He however also did a tour in Sierra Leone Last December at the height of the Ebola outbreak. In his lecture, he thus could talk about the theory behind disease biology but also about its grim reality on the ground. Although the epidemic is over, two new cases were confirmed in Guinea this week and a British nurse who seemed cured is currently back in hospital after the virus returned. The intranet site for the module has an rssfeed to Guardian stories relevant to the module and the continuous flow of ‘big’ news stories is a reminder of how important the issues covered by the module are. Below a picture by Katina Kraemer of a health worker in a field hospital. Note the puddles of bleach; good at killing the ebola virus but used in these quantities also a health hazard in itself.ebolaSean gave a fascinating insight into the workings of a field hospital during an outbreak and about the factors that contributed to its severity. This was followed by a class discussion on how to possibly prevent or mitigate future outbreaks (i.e. a vaccine that seems to work very well was actually available four years ago but was not trialled and mass-produced…). Also, Sean had a student volunteer demonstrate the difficulty of properly removing gloves laced with ‘ebola’ (glowstick fluid). In the Exeter session, Rebecca Lovell spoke about the positive effects that biodiversity could have on human health and well-being. ‘Salutogenic’ places have long been associated with well-being, from walled gardens in ancient Mesopotamia to green spaces in modern urban cities. However, why this is so is not very well understood. The opposite has even been argued, as negative correlations between biodiversity and well-being have also been found (‘the environmentalist’s paradox‘). The following figure by Barton and Grant illustrates the fact that there are many more effects on human health than just genetics or life-style. Although often much more subtle, the outer layers are probably quite important too:SOER-Fig_5-1-The-healt_fmtThe same figure was also used in the lecture by Mat White in Penryn on the effects of  weather and climate on human wellbeing. This exposed the geography and biology students to the field of psychology, which seemed to go down very well. A subjective (self-assessed) momentary measure of wellbeing (mood) can be given by the PANAS system (‘how are you feeling today?’) or by asking for life satisfaction (‘All things considered, how satisfied are you with your life?’). It can be argued that the former measure is more correlated with weather (which also acts momentarily) and the latter with climate (which is also measured over long time-scales). Mat discussed a variety of studies investigating how (the different components of) weather and climate affect wellbeing. Interestingly, in the case of the UK, a warmer climate could actually potentially result in a net positive health effect, for instance by greater levels of outdoors activity. Both Rebecca and Mat used very nice illustrations by former ECEHH member (now at the BMJ) and collaborator Will Stahl-Timmins of which I will show one:salutogenMichiel

Posted in environment and human health, teaching | Tagged , , , , , , , , , , | Leave a comment

Living with Environmental Change I

This semester, head of the European Centre Professor Lora Fleming and myself have started the brand-new undergraduate module “Living with Environmental Change”. Somewhat complicatedly, we are teaching this module to students in different years and in two different locations: the St. Lukes campus in Exeter and the Penryn Campus in Cornwall. At the former campus we mainly teach Biomedical Sciences students and in Cornwall we teach a mix of Geography, Biology and Environmental Sciences students. It has been a steep learning curve setting up a module for the first time, but it seems to be going very well. Very broadly, our module investigates the impact of environmental change on human health. And a broad range of impacts that is! Pollution and resource depletion affect human health directly and indirectly through effects on the environment in myriad ways. Overarching themes include (of course) climate change, effects of social inequality and the ageing of (many) populations. As the module is so diverse, we rely to a large extent on guest lecturers. Luckily, there are many excellent scientist at the university of Exeter (as well as some from other institutions) available to give lectures on their active research in this field. I’d like to highlight the module on the blog as it progresses by showing some slides of these lecturers.Climatechange_engl2012MOne important realization is that we actually know most of the dangers the environment poses to human health, the direct ones and the somewhat less direct ones (such as some of the effects of climate change or long-term exposure to chemicals). So the science behind ‘living with environmental change’ is actually relatively straightforward and the real challenges to try to change things around for the better lie in the domains of politics, society and economy. Dr. Hywel Williams studies how debates on climate change play out on social media (amongst other things such as phage-bacterium coevolution). Social media is now an integral part of most peoples lives; probably most of the students following the course consume their news via news apps and twitter on their smartphone rather than buying news papers. Hywel has studied a number of climate change related hashtags used on twitter and used network analysis how opinions are formed.Picture1

See here a twitter #globalwarming follower network where dots represent users that have been categorized (using a paid army of tweet-scrolling students) as being climate activists (green), climate sceptics (red), non-unanimous (yellow) or other (black, specifically, followers of Aerosmiths Global Warming tour and Pitbulls Global Warming album….). Hywel could glean some very interesting patterns on how opinions are formed, by for instance analyzing different hashtags or differences between retweets and mentions. Unfortunately, figures such as the one above demonstrate that the debate is extremely polarized, and that there is little meaningful dialogue between the two camps. A completely different aspect of Hywel’s work is to use social media as a way of ‘remote sensing’, for instance tracking UK floods using instagram, or California wildfires using twitter (see below). Finally, he highlighted some of the biases associated with this type of work, for instance, most people are not WEIRD.hywel2Another speaker we were fortunate to host was Dr. Duarte Costa who talked about the PULSE project in Brazil. This project is a collaboration between scientists in Brazil and the UK and involves the detailed spatial and temporal mapping of current and predicted climate conditions, disease incidence and socio-economic parameters. We need to take into account all these factors to be able to understand and predict health impacts of climate change, see the figure below (and have a look at the new PULSE Health Mapper website).Duarte1duarte3Average temperatures are set to rise considerably in Brazil, up to 8°C by the end of the century under the ‘business as usual’ scenario. And Brazil is already pretty hot. The government is barely coping to manage day-to-day healthcare issues and is in no way prepared to deal with the adverse health effects prolonged, high temperatures will pose (imagine doing construction work at 40°C and the heat strokes and the extra accidents caused by any dizziness or lapses in concentration). Except for heat, water is a main problem. Sao Paolo had a recent watershortage with reservoirs down to 8% capacity without any measures taken as it was nearing election time. When water restrictions were finally in place, these were mainly in place in the poorest neighbourhoods, resulting in social unrest. At the same time, far away in Acre province, massive floods blocked the only road giving access to the rest of the country. This province thus was for months reliant on neighbouring Peru for supplies, highlighting potential national integrity and security issues. Below the increase over time in ‘heatwave’ days under two climate scenario’s. For more information, see one of Duarte’s recent publications here, and a recent publication by Hywel’s here.duarte2Michiel

Posted in environment and human health, teaching | Tagged , , , , , , , , , , , , , | Leave a comment

Rates of lateral gene transfer: high but why?

I just had a paper out which was an enlightening experience to write. Along with three Dutch co-authors, it was mainly a collaboration with Adam Eyre-Walker at Sussex (see this previous post). The manuscript morphed from a data paper into a ‘verbal theory’ (i.e. no equations) paper (I will spare you the details). To quote from the Abstract:

Lateral gene transfer (LGT) is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.

Briefly, we first reviewed the (very few) studies that have quantified the rate at which prokaryote genomes change due to gene acquistion and loss. The relative dearth of data means that we do not know for sure, but it seems plausible that the rate at which whole genes are gained is on the order of point mutation or perhaps above that. Trying to work out the rate at which genomes changes due to uptake and loss of genes (relative to mutation) was inspired by another study where I found that very closely related Myxococcus genomes (see my personal page for some links to papers on this interesting bacterium) that differ only by several SNPs (point mutations) can differ by hundreds of genes. I was surprised by this finding. I asked a number of colleagues what they thought would happen first when a bacterial cell in the environment would divide for some time: a point mutation or a lateral gene transfer event/gene loss event. Almost all thought that point mutations would be more common. The fact that the Myxococcus isolates were very closely related is important. Most genomic changes are deleterious and will be removed by purifying selection. Comparing closely related genomes means that not enough time has passed for selection to have removed all (but the most severe) changes and thus results in missing many of them. Consistent with this expectation was that the ratio of gene content differences to point mutations decreased when comparing slightly less closely related Myxococcus isolates. (I hope to post about this other manuscript soon, it has been a long time coming and is still in revision at the moment.)

The second part of the paper is concerned with the question: why are changes in gene content so common in many bacterial species when most of them apparently seem deleterious? This question is quite fundamental to understanding bacterial genome evolution, including the evolution of pathogens. We discuss two main scenarios that could explain the high observed rates of lateral gene transfer. In the first scenario, the high rate of gene turnover is optimal: although the majority of LGT events are expected to be detrimental, this is outweighed by a small proportion of highly advantageous events. This is illustrated by the figure below:

Figure 2 CORRECTED PROOFS - CopyOn the x-axis, it shows the distribution of fitness effects (DFE). Mutations, as well as LGT events, have fitness effects that can be broadly divided into three categories. First, there are mutations that decrease fitness. Second, there are ‘neutral’ mutations, which have little or no effect on fitness. Third, there are advantageous mutations, which increase fitness by allowing organisms to adapt to their environment. However, in reality, there is a continuum of selective effects, stretching from those that are strongly deleterious, through weakly deleterious mutations, to neutral mutations and then on to mutations that are mildly or highly adaptive. The distribution of fitness effects refers to the relative frequencies of these types of mutation. We hypothesize that LGT events are generally subject to stronger positive and negative selection. In addition to the many LGT events that insert themselves into ‘native’ genes causing loss of function, result in the expression of proteins that are toxic to the cells or just are utterly useless and result in wastes of energy, there are also events that result in the uptake of whole genes or plasmids that allow for the immediate gain of new functions which could have strongly beneficial effects when adapting to a novel environment.

In the second scenario (I’ll keep it very brief, if you have read this far down you probably should turn to the actual paper), the rate of LGT is actually suboptimal but the fitness costs of preventing LGT events, often mediated by selfish genetic elements, are too high or barriers to gene transfer are impossible to achieve.


Vos M, Hesselman MC, Te Beek TA, Van Passel MWJ and Eyre-Walker A. “Rates of Lateral Gene Transfer in Prokaryotes: High but Why?.” Trends in Microbiology 23, no. 10 (2015): 598-605. cough, cough

P.S. this was the 100th blog post!

Posted in paper out! | Tagged , , , , , , , | Leave a comment

Discovering New Antibiotics

Posted in ongoing work | Tagged , , , , , , | Leave a comment

Microbiomes: belly buttons and plant leaves

The Wellcome Trust-funded Invisible You – Human Microbiome Exhibition at the Eden Project (see here) had a number of cool public engagement events going on in the opening week. One of these projects straddling the boundaries of art and science was by Brooklyn-based Joana Ricou who visited our lab as part of this event. Visitors could have a portrait taken from their non-human self. Specifically, they could swab their belly buttons and have this plated out on an agar plate. Each such portrait thus shows the unique, cultivable microflora at one particular bodysite for each participant. After incubation on site, Joana photographed the plates in Penryn, later added some colour digitally and uploaded them onto the dedicated website All anonimized portraits can be browsed here and project participants can locate and download their own portrait using a personal code. More details about the project can be found here. Below you can see my belly button portrait: quite a lot of diversity at quite a high density. I choose to interpret this as me having a very healthy belly button!010 MichLast week I had the pleasure to host 14 school kids from London as part of a three-day visit to our campus, engaging in a range of biology projects. It is quite a challenge to do a microbial ecology project with students in only an hour or two: any cells that are sampled do not have the time to grow up into colonies. I repeated a session that I did last year with Britt Koskella in another school outreach event focusing on plant leaf bacteria. Just like our belly buttons, plant leaves are covered in bacteria. This ‘phyllosphere’ is likely to be very important in plant health (see here for more information on the topic). After a general introduction, I asked the students to come up with hypotheses on where they would expect to find differences in leaf-associated bacteria. They came up with a variety of good questions. For instance, one group asked whether microbiomes where different on the underside compared to the upper surface. Another group asked whether dead leaves differed in their microbiome from fresh leaves. After some discussion, students ventured out on campus to collect leaves, and then went back into the lab to press leaves on agar plates. I had already pressed a leaf on a plate to be able to show them what their own plates would look like. After the weekend, I took pictures of the student’s plates and send it back to them so they could find out whether their questions were answered. Below an example of a leaf-pressed agar plate:IMG_9048

Posted in art, outreach | Tagged , , , , , , , , | Leave a comment

visiting PhD student Nadia Andreani

I had the pleasure to host PhD student Nadia Andreani from the University of Padova for a six month stay. She wrote the following blog post about her time in Cornwall, which I am publishing now, a day after she returned to Italy, here goes!


I am Nadia Andreani, a third-year PhD student from Italy, visiting the Coastal Pathogen group at the ECEHH. When I had to decide what to do for my internship, I strongly wanted to find something interesting and new and, because of my great interest in bacterial genomics, I straightforward decided to ask hospitality to Michiel.
As in that period (September 2014) I was struggling with some bioinformatics analyses on my PhD project, the first idea for this internship was to apply different bioinformatic tools to try to analyse in depth some data coming from the complete sequencing of the genomes of 4 of my Pseudomonas fluorescens strains.

Just some little notes about my Pseudomonas fluorescens strains: the Pseudomonas fluorescens group comprises several Gram negative, rod-shaped, aerobic, mesophilic and psychrotolerant bacteria, characterized by extreme versatility and adaptability. A major concern about this microbial group is food spoilage. Microbial contamination by these strains can result in unpleasant changes in appearance, texture, flavour and odour that spoil food. In 2010 in Italy, 70000 balls of mozzarella cheese were seized after consumers saw that the white cheese turned blue after the package was opened. The batches of blue mozzarella have been found all over the mozarellaThe first part of my PhD allowed the identification of the strains able to produce this strange blue pigment. However, the chemical nature of the blue pigment is still unknown.
Only just before my arrival here, some genomic analyses revealed the presence of some genes clearly involved in the blue pigment production. As I solved my bioinformatics issues before coming here, the project moved on quite different topics. First of all I performed a random mutagenesis of one of my blue strain to experimentally verify the genes involved in the blue pigment production. As the blue pigment is a clearly visible phenotype, the idea was to randomly insert transposons in the bacterial genome. If insertions end up in a gene involved in the pigment production, the strain will be no more able to produce it and appear white. The sequencing of the genomic DNA surrounding the transposon in these strains then allows confirmation of the genes involved in the blue pigment production.

Next, competition experiments using blue and white mutants was performed to identify the competitive advantage of pigment production: is iron necessary to produce the blue pigment? Is the blue pigment a siderophore (or rather a molecule to catch iron from the environment)? Is the blue pigment protective against low temperatures as it is not produced above 30°C? The experiments I performed here revealed that iron enhances the production of the blue pigment, but it’s not a siderophore. Moreover, the blue pigment seems not to be involved in protection against cold temperatures. In this last week, I also performed a challenge test, inoculating a blue and a white mutant on bacon and mozzarella cheese. The idea was to understand if the blue pigmenting strains were doing better than the white ones in food. Actually, it doesn’t seem so! aThe second part of this internship was spent to isolate bacteriophages from the environment. As Pseudomonas fluorescens is still a problem for the dairy industry, the idea was the use of bacteriophages as a novel and safe option for the treatment of these contaminants . Actually I was really unlucky: I analysed 34 samples of leaves/flowers/grass/mushrooms, 27 samples of soil, 19 samples of water, 32 samples of sewage (yes, sewage!!!) and 10 samples of animal poo (amazing stuff!!), but with no success! I also applied some of Abi’s seaweed extracts to see if some were active against my Pseudomonas strains: a couple of them were… this was a nice result, maybe for a future collaboration!!!
Finally, I worked on a Bioinformatics project, starting from an idea of Michiel. The main questions of this project was: Is there any correlation between homologous and non-homologous recombination in bacteria? The project is based on the use of an online software package, odose, that allows several analyses within bacterial species. Now the system is under maintenance , but I hope to finish soon all the analyses and, maybe, to write a nice paper!

During my stay here I had the opportunity to attend several seminars and two interesting workshops: the first was about storytelling in science and the second one was about Matlab. Even if the Matlab workshop was really helpful for my bioinformatics project, my favourite one has been the workshop about writing science stories for children, because it gave me the opportunity to write my own book. “The Adventures of Flo, the special Bacterium” will be published really soon as part of a science book series for young independent readers! The main character is Flo, a young Pseudomonas fluorescens strain, having some issues in controlling the production of his blue pigment.

And that’s all, I think…I had a great time here and I really hope to come back soon. This experience was great: I can say that I am grown a lot! I have learnt lots of new things and my PhD project sounds to be now close to the end! The research group is amazing and I really want to thank Michiel, Will, Lihong, Anne, Aimee, Amy, Andy and Abi to make me feel at home and for the help during these six months… it was a pleasure to work with you!



Posted in introducing | Tagged , , , , , | Leave a comment