Sow Contact Is a Major Driver in the Development of the Nasal Microbiota of Piglets

Abstract

The nasal microbiota composition is associated with the health status of piglets. Sow-contact in early life is one of the factors influencing the microbial composition in piglets; however, its impact has never been assessed in the nasal microbiota of piglets reared in controlled environmental conditions. Nasal microbiota of weaning piglets in high-biosecurity facilities with different time of contact with their sows (no contact after farrowing, contact limited to few hours or normal contact until weaning at three weeks) was unveiled by 16S rRNA gene sequencing. Contact with sows demonstrated to be a major factor affecting the nasal microbial composition of the piglets. The nasal microbiota of piglets that had contact with sows until weaning, but were reared in high biosecurity facilities, was richer and more similar to the previously described healthy nasal microbiota from conventional farm piglets. On the other hand, the nasal communities inhabiting piglets with no or limited contact with sows was different and dominated by bacteria not commonly abundant in this body site. Furthermore, the length of sow-piglet contact was also an important variable. In addition, the piglets raised in BSL3 conditions showed an increased richness of low-abundant species in the nasal microbiota. Artificially rearing in high biosecurity facilities without the contact of sows as a source of nasal colonizers had dramatic impacts on the nasal microbiota of weaning piglets and may introduce significant bias into animal research under these conditions.

Keywords: artificial rearing; bacterial diversity; piglets’ nasal microbiota; raising environment; sows.

Figure 1

Alpha diversity of the nasal microbiota of 3–4-week-old piglets raised under BSL3 conditions with different degree of contact with their sows. Alpha diversity was measured at a depth of 32,392 by observed ASVs (A), Chao1 (B), Shannon–Weaver (C) and Simpson (D) indices for the different groups under study: piglets with no contact with the sow except for the birth canal (L3-NC, in red); piglets with limited contact of less than 12 h (L3-LC, in blue) and those that had full normal contact with their sows (L3-FC, in green). Group L3-LC included animals treated with ceftiofur (‘Ceftiofur’, in light blue) or non-treated (‘Control’, in dark blue). Significant p values from Kruskal–Wallis pairwise tests are depicted.

Figure 2

Beta diversity of the nasal microbiota of 3–4-week-old piglets raised under BSL3 conditions with different degree of contact with their sows. (A) Principal coordinate analysis representing beta diversity of the nasal microbiota of piglets raised in BSL3 conditions with no contact with sows except the birth canal (L3-NC, in red), limited contact of less than 12 h (L3-LC, in blue) and full normal contact (L3-FC, in green) was computed through weighted UniFrac analysis. The six most relevant genera explaining the differences among groups are plotted in the PCoA space. The length of each of the taxonomic vectors approximates the variance of each taxon throughout the samples. Group clustering distance to L3-NC (B) and to L3-FC (C) computed by PERMANOVA pairwise test with weighted UniFrac distance matrix (p = 0.001 in all cases).

Figure 3

Taxonomical composition at genus level of the nasal microbiota from piglets raised in BSL3 conditions with variable contact with sows. Only taxa with global relative abundance higher than 1% in at least one group is color-coded. All genera with less relative abundance than 1% have been grouped and are shown in grey. L3-NC, no contact with the sows except the birth canal; L3-LC, limited contact of less than 12 h; and L3-FC, full normal contact until weaning at 3 weeks of age. Genera belonging to most relatively abundant phyla have been colored in common color-scheme to simplify its visualization; green for Firmicutes, blue for Bacteroidetes, and red for Proteobacteria. The legend shows the genera ordered by global relative abundance from bottom to top.

Figure 4

Venn diagram of the shared and specific taxa from the nasal microbiota of piglets raised under BSL3 conditions with different degree of contact with their sows: no contact except the birth canal (L3-NC, in red); limited contact of less than 12 h (L3-LC, in blue) and full normal contact until weaning at 3 weeks of age (L3-FC, in green). Taxa was analyzed at family (F) and genus (G) levels. Only taxa present in more than 80% of samples in a group were included.

Figure 5

Principal component plot of the nasal microbiota of piglets raised in farms (FB-FR, in yellow) or under BSL3 conditions with different degree of contact with their sows (no contact except the birth canal (L3-NC, in red); limited contact of less than 12 h (L3-LC, in blue) and full normal contact until weaning at 3 weeks of age (L3-FC, in green)) computed through unweighted (A) and weighted (B) UniFrac analysis. The four most relevant genera explaining the differences among groups are plotted in the PCoA space. The length of each of the taxonomic vectors approximates the variance of each taxon throughout the samples. FB-FR samples have different shapes depending on the farm.

Figure 6

Venn diagrams of the number of taxa at genus (G) and family levels (F) found in the nasal microbiota of piglets raised in farms (FB-FR, in yellow) and under BSL3 conditions with different degree of contact with their sows. No-contact except for the birth canal (L3-NC) in red; limited contact of less than 12 h (L3-LC), in blue and full normal contact until weaning (L3-FC), in green. Only taxa present in more than 80% of samples per group were considered.