Current Project
Profiling of Human Axillary Microbiome in Tropical Climate
Human skin is a complex ecosystem where interaction between the host (human) and microbes happens. Depending on many physiological parameters, the skin provides a suitable environment for the skin microbiota to grow. In the axillary vault, sweat secretion from the apocrine gland is degraded by bacteria and might even act as probiotic. We are interested to profile the microbiome of people living in a tropical climate to find insight on the role of normal microbiome to control tropical diseases.
Human skin microbiome profile is affected by many factors including geographical location, environment, behaviour, and genetics. To understand more about the distribution of human skin microbiome across the globe, we are utilising the RESTful API of EBI metagenomic database to obtain study and sample information and compare it based on the respective metadata. We are utilising Python through Jupyter Notebook to provide reproducible exploration of microbiome data and its metagenome from EBI MGnify.
Publication: M. Nuhamunada et. al. 2018. "Data Mining and Comparative Analysis of Human Skin Microbiome from EBI Metagenomics Database". DOI: 10.1109/BIOMIC.2018.8610588
Biosynthetic Gene Clusters Exploration from Metagenome
Metagenome obtained from environmental samples might contain important information on how microbiome interact and adapt with different variables in the diverse microhabitat found on earth. Many of this interaction are found in the form of “small molecules” or metabolites which are expressed from a Biosynthetic Gene Clusters (BGCs). Using AntiSMASH & other genome mining methods, we are interested to explore potential BGCs from metagenomes (and it’s related product) and how they might play important role in microbiome symbiosis.
Positions Available
Application Period (25 February - 8 March 2019)
Assistant Research Manager (Part-Time, Paid)
The Assistant Research Manager is responsible for the management and coordination of internal and external research work and projects.
This is a part-time paid position with allocated time of 10-20 hours/week for 3 months period. Requirements: Undergraduate in their Final Year or Fresh-graduate are welcome to apply.
You will be working to: (1) plan, coordinate and execute assigned research projects, (2) supervise team members to complete research projects within deadlines, (3) track project progress periodically and report to the PI, (4) monitor and control expenses within allotted budget, and (5) ensure that research deliverables meet quality standards and requirements.
Wet Lab Research Assistant (Volunteer)
The Wet Lab assistant will help to handle sample processing and molecular biology works.
You will receive training on molecular biology techniques and related skills to conduct microbiome research.
You will be working to: (1) prepare microbiome sample, (2) environmental DNA Extraction, (3) 16s rRNA library preparation using PCR, (4) amplicon QC using Gel Electrophoresis and other techniques, (5) amplicon digestion using restriction and (6) preparing sample for sequencing or NGS
Bioinformatics Research Assistant (Volunteer)
The Dry Lab assistant will help to handle sequence data analysis and data mining from several sequence databases.
You will receive training on Python Programming, utilising GitHub, and other related bioinformatic analysis techniques.
You will be working to: (1) optimize primer-enzyme combination for T-RFLP, (2) using Python scripting to obtain information from several sequence databases (NCBI & EBI), (3) manage sequence library using Benchling, (4) perform genome mining using AntiSMASH or other algorithm, and (5) analyze Metagenomic data from NGS using UNIX environment (QIIME, Mothur)
Sponsors
This project is sponsored by:
