Table 5 Differential abundance analysis investigating the pairwise differences in bacterial and archaeal abundances between each of the breeds (i.e. Cheviot, Connemara, Lanark and Perth) in solid, liquid and epithelial ruminal fractions.

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

	Kingdom	Classification	Rank	Log2FC	P.adj	Comparison	Higher In
Solid
ASV27	Bacteria	Coriobacteriales	Order	1.17	0.041	Perth v Lanark	Lanark
ASV17	Bacteria	p-2534-18B5_gut_group (Bacteroidetes)	Family	5.88	0.007	Perth v Cheviot	Perth
ASV17	Bacteria	p-2534-18B5_gut_group (Bacteroidetes)	Family	6.80	0.007	Lanark v Cheviot	Lanark
ASV317	Bacteria	Saccharimonadaceae	Family	5.48	0.007	Lanark v Cheviot	Lanark
ASV317	Bacteria	Saccharimonadaceae	Family	6.89	0.023	Conn. v Cheviot	Connemara
ASV17	Bacteria	F_p-2534-18B5_gut_group (Bacteroidetes)	Genus	5.78	0.012	Perth v Cheviot	Perth
ASV17	Bacteria	F_p-2534-18B5_gut_group (Bacteroidetes)	Genus	6.82	0.014	Lanark v Cheviot	Lanark
ASV55	Bacteria	Sharpea	Genus	4.37	0.000	Perth v Cheviot	Perth
ASV317	Bacteria	Candidatus_Saccharimonas	Genus	5.66	0.014	Lanark v Cheviot	Lanark
ASV37	Bacteria	F_Lachnospiraceae	ASV	3.22	0.010	Lanark v Cheviot	Cheviot
ASV48	Bacteria	G_Prevotella 9	ASV	9.11	0.010	Lanark v Cheviot	Lanark
ASV48	Bacteria	G_Prevotella 9	ASV	7.88	0.009	Perth v Lanark	Lanark
ASV37	Bacteria	F_Lachnospiraceae	ASV	3.38	0.000	Perth v Lanark	Perth
ASV55	Bacteria	Sharpea azabuensis	ASV	4.58	0.000	Perth v Cheviot	Perth
ASV329	Bacteria	G_Pyramidobacter	ASV	5.52	0.018	Lanark v Cheviot	Lanark
ASV337	Archaea	G_Candidatus Methanomethylophilus	ASV	3.21	0.023	Lanark v Cheviot	Lanark
ASV337	Archaea	G_Candidatus Methanomethylophilus	ASV	3.12	0.006	Perth v Cheviot	Perth
Liquid
ASV2	Bacteria	Proteobacteria	Phylum	2.62	0.017	Perth v Conn	Perth
ASV223	Bacteria	Alphaproteobacteria	Class	7.11	0.002	Perth v Cheviot	Cheviot
ASV223	Bacteria	Alphaproteobacteria	Class	7.52	0.012	Conn. v Cheviot	Cheviot
ASV223	Bacteria	Rhodospirillales	Order	6.93	0.005	Perth v Cheviot	Cheviot
ASV223	Bacteria	Rhodospirillales	Order	7.29	0.024	Conn. v Cheviot	Cheviot
ASV219	Bacteria	Betaproteobacteriales	Order	3.03	0.045	Conn. v Cheviot	Cheviot
ASV223	Bacteria	O_Rhodospirillales	Family	7.11	0.021	Conn. v Cheviot	Cheviot
ASV223	Bacteria	O_Rhodospirillales	Family	6.81	0.003	Perth v Cheviot	Cheviot
ASV17	Bacteria	p-2534-18B5_gut_group (Bacteroidetes)	Family	4.75	0.047	Perth v Cheviot	Perth
ASV17	Bacteria	p-2534-18B5_gut_group (Bacteroidetes)	Family	5.87	0.019	Lanark v Cheviot	Lanark
ASV23	Bacteria	Muribaculaceae	Family	2.23	0.015	Perth v Cheviot	Cheviot
ASV461	Bacteria	O_Clostridiales vadinBB60_group	Family	5.82	0.049	Conn. v Cheviot	Cheviot
ASV461	Bacteria	O_Clostridiales vadinBB60_group	Family	6.09	0.004	Lanark v Conn	Lanark
ASV55	Bacteria	Sharpea	Genus	5.05	0.003	Perth v Cheviot	Perth
ASV223	Bacteria	O_Rhodospirillales	Genus	7.03	0.005	Perth v Cheviot	Cheviot
ASV461	Bacteria	O_Clostridiales vadinBB60_group	Genus	5.86	0.013	Lanark v Conn	Lanark
ASV20	Bacteria	F_Lachnospiraceae NK3A20 group	ASV	3.06	0.049	Lanark v Conn	Lanark
ASV23	Bacteria	F_Muribaculaceae	ASV	5.94	0.002	Perth v Cheviot	Cheviot
ASV43	Bacteria	F_Muribaculaceae	ASV	2.51	0.023	Perth v Cheviot	Cheviot
ASV44	Bacteria	G_Acetitomaculum	ASV	10.26	0.034	Conn. v Cheviot	Cheviot
ASV55	Bacteria	Sharpea azabuensis	ASV	4.81	0.006	Perth v Cheviot	Perth
Epithelial
ASV38	Bacteria	Atopobiaceae	Family	1.96	0.014	Perth v Lanark	Lanark
ASV162	Bacteria	Synergistaceae	Family	2.19	0.018	Lanark v Cheviot	Lanark
ASV247	Bacteria	Family XIII	Family	1.41	0.000	Lanark v Cheviot	Lanark
ASV247	Bacteria	Family XIII	Family	1.13	0.008	Perth v Lanark	Lanark
ASV55	Bacteria	Sharpea	Genus	3.13	0.028	Perth v Cheviot	Perth
ASV69	Bacteria	F_Ruminococcaceae UCG-014	Genus	2.77	0.049	Lanark v Cheviot	Cheviot
ASV361	Bacteria	F_Family_XIII AD3011_group	Genus	2.28	0.006	Lanark v Cheviot	Lanark
ASV406	Bacteria	F_Family XIII UCG-001	Genus	3.10	0.049	Lanark v Cheviot	Cheviot
ASV24	Bacteria	G_Succiniclasticum	ASV	24.14	0.000	Conn. v Cheviot	Cheviot
ASV24	Bacteria	G_Succiniclasticum	ASV	23.67	0.000	Lanark v Conn	Lanark
ASV24	Bacteria	G_Succiniclasticum	ASV	25.98	0.000	Perth v Conn	Perth
ASV33	Bacteria	G_Ruminococcus 1	ASV	7.80	0.005	Conn. v Cheviot	Connemara
ASV33	Bacteria	G_Ruminococcus 1	ASV	4.81	0.023	Perth v Cheviot	Perth
ASV37	Bacteria	F_Lachnospiraceae	ASV	2.72	0.046	Perth v Lanark	Perth
ASV74	Bacteria	G_Syntrophococcus	ASV	5.42	0.049	Lanark v Conn	Lanark
ASV118	Bacteria	G_Ruminococcus 1	ASV	5.52	0.046	Perth v Lanark	Perth
ASV123	Bacteria	G_Prevotella 1	ASV	7.85	0.006	Lanark v Conn	Connemara
ASV379	Bacteria	F_Family_XIII	ASV	2.88	0.019	Perth v Lanark	Lanark
ASV633	Bacteria	F_Ruminococcaceae UCG-010	ASV	4.00	0.046	Perth v Lanark	Perth

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 Wald’s pairwise test from DESeq2. Table reports the log10 of normalised counts (Mean ± Sd), BH adjusted P values, Log2 fold change, taxonomic rank and classification, breeds compared and the breed the abundance was increased in for significant findings. 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).

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Table 5 Differential abundance analysis investigating the pairwise differences in bacterial and archaeal abundances between each of the breeds (i.e. Cheviot, Connemara, Lanark and Perth) in solid, liquid and epithelial ruminal fractions.

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