BackgroundPorcine tonsils are the colonization site for many pathogenic as well as commensal microorganisms and are the primary lymphoid tissue encountered by organisms entering through the mouth or nares. The goal of this study was to provide an in-depth characterization of the composition and structure of the tonsillar microbial communities and to define the core microbiome in the tonsils of healthy pigs, using high throughput bar-coded 454-FLX pyrosequencing.ResultsWhole tonsils were collected at necropsy from 12 16-week-old finisher pigs from two healthy herds. Tonsil brushes were also used to collect samples from four of these animals. Bacterial DNA was isolated from each sample, amplified by PCR with universal primers specific for the bacterial 16S rRNA genes, and the PCR products sequenced using pyrosequencing. An average of 13,000 sequences were generated from each sample. Microbial community members were identified by sequence comparison to known bacterial 16S rRNA gene sequences.The microbiomes of these healthy herds showed very strong similarities in the major components as well as distinct differences in minor components. Pasteurellaceae dominated the tonsillar microbiome in all animals, comprising ~60% of the total, although the relative proportions of the genera Actinobacillus, Haemophilus, and Pasteurella varied between the herds. Also found in all animals were the genera Alkanindiges, Peptostreptococcus, Veillonella, Streptococcus and Fusobacterium, as well as Enterobacteriaceae and Neisseriaceae. Treponema and Chlamydia were unique to Herd 1, while Arcanobacterium was unique to Herd 2.Tonsil brushes yielded similar results to tissue specimens, although Enterobacteriaceae and obligate anaerobes were more frequently found in tissue than in brush samples, and Chlamydia, an obligately intracellular organism, was not found in brush specimens.ConclusionsWe have extended and supported our previous studies with 16S clone libraries, using 16S rRNA gene pyrosequencing to describe the microbial communities in tonsils of healthy pigs. We have defined a core microbiome, dominated by Pasteurellaceae, in tonsil specimens, and have also demonstrated the presence of unique minor components of the tonsillar microbiome present in each herd. We have validated the use of non-invasive tonsil brushes, in comparison to tonsil tissue, which will facilitate future studies.

The intestinal microbiota has received a lot of attention in recent times due to its essential role in the immune system development and function. Recent work in humans has demonstrated that the first year of life is the most critical time period for microbiome development with perturbations during this time being proven to have long term health consequences. In this review, we describe the literature surrounding early life events in humans and mice that contribute to intestinal microbiota development and function, and compare this to piglets predominantly during their lactation period, which focuses on the impact lactation management practices may have on the intestinal microbiota. Although extensive research has been conducted in this area in humans and mice, little research exists in pigs during perceivably the most critical time period of development, which is the lactation period. The research reviewed outlines the importance of appropriate intestinal microbiota development. However, further research is needed in order to understand the full extent routine farm practices have on a piglet’s intestinal microbiota.

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. 2001. Small intestinal morphology and bacterial populations in ileal digesta and feces of newly weaned pigs receiving a high dietary level of zinc oxide. Can. J. Anim. Sci. 81: 511-516. A study was carried out to determine the effect of dietary supplementation of 3000 mg kg -1 zinc oxide (ZnO) on the small intestinal morphology and populations of enterobacteriaceae, lactobacilli and clostridia in ileal digesta and feces of weaned pigs. At 17 d of age, 36 pigs from nine litters were fitted with simple T-cannulae at the distal ileum and after a 2-h post-surgery recovery returned to their sows. At 21 d of age, the pigs were weaned and housed in individual metabolism crates. Pigs were allocated to receive a standard starter diet supplemented with or without 3000 mg kg -1 of ZnO. Ileal digesta and fecal samples were collected immediately before weaning and then on days 2, 4, 7, 9, and 11 after weaning and were used to quantify enterobacteriaceae, lactobacilli and clostridial populations by colony enumeration on selective media. Pigs were euthanized following the final sampling, and 2cm sections of tissue were collected from sites 25, 50 and 75% along the length of the small intestine for determination of mucosal thickness (MT), crypt depth (CD), villous height (VH) and villous width (VW). Zinc oxide supplementation altered the mucosal morphology of the small intestine. Mucosal thickness (P < 0.08) and VH (P < 0.05) were increased at sites 25 and 50% along the length of the small intestine by ZnO supplementation. Overall VW also increased (P < 0.01) with ZnO supplementation. Crypt depth decreased (P < 0.05) at 75% along the length of the small intestine with ZnO supplementation. The ratio of VH to CD was higher (P < 0.05) for ZnO-supplemented than for control-fed pigs at sites 25, 50 and 75% along the length of the small intestine. There was no effect (P > 0.05) of supplementary ZnO on bacterial populations in ileal digesta or feces. The present study indicates that supplementing ZnO in starter diets changes the epithelial morphology of the small intestine, which may affect nutrient digestion and absorption in newly weaned pigs.