Reconstruction of selected microbiome-phage interaction network from human gut

Abstract: The Human Microbiome is the collection of all the microorganisms living in association with the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses1. Advances in DNA sequencing technologies have created a new field of research, called metagenomics, allowing comprehensive examination of microbial communities, without the need for cultivation. Particularly, microbial diversity can be determined using two different approaches: (1) Amplicon sequencing or (2) Shotgun metagenomics2. In the second approach, shotgun metagenomics can help to reconstruct large fragments or even complete genomes from organisms in a community without previous isolation3. Due to the important role that microbiome interaction may play in T2D and related diseases, we focused on it and implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Accurate feature extraction and bacteria-phage interaction prediction is important for identifying new probable hosts. The main purpose of this study is to provide a network of phage-microbiome interactions based on metagenomics data.

Keywords:

Microbiome , Bacteriophage , Database , Reconstruction network