Fig. 4

a Pairwise Bray-Curtis dissimilarity between the cloacal microbiota of layers from each poultry house. Greater values indicate higher dissimilarity. ‘Total’ contains all possible pairwise comparisons, for reference. Community composition in the indoor poultry houses was more variable than in outdoor poultry houses (Wilcoxon-Rank-Sum test, p = 0.03) b Bray-Curtis dissimilarities between the cloacal microbiota of layers within a poultry house (Within Poultry House) compared to dissimilarities between cloacal microbiota of layers within a housing type (indoor vs outdoor), excluding within poultry house comparisons (Within Housing Types). The cloacal microbial communities of layers within a poultry house (0.46 ± 0.18, mean ± SD) were more similar to each other than to those within a housing type (mean 0.55 ± 0.15, Wilcoxon-Rank-Sum test, p < 0.001)