By setting up the Quaranskin project, we had to read literature on the skin microbiome and also meet experts in the field. Some discussions with dermatologists during confinement increased our interest in the therapeutic application of synthetic biology to cure skin disorder. Also, we learned that in this context of a pandemic the fact that we need to wash more often our hand is a real problem for people who present symptoms of eczema. You can find more information about these discussions on the Human Practices page. From this point we decided to develop the SynDerma project which aims to engineer S.epidermidis, a commensal bacteria of the skin microbiome to control the population growth of pathogenic bacteria, such as S. aureus which, when overgrown, can be a cause of eczema. Since no synthetic biology tools were developed to engineer S. epidermidis, we decided to develop a MoClo toolkit, EpiFlex, and another project for growth and electroporation protocol optimization.
What our projects bring to the scientific community?
The major aim of this study is to answer these questions:
- 1. Has the social distancing and the changes in hygiene during the COVID-20 pandemic affected the skin microbiome diversity?
- 2. Are there some common characteristics (intrinsic or behaviorial) that are associated with a specific proportion of S. epidermidis? If yes, which are these characteristics?
- 3. By looking at the skin microbiome of our database, can we find the characteristics which are, in the literature, associated with eczema symptoms, such as overgrowth of
S. aureus population? If yes, does the microbiomes presenting these characteristics do come from individuals with eczema symptoms?
The answers to these questions will increase the knowledge we have about the microbiome and more precisely about the external factors that can impact it. We'll also know more about the secondary effect of the COVID-19 pandemic, such as the impact of the lockdown and the changes in hygiene habits on our skin, and our health.
One aim of this study is the creation of an open database of skin microbiome from people in the context of a pandemic. This will allow researchers in the field of the skin microbiome to have a full collection of data to explore. It will also allow to continue on the same road of research and compare skin microbiome in this context of pandemic during which our behaviors and daily life are changed with skin microbiomes during a non-pandemic time if some research teams are interested as us about the impact of the sanitary measure during COVID-19 pandemic on our skin microbiome.
By setting up Quaranskin study we also develop Science@Home, since we tested sending the kit with all materials needed to sample microbiome at home following a given protocol. We also want to check if the variability in protocol completion, since the protocol of sampling will be done by all the participants individually and not by a nurse or other experimented actor from the medical field, doesn't affect the results. This all together provides a useful pipeline and protocol that can be used in the future for other microbiome studies which are based on the ideals of citizen science.
Finally, Quaranskin is also an educational project during which each participant will learn about their microbiome. Indeed, at the end of the study, we will send back to each of them their microbiome.
EpiFlex, EpiGlow and EpiGrow
The development of our MoClo toolkit will be useful for all the research team and also future iGEM teams who would like to engineer S. epidermidis. Indeed, EpiFlex toolkit will allow in the future to construct many plasmids with different genes or even genetic circuits quickly and easily. The standardization of the Golden Gate assembly allows collective work, labs can share parts they design and they will still be usable by anyone.
In the same way, EpiGlow and EpiGrow projects provide scientists who want to work with S. epidermidis optimized protocols for culture and transformation. Transformation of S.epidermidis was still a challenge for the labs working with this bacteria.
What are the challenges of implementing these projects in the real world?
The main challenge of running this study and making accessible an open database of the microbiome is the data protection both for data collected with the questionnaire and microbiome data from sequencing after sampling. All of them have to be anonymized and stored in a safe server. To ensure that the safety measures are respected the project has to be presented to an ethical committee, as the Comité de Protection à la Personne (CPP) in France, and approved by it.
The risk of giving pipeline allowing easy skin microbiome collect from people remotely is that some studies can be developed and set up easily outside of the context of a clinical essay in a hospital, so without a CPP approval. To avoid this we think it's important to communicate about the relevance and significance of having this kind of approval before starting such a study. That's what we tried to do as much as possible in our wiki. You'll find more information about it on the Quaranskin project page.
Epiflex and Epigrow
For EpiFlex to be usable by other teams and labs we need to complete it by adding more parts. And the most important thing is to characterize them. A vision we have for an expansion and rapid construction of an extended kit is to use the Soap Labof the 2020 Imperial College team. This kit was developed with community use in mind, thus it should be a collaborative and adaptable resource. In our design considerations, we allow for anyone to be able to design a part and reference it in the toolkit. For that, we explain how to design a part that is EpiFlex compatible on our wiki. You'll find more information about it on the EpiFlex project page.
As part of the EpiGrow project, we wanted to develop a device to measure the growth in a 2D environment and being able to compare it to the growth in a 3D environment. This part of the project is on going.
As a lot of work is still needed to be done to be able to propose EpiFlex and EpiGrow projects to the scientific community as relevant tools, we would like to continue these projects until their end. Fortunately, the iGEM 2021 Paris Bettencourt Team is already hired and willing to continue working on it! The 2020 team will be mentoring them to present a more complete project for iGEM 2021.