Development of a 16S rRNA metabarcoding method to study the porcine gut microbiota
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The weaning transition period in pigs is linked with several stress factors, increasing vulnerability to enteric disorders. This is partly attributed to microbial shifts which occur in response to weaning stressors, including dietary change. To study porcine gut microbiota composition, we have developed a 16S rRNA metabarcoding method. Sequencing is carried out using the Illumina MiSeq platform, before quality control and analysis using Mothur. The methodology has been validated by sequencing a mock community of 20 organisms, and negative controls to indicate possible contaminants. All mock community isolates were identified at genus level, and 75% of these organisms were quantified accurately. The negative controls showed a negligible number of reads post-analysis. Therefore, this method is currently being used to assess porcine microbiota composition in response to enterotoxigenic Escherichia coli (ETEC) challenge, the primary causative agent of post-weaning colibacillosis. Rectal faecal samples from 32 pigs (16 ETECchallenged and 16 non-challenged) were taken forward for sequencing. All pigs were sampled pre-challenge and four samples were taken post-challenge over a 14 day period. Ongoing analyses will reveal any effects of ETEC challenge on faecal microbiota composition, as well as temporal shifts of the microbiota post-weaning.
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Society of General Microbiology (SGM) Annual Conference, Birmingham, UK
Society for General Microbiology
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