PhD fellowship/scholarship - Unveiling the alternative hydrogen pathway in cattle rumen

Applicants are invited for a PhD fellowship/scholarship at Graduate School of Technical Sciences, Aarhus University, Denmark, within the Quantitative Genetics and Genomics programme. The position is available from 1 September 2025 or later. You can submit your application via the link under 'how to apply'.

Title:
Unveiling the alternative hydrogen pathway in cattle rumen

Research area and project description:
Ruminant animals play an important role in food security by converting low-value plant biomass into high-value animal proteins through microbial-mediated fermentation. The process produces methane (CH4) which is a highly potent greenhouse gas as well. Feed additives offering CH4 emission mitigation opportunities, especially 3-nitroxypropanol (3NOP) approved and marketed in the European Union which can reduce approximately 30% methane emission. There are adverse effects such as feed digestion, energy balance and animal performance impede the improvement of CH4 reduction by these feed additives. To solve this, the direction of Hydrogen flow is curious. Redirection of the Hydrogen by hydrogenotrophs to nutrient compounds other than CH4 or accumulated in the rumen is the desirable strategy. However, the knowledge about the species and pathway involved in this process is unknown.
This project aims to fill these two gaps by integrating state-of-the-art bioinformatics and microbiology. For this, the prospective PhD student will apply state-of-art metagenomic method for discovery and conduct laboratory work for validation. Specifically, the candidate will:

1. Using metagenomic assembly resolve strategy to identify the novel species in cattle rumen. And quantify the species abundance in cattle rumen.
2. Applying statistics analysis to prioritize the candidate species that has been affected by 3NOP.
3. Data mining to predict the gene functions of the target microbial species. The focus is on the methanogenesis pathway and hydrogen pathway.
4. Isolation and cultivation of the target species. The novel species are most likely the uncultured species, which need to use enrichment medium to conduct the isolation and cultivation.
5. Functional validation of the isolated species. The in vitro experiment will be executed to validate the function of the target species.

This PhD project is part of” SustainCattle: mitigating methane emission and improving

food security by unveiling the alternative hydrogen pathway in cattle rumen”, funded by Independent Research Fund, that aims to fill the knowledge gap to develop methane mitigation strategy in cattle. The successful outcome of this project has the potential to find the key species and microbial gene for developing the methane mitigation strategy in cattle and assist the cattle breeding practice towards the environmentally friendly animals. The selected PhD student will gain skills and knowledge in bioinformatics, metagenomics and microbiology. The project will involve close work with colleagues at the Department of Animal and Veterinary Sciences, Aarhus University and Centre for Microbiome Research, Queensland University of Technology.

In the centre for quantitative genetics and genomics (QGG), Aarhus University, we are focused on having a diverse, positive and coheresion work environment. Team members support each other and help out when we see someone physically or mentally struggling. We work respectfully with people from different backgrounds, experiences, and nationalities. To collaborate more efficiently and ensure reproducibility, we implement the principles of open data and open science.

Project description
For technical reasons, you must upload a project description. Please simply copy the project description above and upload it as a PDF in the application.

Qualifications and specific competences:
Applicants must have a relevant Master’s degree (120 ECTS), or equivalent, or receive the Master’s degree before the start date. The Master’s degree should be in microbiology.

The applicants must have a strong skill on culturing. The skill set of inoculation, isolation, culturing techniques and incubation are vital. Especially, the applicants need to conduct high quality work in culturing include the usage of different media: Simple or basal media, Complex media, Synthetic or defined media and Special media for enrichment.

Experience in scientific programming with, e.g., Python and/or R, is required. Basic understanding of metagenomics is an advantage. Interest in conducting isolation and cultivation is highly desirable.
The ideal candidate should demonstrate motivation and curiosity, possess strong teamwork abilities, exhibit the potential to produce high-impact publications, and have excellent proficiency in English.

Place of employment and place of work:
The place of employment is Aarhus University, and the place of work is C. F. Møllers Allé 3B, Building 1130, 8000 Aarhus C, Denmark

Contacts:
Applicants seeking further information are invited to contact:

• Zexi Cai, [email protected]
• Samantha Joan Noel, [email protected]

How to apply:
Please follow this link to submit your application.
Application deadline is 31 May 2025 at 23:59 CEST.
Preferred starting date is 1 September 2025.
For information about application requirements and mandatory attachments, please see our application guide.

Please note:

• Only documents received prior to the application deadline will be evaluated. Thus, documents sent after deadline will not be taken into account.
• The programme committee may request further information or invite the applicant to attend an interview.
• Shortlisting will be used, which means that the evaluation committee only will evaluate the most relevant applications.

Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop. We view equality and diversity as assets, and we welcome all applicants. All interested candidates are encouraged to apply, regardless of their personal background. Salary and terms of employment are in accordance with applicable collective agreement.