Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome

Abstract

Tonsils, lympho-epithelial tissues located at the junction of the oropharynx and nasopharynx, play a key role in surveillance, colonization, and persistence of inhaled and ingested pathogens. In pigs, the tonsils are a reservoir for numerous bacteria and viruses, including host-specific pathogens and potential zoonotic pathogens as well as commensal organisms. However, there are no in depth studies of the development of the tonsillar microbiome in pigs, or any mammal, over time. The goal of this study was to follow the development of the tonsil microbiome in healthy pigs from birth to market weight. Samples were collected using tonsil brushes from 16 piglets (4 each from 4 sows) at newborn, 1, 2, 3, and 4 weeks of age, and from 8 of those piglets at 6, 8, 10, 12, 16, and 19 weeks of age. Bacterial DNA was isolated from each sample and 16S rDNA genes were amplified and sequenced. Sequence analysis showed that members of the Streptococcaceae, Pasteurellaceae, and Moraxellaceae were present at all time points and represent the three most abundant families identified. Other community members appeared transiently or increased or decreased significantly with disruption events or stress. We observed four significant shifts in the tonsil community that coincided with well-defined disruption events: weaning plus addition of Carbadox plus movement to the nursery at week 3, removal of Carbadox and addition of Tylan at week 5, removal of Tylan and habitat change at week 9, and habitat change at week 16. Weaning triggered a bloom of Streptococcaeae and decrease of Moraxellaceae. The shift from Carbadox to Tylan led to reduction in Proteobacteria and Streptococcaceae but an increase in other Firmicutes, accompanied by a dramatic increase in community richness. Cessation of Tylan coincided with a return to a less rich community, and a bloom in Clostridiales. The final shift in habitat was accompanied by a decrease in Clostridiales and increase in Proteobacteria. The tonsillar microbiome of older pigs resembled the previously described mature core tonsillar microbiome. This study demonstrates a temporal succession in the development of the pig tonsillar microbiome, and significant community shifts that correlate with disruption events.

A mammalian commensal of the oropharyngeal cavity produces antibiotic and antiviral valinomycin in vivo

“…For example, on day 20 during the suckling period, the R. nasisuis inoculated litters housed with sows A and B showed differences in the relative abundance of Moraxella plurianimalium and Veillonella spp. In agreement with a previous study (Pena Cortes et al, 2018) changes in microbiota composition were observed during the transition from suckling to weaning. For example, comparing day 20 (suckling period) with day 35 (8 days after weaning) shows decreased relative abundance of Fusobacterium gastrosuis and an increase in Streptococcus porcorum (Fig.…”

“…As Rothia species are frequently identi ed in porcine oral microbiota (Murase et al;Pena Cortes et al, 2018) we investigated whether valinomycin-producing Rothia strains were present in tonsil swabs of piglets using PCR. We designed one PCR primer set (FLANK) to amplify a genomic DNA region spanning the vlm cluster and upstream region, and a second set of primers (INT) to generate an amplicon within the vlm cluster (Fig.…”

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis

“…It is difficult to compare the core genera across studies. Besides age, commonly studies are done in pigs around weaning [ 45 , 46 ], housing and diet may also impact core genera. Moreover, it has been recently determined that when defining the core microbiome in pigs, differences in study protocols have a significant impact and standardization of experimental techniques appear to be important [ 47 ].…”

The porcine respiratory microbiome: recent insights and future challenges

“…Major microbial shifts occur in response to the transition to solid-feed in the gut microbiome of healthy suckling piglets [22]. This holds true also for the URT microbiome, as weaning has been associated with an increase in the relative abundance of Streptococcaceae and a decrease of Moraxellaceae abundance; this might be result of changes in feed, but also in housing conditions and antimicrobial exposure [18,23]. Feeding strategies and the flooring system have been proposed to impact the composition of the URT respiratory microbiome [24,25].…”