Some Streptococcus suis strains are associated with post-weaning disease in piglets and are emerging zoonotic pathogens of humans. The piglet microbiota may positively or negatively influence colonisation of S. suis and invasive disease risk. To identify bacterial taxa correlated with S. suis abundance, samples from the tonsil and small intestine of piglets were collected around weaning for compositional microbiota profiling.