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 microbialart.tumblr.com. 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

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Discovering New Antibiotics

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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!

Michiel

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 country.blue 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!

Nadia

Nadia

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Earth Systems and Environmental Sciences

Will and I are biologists working in the medical school but classified as environmental scientists by the University’s REF program. This week members of this group, including mathematicians, toxicologists, biologists, clinicians, geographers and mining scientists, went on a short retreat at Dartington Hall located inbetween the Exeter and Cornwall campuses. The aim was to discuss which strands of research could form a REF Impact Case study. The university puts forward Impact Cases, which when rated excellent (‘four star’), will result in a financial reward to the university. In order to be rated highly, projects need to be shown to have had significant societal, political or economic impact, and caused demonstrable changes in peoples behaviors. One previous Exeter success story was that by Tamara Galloway and colleagues, who showed a link between the ubiquitous plastic compound bisphenol A (BPA) and negative health effects caused by estrogen-like properties, subsequently resulting on a ban of its use in baby bottles (before BPA was used to make polycarbonate bottles and many other everyday products, it was actually used as a synthetic estrogen). See here for some nice background.

The retreat provided an excellent way to hear what our faraway (100 miles or so) colleagues at Exeter were up to. For example, there were presentations on climate change modelling, an airplane instrument to monitor volcanic ash clouds, noise pollution in the sea, a very cool ocean science education project, transgenic zebrafish that light up when a chemical is detected in water (which has the potential to greatly reduced toxicology monitoring cost and save the lives of warmblooded test animals) and a whole bunch of other projects as well. Hywel Williams  showed a realtime twitter map that was able to track a storm crossing the US and talked about text mining social media to monitor changes in perception and opinions on climate change. ECEHH head professor Lora Fleming mentioned some of the centres success stories, one of which is led by Jess Tyrell. She explaines how her app is helping to tackle Meniere’s disease in the video below:

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A visit to Gabriel Perron at Bard College

This week I have made a short trip to see NERC collaborator Gabriel Perron at Bard College. (Gabe visited the ECEHH last year, see here.) Bard is a small liberal arts college located in the beautiful Hudson Valley about an hour and a half north of New York City by train. Colleges like Bard do not really exist in Europe and so it was a very interesting place to visit! Scattered in the large wooded campus lie a mix of old and very modern buildings, including a concert hall (designed by Frank Gehry), art museum and small baseball stadium. The focus is on undergraduate teaching (there are about 2000 students) which is faciltated by a new state-of-the-art science building where labs, teaching labs and lecture spaces are seamlessly integrated. One of Gabe’s projects is monitoring water quality in the Saw Kill stream adjacent to the campus using molecular biology and chemistry methods. The campus has its own waste water facility, which will allow for sampling strategies that are otherwise generally not possible. (For this project, Gabe is using some of the approaches developed by Will Gaze’s group, see here.) It was great to see the students present their work, walk along the stream where they were doing their sampling (spotting a baby snapping turtle on the way) and talk about new ideas. I gave a presentation on our antimicrobial seaweed extract work (I will post on that soon btw) and the production of antimicrobials in nature was another topic that Gabe and I have been philosophizing over. On to some grant writing to extend this trans-atlantic collaboration!

Michiel

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The Gabrielle H. Reem and Herbert J. Kayden Center for Science and Computation

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The Italian Garden overlooking the Hudson

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3rd International Symposium on the Environmental Dimension of Antibiotic Resistance

Another conference post…This time Will, Lihong, Anne and I went to EDAR3 (the 3rd International Symposium on the Environmental Dimension of Antibiotic Resistance), held from 17th – 21st May in the quaint town of Wernigerode, Germany. As you can guess from the name of the conference, it was extremely relevant to all of our research and there were some excellent presentations by some big names in the field. Will promoted his new, international, collaborative project in his presentation titled, “Class 1 integrons as markers of antibiotic resistance” and signposted the posters being presented by the rest of us:

Co-selection for antibiotic resistant bacteria at sub-inhibitory concentrations of biocides – Lihong Zhang

Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters – Anne Leonard

Investigating co-selection for antibiotic resistance in the environment – Yours truly

Conference season is pretty much over now, but watch this space for the next update!

Aimeewernigerode

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Invisible You: the Human Microbiome Exhibition

In an earlier post, I described plans for an exhibition at the Eden project here in Cornwall that would combine art and the biology of the microbes that live on and in our body. Supported by the Welcome Trust, that exhibition has now become a reality. Located in the Core building (and included in the normal Eden Project ticket), it consists of a variety of art installations that are widely different, but that all focus on the importance of the invisible ‘bugs’ we carry around on our bodies. For example, Rebecca Harris’ ‘Symbiosis’is a textile map of the human body depicting microbes as embroidered knots and Rogan Brown creates bacteria out of layers of cut paper:IMG_7972

IMG_7968There is much more to discover, including music and poetry. The opening week has/had a number of demonstrations/workshops too. I will blog about two of these later. It has been a great experience for Will and myself to be involved in this project, and we urge everyone to go take a look at the Invisible You exhibition!

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