Mots-Clés

Phage, génome, métagénomique, génomique, comparative métagénomique, python, linux

Description

Subject: Skin Phageome Translational Analysis Internship.

Internship Master 2 (6 months)

From February to July 2024 at the EBI (Ecoles de bio-industries, Cergy 95800, France) & Efrei (Engineering school of digital technologies, Villejuif, France)

Human development and health have been improved by the advances and numerous studies on microbiome human. In contrast to microbiome research, the phageome is ignored. Phageome is a term used to describe bacteriophages, viruses that infect bacterial hosts. They are known to regulate the dynamics and diversity of bacterial populations in various ecosystems. Phages were first discovered in the early 1900s and were recognized as an alternative to antibiotic treatment. Most research concentrates on the use of phages for therapeutic and biotechnological purposes, but the analysis of phage communities is relatively young.

There are three methods available to characterize phages: culturing, microscope, and metagenomics. The culture-based method isolates phages from heterogeneous samples by extracting and purifying of virus-like particles (VLPs), enriching phages in bacterial host cultures, and inducing temperate phages from lysogenized hosts. Phages in the gut ecosystem can be observed using electron microscopy and transmission EM. Metagenomic-based approaches are based on the alignment to a reference phageome database.

In this project, you will build a bioinformatic workflow to process the metagenomics dataset (NGS) and explore the phageome of skin communities. Your task is to create an analytical workflow that can process a significant amount of NGS data. You will also use interactive and reproductible workflows and electronic notebook environments to analyze the data and ensure transparency, reproducibility, and reuse of the data analytical work.

Essential prerequisites for this role include robust competencies in Linux/Unix, and programming languages such as Bash, Python, and R. Additionally, skills in leveraging bioinformatics tools for quality control, alignment, and classification are crucial. An understanding with curiosity about metagenomics, genomics, and molecular biology will form the backbone of your contributions to this cutting-edge exploration.

CV and cover letter to thi-p.le@hubebi.com and mano.mathew@efrei.fr