Data Mining and Comparative Analysis of Human Skin Microbiome from EBI Metagenomics Database
Abstract
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, skin microbiome studies available in the EBI metagenomics database were compared. Based on the RESTful API of the database, we demonstrate programmatic access to obtain study and sample information based its respective metadata such as sex, geographical location, and body site. The biological observation matrix (BIOM) from the analysis result of the selected samples was compared using MEGAN Community Edition. Of the 7 studies found, comparative study was conducted for scalp samples between the USA and Brazilian populations, and foot samples between the USA and Australian populations. Data mining of the BIOM files using PCoA and biplot analysis showed the difference in microbiome profile between studies. Co-occurrence network analysis showed a major difference between scalp sample of the USA and Brazilian population due to the difference in microbiome richness and abundance. Foot samples between the USA and Australian samples, even though different in profiles, suggest a similar pattern in the network of bacterial interaction.
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Matin Nuhamunada
Lecturer
My research interests include natural products genome mining and bioengineering.