Microbial NGS data analysis

Job Location

Ten private companies of the animal production sector and INRA have partnered in a research
consortium to conduct studies around the methanogenesis in ruminants. This Consortium aims
ultimately to develop operational solutions to reduce emissions of greenhouse gas from ruminant
Two main research areas have been selected:
-The development of indicators for methane production;
-The study of the functioning rumen and its microbial ecosystem (microbiome) to reduce methane
In this context, three animal experiments were conducted and methane emissions recorded along with average daily gain, milk production, milk quality, rumen fermentation products. All animals were sampled for rumen contents and total DNA or total RNA were extracted. DNA and/or RNA amplicon libraries were constructed for bacteria, archaea, fungi and protozoa and sequenced using the MiSeq technology. Shotgun RNA sequencing will also be performed in a meta-transcriptomic approach. The finality of the work is to explore relationship between the diversity and activity of rumen microbiota and animal performances.

Job Description

The engineer will be responsible for data collection and processing to answer questions dealing with changes in microbial diversity and transcriptional regulation of gene expression. He/she will use existing software and bioinformatic pipelines for routine analyses, as well as programming skills for specific analyses. The candidate will also perform statistical processing and associated data representations. He/She will be part of a multidisciplinary team studying ruminants’ metabolism.


We are looking for a highly motivated individual with:
 PhD / Engineering degree in bioinformatics / biostatistics
 Statistical knowledge applied to microbial ecology
 Experience in NGS Data Analysis
 Experience in RNAseq data analysis
 Advanced use of R software
 Ability to interact with biologists

How to Apply

Send CV and a cover letter to [email protected]

About Our Organization

UMR1213 Herbivores is a joint research unit associating Inra and VetAgro Sup. It contributes to the design of sustainable farming systems for herbivores that seek to reconcile production efficiency, product quality and socio-economic viability with environmental protection and valuation, and animal welfare. UMR1213 Herbivores assesses both on-farm practices and predominant and alternative systems of herbivore farming, and proposes innovative techniques with high environmental value. To achieve this aim, UMR1213 Herbivores analyses and integrates the underlying biological mechanisms, and establishes laws for animal responses with approaches ranging from high-throughput techniques to modelling and decision support tools for various stakeholders (producers, consumers, citizens, and policy-makers).

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