Internship - Method for integrating transcriptomics and microbiome data

Starting date: To be determined
Contract: Internship, 6 months
Location: Bordeaux, France
Laboratory: Bordeaux Bioinformatics Center (CBiB)
Address: CBiB 146 Rue Léo Saignat 33076 Bordeaux Cedex
Amount of internship compensation: statutory internship compensation


A master's 2 internship (6 months) is open to work jointly within the IGBC (UMR 5164) and the Bordeaux Bioinformatics Center in Bordeaux (France), under the supervision of Domitille Chalopin-Fillot and Ulysse Guyet and by Dr. Macha Nikolski.

The main objective of the internship is to model host-bacteria interactions via gene expression. Based on the annotation of the function of genes, the student will have to propose and implement a method of network analysis which would allow to extract the modules of human and bacterial genes which share the same function (for example, the production vitamin B12, the biosynthesis of short fatty acids, etc.). The search for modules linking the functions of human and bacterial genes will allow from a bioinformatics point of view to automate the integration of RNA-seq data and 16S sequences, and from a biological point of view to better understand the influence of the microbiome on the expression of the genes of its host. The new integration method including human-bacteria interaction modules can be validated using real data available in the team and from patients with liver cancer (RNA-seq and microbiome).

The Bordeaux Bioinformatics Center (CBiB) is a bioinformatics research team at the IBGC (UMR 5095) and a core facility that provides access to high-performance computing resources, develops bioinformatics methodologies and performs data analysis. We bring to researchers the best tools to manage and understand biological data. We focus mainly on the development of bioinformatics for analysing datasets acquired using high-throughtput omics technologies and offer state-of-the-art technologies for working with clinical, translational, and basic science data – from acquisition and storage to analysis and sharing. From a few samples to several tens of thousands, the Innovation Centre provides complete DNA, RNA, metabolomics and proteomics analysis.


Metagenomics makes it possible to study the microbiome, all living microorganisms (bacteria, viruses, fungi, yeasts) in a specific environment (oceans, soils, intestines, etc.). The study of the human microbiome has so far included the characterization of the diversity of microorganisms regardless of their impact on the expression of host genes. Indeed, it has not been proven that the functions performed by the microbiota, for example the production of vitamins, could influence the expression of the genes of their host. However, it was recently shown that the bacterial diversity within tumors could have an immunosuppressive or immuno-activating effect (Riquelme et al. 2019), suggesting that the bacterial presence influences the recruitment of certain immune cells and therefore the expression. of genes. Samples taken from patients, during biopsies or surgery, can be used for many analyzes, including gene expression analysis based on transcriptomic data (expression of host genes) or microbiome analysis based on 16S sequencing. (diversity and abundance of microorganisms). Nevertheless, the joint analysis of these two types of data has still been very little investigated (Huang et al. 2020) and bioinformatics methods remain to be developed (Wang et al. 2019).


  • Knowledge of concepts and terminologies of bacterial and human genomics
  • Knowledge of biological analysis and statistics of high throughput data
  • Use of at least one programming language and / or analysis (Python, R, ...)
  • Mastery of the Unix / Linux environment and the Bash language


The internship will take place at the IBGC under the supervision of Domitille Chalopin-Fillot and Ulysse Guyet. Contacts:


Cover letter, CV and references contacts may be directed to domitille.chalopin-Fillot@u-bordeaux.fr, ulysse.guyet@u-bordeaux.fr and macha.nikolski@u-bordeaux.fr .


Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma - Genome Medicine
Background The gut-liver axis plays a pivotal role in the pathogenesis of hepatocellular carcinoma (HCC). However, the correlations between the gut microbiome and the liver tumor transcriptome in patients with HCC and the impact of the gut microbiota on clinical outcome are less well-understood. Met…
Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes - PubMed
Most patients diagnosed with resected pancreatic adenocarcinoma (PDAC) survive less than 5 years, but a minor subset survives longer. Here, we dissect the role of the tumor microbiota and the immune system in influencing long-term survival. Using 16S rRNA gene sequencing, we analyzed the tumor micro…
Host and microbiome multi-omics integration: applications and methodologies
The study of the microbial community—the microbiome—associated with a human host is a maturing research field. It is increasingly clear that the composition of the human’s microbiome is associated with various diseases such as ...