若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 応募書類

Name: Zhao Jin
Title: Comparative metagenomics analysis of microbial communities across bacteria
Institute: Bioinformatics Center, Institute for Chemical Research, Kyoto University
Partner institute of your choice：Bioinformatics Program, Boston University
Duration of your choice: January 16, 2012 ~ April 8, 2012
Plan：
Research Objectives:
I would like to apply for the ITP program for three months' study in Dr. Daniel Segre'slaboratory, which belongs to Department of Biology & Department of Biomedical Engineering,
Bioinformatics Program, Boston University.
There are various research interests in this partner laboratory which attract me very much,mainly using mathematical, computational and experimental approaches to study the dynamics
and evolution of metabolism in individual microbes and in microbial ecosystems. They approachthe questions of whether optimality principles are helpful in understanding the architecture andutilization of metabolic networks both in simplified artificial chemistries and in the global map ofknown biochemical reactions across all organisms; what role the metabolism played in theemergence of complex multicellular life (joint project with the NASA Astrobiology Institute (NAI)
MIT team); the prediction of evolutionary trajectories of microbial metabolism; also the analysis on
microbial community dynamics and synthetic ecology, and so on.
I used to focus on several bioinformatics studies such as oncogenic pathway characterizationaccording to virus analysis and target prediction of viral miRNA. I believe this visiting would
provide a great chance to apply and improve my research skills. Also during the communications
with researchers and students joint with different programs from various countries, it will bebeneficial to my professional vision and English communicating skills.
Research Plan:
Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms
to understand the true diversity of microbes, their functions, cooperation and evolution, inenvironments such as soil, water, ancient remains of animals, or the digestive system of animals
and humans. Comparative analysis between metagenomes can provide additional insight into thefunction of complex microbial communities and their role in host health.

若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 応募書類

Plan (Continued)
Because bacteria species can be identified on the basis of 16S rRNA from the metagenomic
datasets, our research would like to focus on the functional comparisons between metagenomes
across bacteria made by comparing sequences against reference databases such as COG or KEGG,
and tabulating the abundance by category and evaluating any differences for statisticalsignificance in order to reveal the effect of habitat upon community structure and function.
Besides, metagenomic sequencing is particularly useful in the study of viral communities, which
could be applied in one of my past studies on virus. As viruses lack a shared universal phylogenetic
marker (as 16S RNA for bacteria), the only way to access the genetic diversity of the viralcommunity from an environmental sample is through metagenomics.
What’s more, understanding metabolism is one of the major research interests in Dr. DanielSegre's laboratory, they usually focus on microorganisms and try to model the metabolism throughFBA (Flux Balance Analysis), which is a mathematical method for analyzing metabolism, to someextent. Therefore, the second plan during my stay is to understand the details of FBA and learn towork with this model, which may provide a new angle to my pathway research.
In conclusion, I will take part in not only researches but also events and communications
actively during the three months’ stay in Boston, trying to explore and experience various things
that can only be obtained in this opportunity.