Team:Tongji Software/Contribution
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Overview
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Database & Software tool
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For synthetic biology
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For iGEM community
CONTRIBUTION
★Overview
Since the launch of Human Microbiome Project (HMP) and Metagenomics of The Human Intestinal Tract (MetaHIT) in 2007, studies on microbes, especially gut microbiota, have surged, and interactions between microbiota have become a hot topic, including phage-bacteria interactions. Many synthetic biologists have also been engaging in related fields. At the same time, with the abuse of antibiotics, superbugs become increasingly harmful to human health. As the natural enemy of bacteria, bacteriophage has become the focus of researchers, so bacteriophagotherapy has been developed and is promising. However, the vexing question of how to choose the right phage has plagued many researchers and iGEMers. To meet these needs, we launched Phage-MAP, hoping to recommend the most suitable phages for bacteria by studying phage-bacteria interactions, in order to assist phagotherapy and related scientific research.
Fig. Literature on phagotherapy in the last 20 years
★Database & Software tool
Our project, Phage-MAP, adopting alignment-based method and alignment-free methods, integrated information from NCBI, CRISPR-CasDB, Taxonmy and other databases, and finally drew a MAP to describe phage-bacteria interactions. The MAP covers interactions between 10,819 bacteria and 12,041 phages. It is an improvement on the current lack of phage-bacteria relationship data and provides information for future iGEMers interested in the study of the microbiome.
Based on the MAP, we developed software tool Phage Finder, which integrated CRISPRdetect, BLAST, PHP, WISH and other tools & models. It can recommend top-N phages that have the strongest interaction relationship with the user's query bacterium, to provide reference for phage selection in phagotherapy.
Fig. A graph of our software
It's also worth noting that not only did we share the database, we also organized the data analysis process into a workflow, click on Github for more details. According to the readme documentation, future iGEMers can easily process their own data.
★For synthetic biology
For Synthetic biologist
Superbug has long been a burning problem in both synthetic biology and entire scientific community. Single phagotherapy may be effective, but most phages only bind to a single receptor on bacteria by tail filaments, which makes it easy for bacteria to develop resistance to phages as well. Phage modification through synthetic biology may be an effective way to solve this problem, and Phage-MAP can exactly provide reference and help for the study of synthetic phages.
Fig. Synthetic phage
For Public
In order to expand the influence of synthetic biology, we established a popular science website xtphage.com in cooperation with XJTLU-China, which is mainly used to introduce the knowledge about synthetic biology, bacterial resistance and phages. At the same time, we developed a "Cell Defense" game based on bacterial CRISPR system to simulate the defense process of cells fighting against pathogen invasion. This game has well promoted synthetic biology and iGEM, deepened people's further understanding of superbugs as well. Clicking Communication for more details.
★For iGEM community
We have participated CRISPR Conference with a lot of CRISPR-themed teams around China, and collaborated on the compiling of CRISPR manual. The manual includes an introduction to CRISPR and the topic selection ideas of previous iGEM teams, hoping to provide reference for future iGEMers.
In addition, we opened our own account on bilibili, the largest social media for young people in China. We have uploaded a series of videos and articles, which includes the process of iGEM competition, methods to build a wonderful wiki, and the popularization of some software tools related to synthetic biology. We did these in order to promote the iGEM competition and bring our youth closer to the iGEM stage. And we sincerely hope to provide information and help to future iGEMers, solving their difficulties in carrying out projects.
Figure: Our bilibili account
Moreover, many iGEM teams associated with artificial phages, such as, Heidelberg-2017, Munich-2018, TUDelft-2020, DUT-China-2020, and so on, have shown us our project phage-bacteria interaction network can help the future iGEM teams.
Fig. Some iGEM teams associated with artificial phages
Tongji University, Shanghai, China
