Table 4 Differential abundance analysis investigating the effect of breed on the abundance bacterial and archaeal taxa in solid, liquid and epithelial ruminal fractions.

From: Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

 

Rank

Classification

Cheviot

Mean ± Sd

Connemara

Mean ± Sd

Lanark

Mean ± Sd

Perth

Mean ± Sd

P.adj

Solid fraction

 ASV55

Genus

Sharpea

1.37 ± 0.35b

1.90 ± 0.71ab

1.55 ± 0.84ab

2.28 ± 0.51a

0.009

 ASV55

ASV

Sharpea azabuensis

1.34 ± 0.34b

1.93 ± 0.73ab

1.58 ± 0.87ab

2.24 ± 0.51a

0.023

 ASV37

ASV

F_Lachnospiraceae

2.22 ± 0.46a

2.40 ± 0.49ab

1.92 ± 0.50b

2.60 ± 0.53a

0.024

Epithelial fraction

 ASV247

Family

Family XIII

2.84 ± 0.22b

3.03 ± 0.17ab

3.33 ± 0.28a

2.95 ± 0.18b

 < 0.001

 ASV379

ASV

F_Family XIII

1.15 ± 0.39ab

1.44 ± 0.19ab

2.02 ± 0.47a

1.05 ± 0.43b

0.005

  1. Analysis was conducted across all taxonomic ranks for bacterial populations (Phylum, Class, Order, Family, Genus and ASV), and lower taxonomic ranks for archaeal populations (Genus and ASV) using the LRT and Wald’s test from DESeq2. Table reports significant findings along with the log10 of normalised counts (Mean ± Sd), BH adjusted P values, pairwise comparisons (superscripts), taxonomic rank and classification. Solid (Cheviot n = 8, Connemara n = 5, Lanark n = 9, Perth n = 7), liquid (Cheviot n = 9, Connemara n = 5, Lanark n = 9, Perth n = 5), epithelial (Cheviot n = 9, Connemara n = 3, Lanark n = 6, Perth n = 8).