Browsing by Author "Jones, Sophia"

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    Investigation of the microbiomes of sow skin, milk and piglet hind gut : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Animal Science at Massey University, Manawatū, New Zealand
    (Massey University, 2024) Jones, Sophia
    There is a lack of information on the microbiome of sow skin, sow milk and piglet faeces from New Zealand production systems. Therefore, we have a current lack of data on the bacterial populations present and the potential pathways of transmission to colonise the gut of neonatal pigs. Knowledge of these aspects would allow the identification of common probiotics, pathogens and commensal bacteria in pigs and provide information to help identify the pathways of colonisation for bacteria within the gastrointestinal tract of neonatal pigs. Samples were collected from 21 sows (N = 17 milk samples and N = 20 udder skin swabs) and 63 piglets (N = 63 piglet faecal samples) within 72 hours of parturition, on a commercial farrow-to-finish indoor pig farm. The DNA extracted from these samples underwent metabarcoding analysis using the greengenes 16S database and Kraken2 pipeline. The number of reads varied by different samples, even from within the same pen. For example, the milk sample of sow 676 only had 25,000 reads whilst the piglets suckling from this sow had between 125,000 – 160,000 reads. Piglet samples were dominated by populations of Firmicutes and Bacteroidetes bacteria, whilst the sow udder skin and milk samples were dominated by populations of Firmicutes and Proteobacteria bacteria. Milk samples displayed a greater presence of lesser common phyla compared to sow skin or piglet faeces, but these phyla are present at relatively low levels of reads, such as Cyanonbacteria, Chloroflexi and Acidobacteria. There were no reads for Escherichia coli bacteria present in any samples taken for this study which is an unusual but incredibly positive finding. Clostridium, a similar pathogenic bacteria in neonates, was found abundant in piglet faecal samples so we cannot be sure if E. coli did not exist on-farm at all due to upkept disinfection protocols or if the piglets had not yet picked it up. Probiotic bacteria were identified across the piglet faecal samples, namely Pediococcus and Lactococcus, including species of the phyla which are known to increase production and performance, as well as providing a protective function against E. coli bacteria. As probiotic bacteria are typically given as feed additives pre-weaning due to benefits aiding in gut microbiota development, these piglets seem to already have a good basis of these bacteria. The research was successful in what was set out to be completed, despite any limitations that were discovered, and resulted in future recommendations to continue characterising important microbiomes in the New Zealand pork industry, as well as their interactions and pathways of transmission to neonatal piglets.