“Investigating host-microbiome interactions by droplet based microfluidics” – a New Joint MetaFluidics Publication

Discover the latest publication by MetaFluidics partners INSA Toulouse and The University of Cambridge:

  • Tauzin, A.S., Pereira, M.R., Van Vliet, L.D. et al. Investigating host-microbiome interactions by droplet based microfluidics. Microbiome8, 141 (2020). https://doi.org/10.1186/s40168-020-00911-z https://doi.org/10.1186/s40168-020-00911-z

You can also watch the video abstract below:

Meet the MetaFluidics Team! (Episode 11)

Today, let’s introduce Dr. Emna Bouhajja, from Partner INSA Toulouse (France)

Emna Bouhajja is currently a postdoctoral research fellow at Toulouse Biotechnology Institute, one of the most innovative bio & chemical engineering laboratories in France, located on the Institut National des Sciences Appliquées (INSA Toulouse) campus. Emna is part of the Catalysis and Enzyme Molecular Engineering Team (CIMEs), whose research focuses on in-depth mechanistic and structure-activity relationship studies of a broad range of enzymes. Let’s find out more about her and her experience with MetaFluidics in this latest “Meet the MetaFluidics team” interview!

  • What exactly are you working on ?

I’m using microfluidic techniques to screen large metagenomic libraries from extreme environments such as bovine rumen gut, salterns and antarctic rizospheres. Our main targets are the yet-unknown carbohydrate enzymes from uncultivated bacteria. We are looking to characterize them in order to enrich the catalogue of enzymes for biotechnological applications.

Left : Fluorescent bacteria growing in picoliter-scale droplets, one green dot is one bacterium (microscopic picture)

Right: Fluorescent bacteria from picture 1 forming visible colonies on growth medium, one green dot is 1 million bacteria
  • Which problem would you like to solve / contribute to in the future?

The main problem I would like to solve is the limitation of commercially available chromogenic carbohydrates, which are key components in conventional screening procedures, thereby enhancing the novelty of enzymes discovered. Moreover, the high price of these reagents is always a limiting factor when we plan for a screening campaign. For example, the average current price for several carbohydrate active enzyme substrates is 50 euros per 10 mg. Theoretically, if you want to screen a 20,000-clone library twice, you will need at least 100 g of substrate, which costs 500,000 euros. My work is to miniaturize the screening assays from the ml- to the µl-scale to drastically reduce the cost and make use of natural substrates that have no chromogenic analogues in the market.

  • Will the MetaFluidics project change your career prospects?

Yes, I have gained a considerable expertise in the field of enzyme discovery from the environment, using not only powerful but also in vogue mining tools, which is very important in my professional career. Within our project, I could see my working network increase thanks to the multiple collaborations with partners from different European universities and from the industry. This is definitely a boost for me to move gradually from fundamental research to applied research. 

  • A more personal question now… Name the one time in your life when you were the happiest.

The happiest time in my life was when I got my PhD. I knew that it was the starting point for an adventurous life as a researcher, which is full of challenges.

For more information about Toulouse Biotechnology Institute at Partner INSA Toulouse, please visit their webpage: http://www.toulouse-biotechnology-institute.fr/en/index.html

Meet the MetaFluidics Team! (Episode 10)

Today, let’s introduce Dr. Eduardo González Pastor, from Partner CSIC (Spain)

Eduardo González Pastor is a Senior Research Scientist at the Center of Astrobiology (CSIC-INTA) in Madrid, Spain. His research focuses on the mechanisms of adaptation of microorganisms to extreme conditions using metagenomic and metatranscriptomic approaches. Find out more about him in this latest “Meet the MetaFluidics team” interview!

  • How did you become a scientist ?  

From a young age, nature fascinated me, I spent hours in the field, observing and collecting plants and insects and also had a microscope with which I observed microorganisms. My passion was to become a naturalist. Finally, I did a degree in Biology and specialized in microbiology and molecular biology. Until my postdoctoral stage I was studying model bacteria and when I was an independent researcher at the Center for Astrobiology, I resumed contact with nature and began studying microorganisms in their natural environment. This has led me to study microbial communities in various extreme environments such as Rio Tinto, Andean hypersaline lakes, Atacama and Antarctica.

  • What are the main topics you are currently working on?

My research work is basically focused on the study of the adaptation mechanisms to extreme conditions in microorganisms, such as UV radiation, high salinity, acid pH, toxic metals, etc. The main objective is to understand how extremophilic microorganisms can adapt to these conditions. On the other hand, the information obtained is being used to expand the capacity of other organisms such as plants to resist more extreme conditions. In addition, I am interested in the social behavior of microorganisms, and in the laboratory, we are studying the ability to produce extracellular DNA by Bacillus subtilis and its relevance in communities formed by this bacterium.

  • Which problem would you like to solve / contribute to in the future?   

I am concerned about the emergence of multiple antibiotic resistance in pathogenic microorganisms, and I would like to contribute to the development of new strategies and antibiotics. But for that, we need to understand even better how microorganisms work. Even in the best studied model bacterium, Escherichia coli, we do not know the function of 2000 genes, almost half of the proteins that are encoded in their genome. The lack of knowledge of the functioning of microorganisms makes it difficult to address more sophisticated strategies to combat those that are pathogenic.

  • What is exactly your role in the MetaFluidics project?  

I am the PI of the CSIC group and we are contributing to generate molecular tools and protocols to express metagenomic libraries in hyperhalophile hosts to perform functional searches. On the other hand, we are also identifying new genes and adaptation mechanisms to extreme conditions, such as UV radiation and cold temperatures.

  • What have you learnt from the international / European experience within the MetaFluidics project?  

Collaboration between research teams from different disciplines and countries must be encouraged more strongly to successfully address any scientific problem, without damaging the individual creativity that has allowed scientific knowledge to advance.

  • A trickier question now… In your opinion, could humans live on other planets like Mars?   

Yes, it will be possible, but we are still far from being able to do so. More research is still needed to create life support systems that allow human communities on Mars to be supplied autonomously, without having to transport food from planet Earth.

Dr. Eduardo González Pastor was also one of the main organisers at the EMBO Practical Course: Microbial Metagenomics: A 3600 Approach (12 – 19 June 2019). You can read more about him in the following interview:

For more information about the Center of Astrobiology at Partner CSIC, please visit their webpage: http://www.cab.inta.es/en/inicio

Bye Milton…

The MetaFluidics consortium is very sad to communicate the recent loss of our colleague Professor Milton da Costa from the University of Coimbra. On behalf of the whole MetaFluidics team, we send our sincere condolences to his family and friends. We will remember Milton’s deep kindness and his fine wit, as well as his numerous contributions to the project. Bye Milton…

Meet the MetaFluidics Team! (Episode 9)

Today, let’s introduce Mercedes Sánchez Costa, from the Universidad Autónoma de Madrid (Spain)

Mercedes Sánchez Costa is currently a PhD research fellow at the Center for Molecular Biology “Severo Ochoa” at the Universidad Autónoma de Madrid. Let’s find out more about her and her experience with MetaFluidics in this latest “Meet the MetaFluidics team” interview!

  • What exactly are you working on?

My work is mainly focused on developing and optimizing the workflow for the screening of thermozymes from Metagenomic libraries using Microfluidics. For this purpose, I am testing a system to express enzymes from a thermophilic bacteria, directly in droplets, and studying methods to recover the genetic information bearing in different vectors, such as plasmids or fosmids. 

  • Why did you choose to become a scientist? 

The main reason to become a scientist was my interest in finding answers and explanations either to how “things” work, in general terms, or the why of several daily aspects that we face. So, I could contribute to society. 

  • Which problem would you like to solve / contribute to in the future? 

I would like to contribute, as much as possible to decreasing the current lack of environmental awareness that, unfortunately, is present in a vast number of regions on the planet.   

  • What is your favorite aspect in the MetaFluidics project? 

My favourite aspect of Metafluidics is that this project links the classical knowledge in the microbiology field together with really new and revolutionary techniques, such as microfluidics. Besides, the project covers the study of a vast variety of enzymes, using different approaches and microorganisms, being represented many extreme environments.   

  • A more personal question now… Which causes would you be ready to fight for? 

I consider that I am ready to fight  to revert climate change and the state of emergency that is determining the future of the planet and the species that inhabit it. 

For more information about the “Center for Molecular Biology Severo Ochoa” (CBMSO) at Partner UAM, visit their webpage: http://www.cbm.uam.es

Meet the MetaFluidics Team! (Episode 8)

Today, let’s introduce Dr. Liisa Van Vliet, from Partner Drop-Tech (UK)

Liisa Van Vliet is the Managing Director of Drop-Tech, a Cambridge-based company commercialising a patented droplets-on-demand sampler that allows the creation of microfluidic droplet sequences from up to 24 samples. This technology was created through a collaboration between microfluidic groups at Imperial College London and the University of Cambridge.

Liisa has an M.Phil and Ph.D. in the field of drug discovery and over 10 years research in miniaturisation and microdroplets at the University of Cambridge. She worked for a global business consulting firm before returning to science with a BBSRC/RSE Enterprise Fellowship award to found Drop-Tech. Find out more about her in this latest “Meet the MetaFluidics team” interview!

  • How did you become a scientist ?   

It’s in my genes ! And also thanks to several incredibly inspiring Science teachers in school and especially thanks to the encouragement from my Undergraduate and PhD supervisors.

  •  What are the main topics you are currently working on? 

Microfluidics, Metagenomic screening, Alzheimer Diagnosis, Drug development… Quite varied indeed and always trying to bring some benefit to society!

  • What things give you the greatest satisfaction at work?    

Learning something new every day,  seeing people make their first droplets! And  working on something that will have a serious impact on the health of people and our planet.

  • What things frustrate you the most in your research? How do you usually cope with these?

Fighting for funding, when the applications are clearly for the benefit of society. And currently, not having enough time to have fun in the lab, but having to deal with the necessary other responsibilities. Sometimes the workload is overwhelming, but family, friends and travelling keep me sane.

  • What is exactly your role in the MetaFluidics project?  

Drop-Tech is responsible for helping the academic groups in the consortium prepare for the commercialisation of their innovations, by identifying the key benefits of their research and mapping out the potential markets for their research outcomes. We also provide advice for the partners who are new to the exciting world of microfluidics. 

  • Can you give us an example of MetaFluidics applications?  

The microfluidic techniques developed by our University of Cambridge partner can be used for a variety of applications: from drug discovery to improving enzymes for use in the food, textile, chemical and biofuel industries for example. Nature has evolved over millennia to perform highly specialised reactions, and we have barely scratched the surface when it comes to exploring genomic sequence space. Screening the huge landscape of genomic material from the environment will provide new, interesting and useful enzymes over the next decade.

  • A more personal question now… If you were stuck on an island, what three things would you bring and why?   

A musical instrument (guitar or flute), Rayuela by Cortázar,  a water desalinisation kit.

For more information about Partner Drop-Tech, visit their webpage: http://drop-tech.com/

Meet the MetaFluidics Team! (Episode 7)

Today, let’s introduce Dr. Morten Vinther Lund, from Partner QIAGEN Aarhus (Denmark)

Morten Vinther Lund is a Senior Bioinformatics Scientist at QIAGEN Aarhus, Denmark, the world’s leading software provider for Next Generation Sequencing data analysis. Let’s find out more about him and his experience with MetaFluidics in this latest “Meet the MetaFluidics team” interview!

  • What is your professional background?

I was educated as a physicist with a Master’s degree from Aarhus University, Denmark. After this, I was accepted on a Ph.D. program at the same university. My Ph.D. research was in experimental nuclear astrophysics studying low-mass exotic nuclei close to the proton dripline relevant for understanding super-novae’s. As part of my Ph.D., I worked at CERN, Geneva, Switzerland, in a prolonged period of time and this is also where most of my experiments were performed.

After finishing my Ph.D. I accepted a job at QIAGEN Aarhus as a Senior Bioinformatics Scientist. In this position, I take an active part in developing the CLC Microbial Genomics Module and other software. I have worked at QIAGEN for 3 years now.

  • What things give you the greatest satisfaction at work? What things frustrate you the most?

For sure, the most frustrating bit of my work is debugging the software when the error message gives you no clue about the cause. Sometimes I end up spending hours finding the mistake. However, the greatest satisfaction is then to see a finished product being sent out to the customers and to hear customer feedback on the product. It is always a great help when customers take their time to provide input for improvement.

  • What is exactly your role in MetaFluidics?

I am taking part in developing the bioinformatics tools and pipelines that will help support the researchers. I act as a developer, a bioinformatician, and a test manager on the Microbial software project at QIAGEN Aarhus. We have the development and maintenance responsibility of the CLC Microbial Genomics Module, the CLC Genome Finishing Module and the CLC MLST Module.

  • Will the MetaFluidics project change your career prospects?

The MetaFluidics project has certainly been an enormous help and inspiration in my current job at QIAGEN. Since I started working in a (for me) completely new field 3 years ago, the meetings with the MetaFluidics partners have been a welcome opportunity for me to develop a deeper scientific understanding of the microbial world that I work with now.

  • A more personal question now… What is your favorite book (or author)?

Currently, I think my favorite author is Bernard Cornwell since I am a big fan of historical fiction and he has written a very good series called Saxon Stories/The Last Kingdom about the Viking invasions of England and the birth of England as one country. I also enjoy very much reading books by Ken Follett, George R.R. Martin and Philip Pullman among others.

The Flame Bearer

For more information about Partner QIAGEN Bioinformatics, visit their webpage: https://www.qiagenbioinformatics.com/

Meet the MetaFluidics Team! (Episode 6)

Today, let’s introduce Dr. Josefa Antón Botella, from Partner UA (Universidad de Alicante)

Josefa (aka Pepa) Antón Botella is a Senior Lecturer at the University of Alicante, a diverse-oriented and welcoming university with one of the best campuses in Spain, not only in terms of infrastructure, but also in terms of landscaping, sustainability and gender equality. Pepa Antón carries out research in microbial biodiversity, molecular microbial ecology, and marine and hypersaline environments (among other interests) at the Multidisciplinary Institute for Environmental Studies. She also teaches at the University’s Department of Physiology, Genetics and Microbiology. Find out more about her in this latest “Meet the MetaFluidics team” interview!

  • How did you become a professor at the University of Alicante?  

I did my PhD here after studying in Valencia. Afterwards I went to Madrid and Berkeley and they offered me a position of Assistant Professor, so I decided to come. Then I started my group and finally got the professorship.

  • What do your students learn in your classes?

Now I teach Advanced Microbiology, but I’ve taught all the possible micros we have at this university. I try to teach them to think and be critical and how fascinating microbiology is.

  • What are the main topics you are currently working on as a researcher? 

Viruses, microorganisms and their interactions with one another and with the environment in hypersaline systems and in some marine environments such as corals and sediments.

  • What are you most proud of in your life & career?

My group! 🙂

  • What is exactly your role in the MetaFluidics project?  

We are the ecological part and the providers of environmental samples (that we analyze through metagenomics). We are developing microfluidics-based approaches to study viral/microbial assemblages in nature.

  • What is your favorite aspect in the MetaFluidics project?

The interaction with the rest of the teams and the cutting edge science

  • A more personal question now… What helps you to overcome the difficulties of life?  

“With a little help of my friends” (and family) 🙂

Meet the MetaFluidics Team! (Episode 5)

Today, let’s introduce Laure Fabre, from Partner INSA Toulouse (France)

Laure Fabre is in charge of the “Communication and Dissemination” Work Package in the MetaFluidics project. She has been working at INSA Toulouse for 11 years now, carrying out many different activities in this engineering university. Find out more about her in this latest “Meet the MetaFluidics team” interview!

  • What is your professional background?

It might come as a surprise, but my main job is actually as an English teacher! I have always loved learning and studying languages, which is why I graduated with both a Master’s degree in English and a Bachelor’s in German in the early 2000s, and after teaching in high school for 5 years, I joined INSA Toulouse where I have been teaching English since 2008. I have always wanted to work at an international level though, and in 2013, I had the opportunity to do another Master’s degree in European studies and European grant proposal writing. Now I wear 2 main “hats” at INSA Toulouse: still teaching English to our students and helping INSA researchers write their proposals to apply for Horizon 2020 funding. When I helped write the MetaFluidics proposal in 2015, Aurelio, our coordinator, offered me to take on the Communication & Dissemination Work Package and I found this a great way to get actively involved at a European level and interact with people from many different countries, while discovering the “other side” of European projects: how they are actually put in place! So far it’s been a very enriching experience!

  • What is exactly your role in MetaFluidics?

I am in charge of coordinating all the MetaFluidics communication and dissemination activities and presenting them in reports and meetings with the European Commission. For dissemination, the scientists in the consortium are fairly autonomous and I mainly synthesise what has been done in the past review period. For communication, my role is a lot more active. Since the first few months back in 2016, this has meant coordinating the preparation of the project’s visual identity and tools, website, video and social media, and then updating the website and social media on a regular basis.

I have also taken part in some of the project’s outreach activities, e.g. ESOF 2018 in Toulouse. Although it was a real challenge for me at the beginning to really understand what the scientists in the consortium were doing and be able to explain it to visitors, it ended up being a fantastically rewarding experience! I’m still proud today of being able to explain the project to family and friends in simple terms, whereas I knew so little about it just a few years ago!

  • Why is science communication important?

Science communication is essential to enable the general public to understand what scientists do in their labs, strengthen the links between science and society and also encourage children to become the scientists of tomorrow. There is a clear lack of engineers and scientists in Europe today and it is vital for the future of Europe to generate interest in science among young people. They also can make it! Of course, the very detail is very complex to understand but with good science comm’, it is possible to see the point of (almost) any experiment and more importantly, relate it to our everyday life.

Through my experience at ESOF, I could discover some of the techniques used to communicate to the general public and I feel there is a lot to do in this field. Science communication is also a very good exercise for scientists, which can help them think differently about their own research. This is actually a bit what we teach our final-year students to do in English classes at INSA, or when I meet a scientist who has a European project idea in mind. They try to explain to me what they want to do and I ask all these “silly” questions in return to fully understand everything. In general, when they come out of the meeting, their own project idea has evolved and they can see better how to present it when writing the proposal. The challenge is even greater when talking to children or non-science-savvy people but the activities that can be put in place in this case are much more fun: games, quiz, lab experiments and even looking for microbes in a ball pool as we did for ESOF! Imagination has no limit!

  • Will the MetaFluidics project change your career prospects?

I’m not sure yet but adding skills in science communication, communication in general, as well as European project management, will certainly open up new opportunities for me. For the moment, I feel like focusing more on teaching English and European proposal writing in the next few years, but the new skills on my CV definitely give me many different career options for the future. I’m really lucky in that sense!

  • A more personal question now… If you had to name the all-time best song, which would you pick?

That’s a difficult question (but I’m partly responsible for it so I won’t evade it! ;-))

Although my tastes in music are quite diverse, I have a slight preference for French music so I would pick “Ne me quitte pas” by Jacques Brel (who was actually Belgian by the way…)

Although the lyrics are a bit sad, I find this song quite powerful and it gives me goose bumps every time I hear it!

For more information about Partner INSA Toulouse, visit their webpage: http://www.insa-toulouse.fr/en/index.html

Meet the MetaFluidics Team! (Episode 4)

Today, let’s introduce Che Fai Alex Wong, from Partner NTNU (Norway)

Alex (right) presenting a MetaFluidics poster with colleague Swapnil Vilas Bhujbal from NTNU

Alex Wong is currently a PhD research fellow at the Department of Biotechnology and Food Science of NTNU, the Norwegian University of Science and Technology. Let’s find out more about him and his experience with MetaFluidics in this latest “Meet the MetaFluidics team” interview!

  • What exactly are you working on ?

In Biotechnology, we generally utilize bacteria as “micro-factories” with the usual aim to produce valuable products, such as enzymes. Expressing and producing an enzyme in large quantities is not always a straightforward matter, which requires the development of molecule parts/ tools to overcome different challenges. As an example, I am trying to expand the promoter repertoire in alternative expression hosts, which should provide additional flexibility when working with these unusual bacteria.

  • What work have you accomplished so far for your PhD and what are your remaining objectives?

I am currently “wrapping” up work from two projects and hopefully convert them into publications. As a team, we have presented the MetaFluidics project in different local and international podiums, such as the Centre for Digital Life Norway, the Synthetic and Systems Biology Summer School etc.. My remaining objective is to (hopefully) defend my PhD and gain my title (not sure) in less than a year.

  • What is the most important thing you are looking for in your professional life?

For me, one of the most exciting parts of research is to learn new ideas from others, usually from reading articles but sometimes from chit-chats during conferences. You are often amazed by other achievements, and it’s even greater if you can integrate these ideas into your own work.

  • What have you learnt from the international / European experience within the MetaFluidics project?

The MetaFluidics project brings in expertise from all around Europe, and it’s an incredible experience to meet and work with people across research disciplines, e.g. extremophile studies, development of microfluidic devices etc.. I received consistent help from our Spanish partner on the usage of thermophilic bacteria, and in return we try to provide useful molecular tools for their work.

  • A more personal question now… What helps you to overcome the difficulties of life?

Often difficulties of life are beyond one’s control, and the most important issue is (try) to stay calm and keep going till the situation gets better. Sometimes it’s easy to forget your work is not your whole life, which requires a self-reminder from time-to-time.

For more information about Partner NTNU, visit their webpage: https://www.ntnu.edu/