To characterize and compare microbiome development patterns between robust (healthy) and diarrhoea piglets from birth to slaughter using rectal swabs

Background and research interests

This research project is a part of a larger multidisciplinary consortium named PIG-PARADIGM that has the strategic aim to reduce the need for antibiotic use and risk of Anti-Microbial Resistance (AMR) in pork production by deciphering the key-determinants of intestinal health in pigs and translating this knowledge into strategies to enhance pig health and robustness. The primary aim of this project is to characterize gut microbiome development patterns in robust, resilient and antibiotic treated diarrhoea piglets using rectal swab time-series sampling. All rectal swab and fecal samples (Total=378 samples) will be subjected to 16S rRNA gene metataxonomic profiling. The resultant microbiota composition will be analysed to reconstruct time-resolved microbiota-development patterns (early life microbiome) during the first 10 weeks of life of these piglets, where we intend to differentiate between robustness classes and investigate to what extent, and at what rate the microbiota composition in “Resilient” and “Antibiotic Treated” animals is able to recover in comparison to the animals belonging to the “Robust” class. These analyses will take all of the recorded metadata for these groups of pigs into account, either as potential confounding factors, or as interacting parameters of the classification.

Objectives

The aim of the study is to compare the microbiota development pattern between the three robustness classes of piglets (1: Robust, 2: Resilient and 3: Antibiotic Treated) from birth to 6 weeks post-weaning.

Methodology / what students can learn

Students will work on Rstudio platform on HMI lab’s server for microbiome data analysis. Students will be able to learn coding in R language to generate different types of (statistical) analysis graphs like alpha/beta diversity, box/bar plots, heatmap/correlation plots (see above figures) and will also be able to learn different software like GraphPad Prism, Canoco, etc. Different aspects of clinical metadata will be correlated with microbiota composition in 3 distinct classes of piglets.

Requirements

We are looking for MSc students with background in Bioinformatics, Biotechnology or Microbiology interested in learning microbiome data analysis and some basic bioinformatic techniques. The project will start preferably from March 2024 onwards and will have a duration of 6 months.

Contact information

Mohak Gujare, Host-Microbe Interactomics, Animal Sciences – mohak.gujare@wur.nl

Prof. Michiel Kleerebezem, Host-Microbe Interactomics, Animal Sciences – michiel.kleerebezem@wur.nl