Assembly and Resilience of Pig Intestinal Microbiomes

The pig industry is a main user of antimicrobials to treat and prevent microbial infections. Current pig production procedures, in particular the commonly applied early weaning age (3-4 weeks of age), are challenging pig development and health. A commonly encountered consequence is the relatively high frequency of infectious post-weaning diarrhoea, which requires the use of antimicrobials. However, antimicrobial resistant bacterial infections are a global health and economical hazard, with the mis- and overuse of antimicrobial treatment as main driver.

Therefore, this project intends to improve our ecological understanding of the pig intestinal microbiome development during early life to define pig management scenarios that enhance pig robustness and resilience to minimize the use of antimicrobials. Early life intestinal microbiome colonization patterns are known to be highly dynamic and the underlying assembly rules remain largely unknown.

Here, we aim to identify the key microbes and their functions that govern proper early assembly towards a resilient and robust intestinal ecosystem.

Techniques:

DNA isolation, qPCR, 16S rRNA gene amplicon sequencing, shotgun metagenomic sequencing, (meta)transcriptomics, metabolomics, anaerobic culturing, bacterial isolation

Potential BSc and MSc thesis project topics include:

• Anaerobic cultering of synthetic communities
• Isolation of new bacterial species from the pig's gut