Canine faecal metagenomes with Providencia alcalifaciens

Acute haemorrhagic diarrhoea syndrome (AHDS) in dogs is a condition of unknown aetiology. Providencia alcalifaciens is however suspected to play a role in some cases of disease as it occurred in high prevalence in an outbreak in Norway in 2019. The role of this bacterium as a constituent of the canine gut microbiota is unknown, hence this study set out to investigate its occurrence in healthy dogs through metagenomics. This project contains two types of samples. Sample type 1 consists of two samples that were culture-negative for P. alcalifaciens. These two samples were spiked with different concentrations of P. alcalifaciens before qPCR and shotgun sequencing was performed. The limit of detection of Providencia alcalifaciens was used to generate a metagenomic threshold for the analysis of other samples in this study. Sample type 2 consists of 13 samples with a known cultivation status for P. alcalifaciens. These samples were used to test the metagenomic threshold for Providencia alcalifaciens that was set with the spiked samples.