PhD student in the field of culturomics of the infant microbiome

13 Mar 2024
Job Information

Organisation/Company

University Medical Centre Groningen (UMCG)

Research Field

Medical sciences

Researcher Profile

Recognised Researcher (R2)
First Stage Researcher (R1)

Country

Netherlands

Application Deadline

21 Apr 2024 - 22:00 (UTC)

Type of Contract

Temporary

Job Status

Not Applicable

Hours Per Week

36.0

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

The work of our group has characterized the colonization of the infant microbiome using several different data layers. These data layers include: (1) sequencing of the bacterial and viral microbiome throughout the infant’s first year of life; (2) characterization of the oligosaccharide content of breast milk, a potential ecological driver of selection for the infant’s microbiome; (3) and the metabolic profile of the infant’s blood plasma, which contains signatures of the interplay between host and microbiome. Important findings of these surveys indicate that particular species, such as Bifidobacterium spp. and Bacteroides spp., may serve as keystone species that promote the diversity and colonization of the microbiome. Other species, such as Staphylococcus spp., appear to be selected by oligosaccharides found in the mother’s milk. The aim of this PhD project is to study the role of such key species by culturing them from stool samples, characterizing their function via wet and dry lab approaches, and creating synthetic microbial communities from these isolates to test ecological and evolutionary theories of ecological succession and colonization. The focus of this project is therefore primarily lab based, although statistical and analytical experience is important to interpret results. Bioinformatic experience or an interest in learning the bioinformatic analyses is also a plus.

Information about our team and work:
Our team's website .

Links to recent papers from our team:
Paper: Environmental factors shaping the gut microbiome in a Dutch population
Paper: Host genetic regulation of human gut microbial structural variation

PhD student working on this project will be expected to:
- Perform microbiological analyses such as isolating and culturing isolates in both anaerobic and aerobic conditions.
- Perform molecular microbiology tasks such as DNA extraction and PCR.
- Set up and execute culture-based experiments.
- Process and analyze data from experiments.
- Summarize and report key analytical findings in both oral and written form at work meetings, at international scientific conferences and in scientific publications.

Requirements
Specific Requirements

- An MSc in biology , microbiology, molecular biology or related field.
- Experience in a molecular or microbiological lab.
- Experience with statistics and performing analyses in R or python.
- Familiarity with ecological concepts.
- Excellent oral and written communication skills in English.

Bonus experience would be:
- Bioinformatic experience, such as genome assembly, annotation. Familiarity with shell scripting.

The UMCG has a preventive Hepatitis B policy. The UMCG can provide you with the vaccination, should it be required for your position.
In case of specific professions a ‘Certificate of Good Conduct’ is required.

Additional Information
Benefits

You wil get a contract 32-36 hours a week for 4 years. Your salary will be a minimum of € 2.901,- gross per month in the first year and a maximum of € 3.677,- gross per month (scale PRO) in the final (4th) year, based on a full-time appointment.In addition, the UMCG will offer you 8% holiday pay, and 8.3% end-of-year bonus. The conditions of employment comply with the Collective Labour Agreement for Medical Centres (CAO-UMC).

Interested candidates should include a cover letter, CV, and references in their application.

Selection process

dr. Alexandra Zhernakova, [email protected]
dr. Cyrus Mallon, [email protected]

Additional comments

dr. Alexandra Zhernakova
[email protected]

dr. Cyrus Mallon
[email protected]

Website for additional job details

https://www.academictransfer.com/338940/

Work Location(s)

Number of offers available

1

Company/Institute

University Medical Center Groningen (UMCG)

Country

Netherlands

City

Groningen

Postal Code

9713 GZ

Street

Hanzeplein 1

Geofield

Where to apply

Website

https://www.academictransfer.com/en/338940/phd-student-in-the-field-of-culturom…

Contact

City

Groningen

Website

http://www.werken.umcg.nl/

Street

Hanzeplein 1

Postal Code

9713 GZ

STATUS: EXPIRED