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Fig. 1 | Microbiome

Fig. 1

From: Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

Fig. 1

Microbial diversity and community structure. a Alpha diversity (Richness and Shannon entropy) and environmental filtering (NRI/NTI) measures respectively. Lines (a) connect two categories where the differences were significant (ANOVA) with *P < 0.05, **P < 0.01, or ***p < 0.001. b Beta diversity using Bray-Curtis distance measure along with top-25 genera observed in all samples grouped by categories. The tables represent taxa that were found to be significant based on subset analysis (Supplementary S1), i.e. those genera selected in the subsets that explain roughly the same distance between samples as all the genera. Additionally, if the taxa were found to be differentially expressed based on other analyses, such as DESeq2 (Supplementary S11), MINT (Supplementary S2) and differential heat tree (Fig. 2), the categories they up- and downregulated are represented with corresponding up and down arrows. For example, in HW30 vs O30 comparison, ‘(S), O30 (D, H)’ for Phascolarctobacterium should be read as selected in subset analysis: (S) and upregulated in O30 according to both DESeq2 and Differential Tree: O30 (D, H)

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