Postdoctoral Researcher on the impact of antibiotic use on the infant microbiome development and resistome in low-and middle-income countries

Postdoctoral Researcher on the impact of antibiotic use on the infant microbiome development and resistome in low-and middle-income countries

Published Deadline Location
8 May 17 Jun Amsterdam

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The Amsterdam Institute for Global Health and Development (AIGHD) strives for equal opportunities for health and well-being for all.
For our research department we are looking for a Postdoctoral Researcher – Impact of antibiotic use on the infant microbiome development and resistome in low-and middle-income countries.

Job description

The position

The infant gut microbiome is important in protecting against infections with enteric pathogens, for the maturation of the human immune system, and in supporting nutrient metabolism and growth. Antibiotics massively disrupt the intestinal gut microbiome, impacting these functions of the gut microbiota and accelerating selection for antimicrobial resistance. Children in low- and middle-income countries have high burden of infectious diseases, high exposures in early-life to antibiotics, and high risk for infections with antimicrobial resistance. There is an urgent public health need to better characterize the impact of early life antibiotics on the developing microbiome in young infants in low- and middle-income settings to help prevent the development of antimicrobial resistance and preserve maturation and function of the infant gut.

The postdoctoral researcher will analyze metagenomic data of two large infant cohorts (> 1300 children, the ROTA-biotic study) in Zambia and Ghana, to characterize the association between antibiotic use and antimicrobial resistance (resistome), gut function, and risk of infection with enteric pathogens. The analysis will require the development and/or application of computational approaches to integrate quantitative readouts with antibiotic usage, vaccination status and demographic variables with the aim of better understanding the occurrence, stability, and evolution of antibiotic resistance genes. The sampling for the ROTA-biotic study has concluded, meaning that analysis can begin immediately.


The Amsterdam University Medical Center is a leading academic medical center that combines complex highquality patient care, innovative scientific research, and education. Global Health, Microbiology, and Infectious Diseases represent one of the major research topics at the Amsterdam University Medical Center and are integrated in a multidisciplinary fashion at the Amsterdam Institute for Infection and Immunity (AII&I).

This research will take place at the Department of Global Health/Amsterdam Institute for Global Health and Development (AIGHD) and the Department of Medical Microbiology, Evolutionary Biology of the Amsterdam UMC.

The mission of the Dept of Global Health/AIGHD is to address challenges in global health and development by conducting collaborative interdisciplinary and intersectoral research, generating insights and solutions, and educating the next generation of global health experts. A key departmental research priority is curbing the global development and spread of antimicrobial resistance.

Dr. Harris and Dr. Mende will work closely with the postdoctoral researcher.

Dr. Harris’ group works on understanding how interactions between the intestinal microbiome and host immunity can drive vulnerabilities to infectious diseases in global health. The laboratory uses a translational approach, generating needed clinical data from relevant low- and middle-income country (LMIC) patient populations to fuel mechanistic hypotheses underpinning microbiome, pathogen, and host interactions. Epidemiologic studies are combined with computational, cell culture and animal model approaches. A key research area is understanding how antibiotic administration drives risk of infection with antibiotic-resistant enteropathogens. A second key research area is understanding whether the microbiome is a determinant of vaccine immunogenicity and if it can be employed to improve vaccine performance in LMIC.

Dr. Mende’s group studies the evolution and biology of microbial communities (e.g., the human microbiome) as well as pathogens. The focus of the group is on the analysis of metagenomics and genomics data. The group uses statistical and machine learning methods to integrate different datasets and data types to gain a better understanding of the biological principles behind microbial evolution and host/environment-microbe interactions. The group is further involved in the development of state-of-the-art methods for metagenomics data analysis such as the mOTUs tool. In a world, where sequencing data has become ubiquitous, our vision is to combine local expertise with global data to understand the mechanisms and underlying evolutionary history of our relationship with our microbial companions and opponents.



Amsterdam Institute for Global Health and Development (AIGHD)


The ideal candidate is experienced in the field of microbiome data analysis (e.g., human microbiome data analysis, comparative genomics, biostatistics).

Essential qualifications include:

  • excellent teamwork and communication skills
  • demonstrable experience in (meta)genomic data analysis
  • experience in microbiome analysis
  • basic programming skills (e.g., Unix/Bash, R, basic Python)

The following additional qualifications would be advantageous:

  • background in clinical microbiology, microbial ecology, and/or studying microbiome-related disease associations
  • experience in experimental work in the laboratory

Conditions of employment

Fixed-term contract: 1,5 years, with opportunity for extension depending on funding availability.

We offer a Postdoctoral Researcher position within a creative and interactive team for 36-40 hours per week for 1,5 years, with opportunity for extension depending on funding availability.

We believe in the strength of an inclusive culture and think it is important that everyone can be themselves. 

  • A gross monthly salary is in accordance with CAO-VSNU, scale 10 with a range between EUR 3.195 and EUR 5.041 based on a fulltime contract (40 hours per week), depending on year of work experience and expertise.
  • An excellent job opportunity in a cutting-edge working environment in global health and development
  • 27 holidays per year based on a fulltime workweek of 40 hours.
  • An attractive collective pension plan.
  • A comprehensive collective health insurance scheme.
  • Working 50% hydrid: complete equipped ergonomic home workplace with a screen and chair.
  • Training and development opportunities. 
  • The possibility to work a few weeks on remote abroad.
  • Reimbursenent living and work permit (VISA) costs reimbursement


The Amsterdam Institute for Global Health & Development (AIGHD) is a collaborative institute of various faculties and schools of the Universiteit of Amsterdam and Vrije Universiteit Amsterdam with a mission to address challenges in global health and development trough research and education. AIGHD conducts collaborative, interdisciplinary research on major health themes of global importance in relation to human development and aims to educate and inspire the next generation of global health leaders at undergraduate, post-graduate, and professional. AIGHD aspires to accelerate progress on global health objectives by sharing knowledge and insights with global agencies, governments, NGOs, and the scientific community.

More information on AIGHD and our projects can be found on


  • Postdoc; Research, development, innovation
  • Health; Natural sciences
  • 36—40 hours per week
  • €3195—€5041 per month
  • Doctorate
  • AT AI 20230508


Amsterdam Institute for Global Health and Development (AIGHD)

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Meibergdreef 9, 1105 AZ, Amsterdam

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