Computational protocol: Metabolic response of porcine colon explants to in vitro infection by Brachyspira hyodysenteriae: a leap into disease pathophysiology

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Protocol publication

[…] Histopathology and gene expression data analyses were carried out using SPSS version 24 (SPSS Inc., Chicago, USA) and R Studio version 0.99.893 (RStudio Team 2015), respectively. Necrosis scores were compared using Kruskall–Wallis test adjusted by the Bonferroni correction for multiple tests followed by Dunn’s post-hoc test. This data is presented as median ± interquartile range. Explant mRNA levels were compared using the MCMC.qpcr (version 1.2.2) R package (Matz et al. ). This method applies generalized linear mixed model with Poisson-lognormal errors and a Bayesian Marco Chain Monte Carlo sampling scheme to infer fold changes in mRNA levels in response to fixed factors and random differences attributable to technical replicates. Gene expression data were graphed as mean fold-change (±standard error of the mean) using PBS samples as a reference group.Metabolomics data were log-transformed, scaled by each variable standard deviation, and analyzed by multivariate PCA, orthogonal PLS-DA, and univariate ANOVA with pairwise comparisons and post-hoc correction for multiple hypothesis testing using Fisher’s least significant difference method embedded in the MetaboAnalyst 3.0 suite (Xia et al. ). The latter was also used for integrated enrichment and pathway topography analysis, which employed the Homo sapiens library as a reference since a Sus scrofa library is not available. […]

Pipeline specifications

Software tools MCMC.qpcr, MetaboAnalyst
Application qPCR
Organisms Brachyspira hyodysenteriae, Sus scrofa
Diseases Dysentery