Scouring weaner pigs have a lower abundance of butyrate-producing bacteria

Scouring caused by pathogenic bacteria leads to poor weight gain, dehydration and (or) sudden death in newly-weaned pigs (Fairbrother et al. 2005). Commensal bacteria, including butyrate producers, are thought to reduce scouring by preventing colonisation of enterotoxigenic E. coli, whilst improving growth performance and intestinal function through increased villous height (Wen et al. 2012). This study hypothesised that scouring weaner pigs would have a lower abundance of butyrate-producing bacteria in faeces than non-scouring pigs.

Individual faecal samples classified as either non-scouring (n = 47) or scouring (n = 26) were submitted from pigs 2 to 3 weeks after weaning from six Australian piggeries; four medicated and two non-medicated. Faecal DNA was extracted using the MagMAX Pathogen RNA/DNA Kit and bacteria were sequenced using universal 16S rRNA primers V4/5 (515F and 806R). Sequences were analysed using the QIIME pipeline with appropriate quality controls and bacterial groups were expressed as abundance relative to total bacteria. The impact of scouring and farm factors on the relative abundance of bacterial taxa was assessed using canonical correspondence analysis (CCA) approaches (R, version 3.1.2). Microbial groups in the upper right quadrant are more abundant in scouring weaners, whereas those in the lower left are more abundant in non-scouring weaner pigs (Fig. 1).

Fig. 1.  Canonical correspondence analysis showing the influence of farm effects (A) and scouring (B) on pig faecal microbiota and individual taxa distributions (C), where plots represent: ● Farm 1, Farm 2, Farm 3, Farm 4, Farm 5, ○ Farm 6, ▴ scouring, ▵ non-scouring and microbial groups.

Faecal microbial communities from scouring and non-scouring pigs clustered separately (Fig. 1B), despite a farm effect (Fig. 1A). The faecal samples from scouring pigs were dominated by Clostridium (#21), Lactobacillales (#14), Enterobacteriaceae (#53) and E. coli (#54), whereas a higher abundance of butyrate-producing bacteria such as Pseudobutyrivibrio (#27), Roseburia (#28) and Veillonellaceae (#39) were recovered from the non-scouring pigs (Fig. 1C). Faecal samples from Farm 1 contained more Ruminococcaceae, Farm 5 had higher numbers of Lactobacillales and Actinobacteria, and Farm 6 had a greater abundance of Porphyromonadaceae and Erysipelotrichaceae (data not shown). The pigs at the remaining farms shared a similar faecal bacterial composition.

This study demonstrated an increased abundance of butyrate-producing bacteria and reduced E. coli and Enterobacteriaceae in non-scouring pigs, suggesting that butyrate plays an important role in gastrointestinal tract health, as described previously (Wen et al. 2012). The high abundance of Lactobacillales in scouring pigs could reflect increased antagonistic activity of Lactobacilli against Enterobacteriaceae (Looft et al. 2014). Further studies would help to separate the impact of scouring from farm factors, including diet, antimicrobial use, hygiene and genetics.