Job ID: 54764

Early Stage Researcher / PhD student for Marie Skłodowska Curie ITN Gut-brain-axis: Targets for improvement of cognition in the elderly (SmartAge)

Position: Ph.D. Student

Deadline: 30 June 2021

Employment Start Date: 15 July 2021

Contract Length: 3 years

City: Copenhagen

Country: Denmark

Institution: Clinical Microbiomics

Department: Microbiome Lab / R&D Department


Clinical Microbiomics, Denmark (head of project: Dr. Henrik Bjørn Nielsen), offers a PhD position for an Early-Stage Researcher (ESR) for the Project #14: “Bioinformatics analysis of the gut-microbiome during aging and following late-life interventions with respect to cognitive functions.” The position is part of the EU-funded Innovative Training Network SmartAge (“Gut-brain-axis: Targets for improvement of cognition in the elderly”) with full-time employment for a duration of 3 years, starting in July/August 2021.

Objective of the project: The Aim of this project is to identify mechanistic links that connect the ageing gut microbiome to cognitive decline. This will be achieved by multi-layered association between microbiome functional potential, microbiome dysbiosis (i.e. aging associated ecological biases in the microbiome) and cognitive readouts, multi-tissue and inflammatory measures and host metabolomics data.

For this we will explore and develop different microbiome bioinformatics analysis and machine learning (ML) techniques. Hence, the project will entail building data infrastructures and frameworks for analysing the link between age-related cognitive decline and microbiome changes. This effort will take advantage of and expand Clinical Microbiomics’ metagenomic species framework (Nielsen et al., 2014, Nature Biotechnology, and smart three-based data structures for making associations to ultra-high-resolution microbiomics (SNV level) data. Furthermore, longitudinal changes of the microbiome incl. microbiome stability, richness and microbial species persistence will be analysed and connected to measures of inflammation and intestinal permeability.

Enrolment in Doctoral degree(s) / ETN if applicable: Technical University of Denmark, Department of Bio and Health Informatics

Requirements:  The candidate must have a 2 years relevant master degree (with bioinformatics, ML and/or microbiome experience) and cannot have worked or studied more than 12 month in Denmark within the last three years. Moreover, experience with phylogenetic analysis or population biology will be an advantage. Furthermore, the applicant should be able to perform team oriented as well as independent work. Desirable methodological skills: excellent background in bioinformatics, machine learning and phylogenetic analysis and computer programming.

The applicant must be fluent in both oral and written English.

Selection process: Interested candidates please send a motivation letter, a CV including publications (if available), copies of university degrees and courses (including obtained grades), and the names and e-mail addresses of two scientists who can provide references (all summarized in one pdf) to

Closing date for receipt of applications is Wednesday 30th June 2021

For more information concerning the research project please contact Henrik Bjørn Nielsen, PhD., CSO. (Phone:  +45 93 51 12 53 ; email: with subject line: “SMARTAGE ESR14”)

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For further information, please visit: ITN SmartAge and Clinical Microbiomics