Microbiome fortification for healthier pigs through metagenomics-driven microbial biomarker discovery

This project investigates microbe-microbe and host-microbe interactions within the microbial communities inhabiting porcine tonsils. The commensal bacteria associated with animals are important for host health due to shaping host immunity as well as preventing infectious disease. Infectious disease in pig farms decrease animal welfare and cause wide use of antimicrobials, leading to antimicrobial resistance. Thus, promoting a healthy microbiota in pigs is of importance.

Tonsils are of special interest when investigating interactions between bacteria and the host innate immune system. Tonsils are lympho-epithelial tissues important in immune detection of inhaled and ingested pathogens, and harbour a highly diverse microbiota. Thus, tonsils are a major niche for commensal and pathogenic bacteria. Tonsils provide entry for pathobiont Streptococcus suis bacteria, a significant problem for pig industry worldwide, and an important emerging zoonotic pathogen in Asia. There are large gaps in our understanding how S. suis and similar pathogens cause infectious disease of pigs. Studying these gaps allow us to answer questions of fundamental interest which may be translated into applied solutions.

This project utilizes high-throughput sequencing technology to characterise microbial communities. Shotgun and amplicon-based sequencing are applied to detect bacterial, fungal and viral organisms in environmental samples collected from pigs in commercial farms. We aim to detect genes of interest including virulence – and antibiotic resistance genes, biosynthetic gene clusters and other traits in metagenomes from healthy and diseased animals, as well as in farms with and without S. suis disease records. In a related project at HMI, bacteria from the same farms and animals will be cultured and whole-genome sequenced (Loes: link to project Isabela). Thus, bacteria of interest that stand out in the metagenomic analyses can be cultured using dedicated growth media and – conditions and eventually obtained in pure culture. Bacteria of interest will be characterised further using in-vitro assays, organoids and ultimately, in-vivo experiments.