Fig. 2
Analysis of microbiota β-diversity by type of sample (consistency), day post weaning and treatment. (A-C) Samples ordination using Bray-Curtis distances at species (A-B) and functional level (C) in a NMDS; coloured according to faecal consistency and dpw factor (Consistency-dpw). (A) Arrows display the top 15 species with the highest mean abundance returned by “envfit” model, influencing the ordination of samples (Arrows showing BH p.adjusted significant species; Arrows length shows the strength of each species influencing the ordination of samples). Species fitted onto ordination are indicated as numbers, ordered according to its NMDS coordinates. 1: Oscillibacter sp. PEA192, 2: Clostridiales bacterium CCNA10, 3: Escherichia coli, 4: Megasphaera elsdenii, 5: Limosilactobacillus reuteri, 6: Anaerobutyricum hallii, 7: Faecalibacterium prausnitzii, 8: Roseburia hominis, 9: Prevotella ruminicola, 10: Eubacterium rectale, 11: Prevotella dentalis, 12: Hoylesella enoeca, 13: Prevotella oris, 14: Blautia pseudococcoides, 15: Lachnospiraceae bacterium GAM79. (B) Ward Clustering of Bray Curtis distances ploted onto a NMDS. The dendrogram was split into four branches and coloured according to the samples’ arrangement within the NMDS space. (C) Ordination of samples using Bray-Curtis distances at functional level of Super-focus level 3 category. (D) Ordination of 7dpw diarrhoea samples, using Bray-Curtis distances, onto a NMDS, coloured by treatment both at species (top) and functional (bottom) levels. (E) Ordination of 14dpw faecal samples, using Bray-Curtis distances, onto a NMDS, coloured by treatment both at species (top) and functional (bottom) levels. Ellipses represent covariance for each factor level: faecal consistency and dpw in figures A-C; and treatment in figures D-E. Treatments to which each sample belonged to are indicated for diarrhoea samples in figures A-C as CT(Ct), AB (Ab) and ZN (Zn). Farm factor is indicated by the shape of the points in figures B-E, coloured according to faecal consistency and dpw (B-C) or treatment (D-E)