Extended Data Fig. 2: Characterizing the age- and location-specific composition of the intestinal microbiome of the healthy pig.

(a) Definition of a core intestinal microbiome of the pig. A total of 58 OTUs that were annotated to 21 taxa were identified in >95% of day 120 and 240 faeces and caecum content samples of both F6 and F7 generations, hence defined as core bacterial taxa. (b) The compositions of the porcine and human intestinal microbiota are closer to each other than either is to that of the mouse. Boxplots are as is Fig. 1c. The number of samples available for analysis were 1281 pigs, 106 humans and 6 mice. (c) Abundances (F6-F7 averages when available) of the 43 families represented in Fig. 1b in the seven sample types relative to the sample type in which they are the most abundant (red – blue scale). The families are ordered according to the sample type in which they are the most abundant. The colour-code for phyla is as in Fig. 1b. Columns are added for comparison with mouse and human. Mouse data are from Fig. 1 in Suzuki & Nachman¹¹⁶, and human data from Fig. 6 in Vuik et al¹¹⁷. P_I: proximal ileum, D_IL: distal ileum, C: caecum, CO: colon, RE: rectum, F: faeces. The families differing the most with regards to location-specific distribution between species include Helicobacteriaceae, Veillonellaceae, Lactobacillaceae and Streptocaccaceae.