The Palatine Tonsil Bacterial Microbiota in Pigs: Diverse, Underexplored, Yet Functionally Relevant

The palatine tonsils play a pivotal role in porcine upper respiratory tract immunity by acting as an interface between the host and the external environment. As such, the tonsillar microbiota represents a critical yet insufficiently characterized microbial ecosystem. This review provides an overview of current knowledge on the porcine tonsillar microbiota, beginning with a description of sampling strategies and laboratory approaches, including metabarcoding, shotgun metagenomics, and culturomics. The development of the tonsillar microbiota over time and the main environmental, host-related, and management factors shaping its composition are examined. Particular emphasis is placed on the core bacterial communities commonly identified in the palatine tonsils, which are largely dominated by members of the Pasteurellaceae, Streptococcaceae, and Moraxellaceae families. The review further discusses how infectious and non-infectious diseases can disrupt tonsillar microbial homeostasis, as well as the effects of antimicrobial treatments, vaccination, and other prophylactic interventions on microbial structure and function. Finally, methodological biases inherent to current studies are highlighted, key knowledge gaps are identified, and future research directions are proposed to advance metagenomic investigations and better elucidate the role of the tonsillar microbiota in swine health and disease.