Fig. 4. Faecal microbiome profiles differ most in frankfurter-fed mice with reduced micribial diversity and a profound shift in abundance of taxa between feeding groups.

Faecal samples were collected at 56 days from each mouse cage for metagenomic sequencing providing cage replicates (n = 3) for each treatment. a shows scores plots of unsupervised PCA based on the first three principle components (PCs). Species level microbiome data explained 73.4% of the total variation (42.9, 15.5, and 15.0% for PC1, PC2, and PC3, respectively). b the Shannon diversity index as calculated by Qiime 2 indicates a reduction in microbial diversity in the frankfurter-fed animals. Individual values are shown along with means (dotted lines), and the error bars shown represent s.e.m. c Relative abundance of microbial taxa is shown at the level of the phylum, the family, and the species. The taxa differed most profoundly in the frankfurter-fed animals. Bacterial species with an abundance of <1% were aggregated and referred to as ‘All others’ (white bars in figure). At the species level the dominance of Dubiosiella Newyorkenesis in the frankfurter group was a particularly striking observation. Control samples are shown in red, minced pork in dark blue, nitrite-free sausage in light blue, and frankfurter (nitrite-containing) in green. uncult. uncultured bacteria, ambig. ambiguous taxa.