Table 9 Differential abundance analysis investigating the pairwise differences in bacterial and archaeal abundances between each of the fractions (i.e. solid, liquid and epithelial) in the Cheviot, Lanark and Perth breeds.

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

	Kingdom	Classification	Rank	Log2FC	P.adj	Comparison	Higher in
Cheviot
ASV141	Bacteria	Epsilonbacteraeota	Phylum	5.42	0.000	Solid v epithelial	Epithelial
ASV3	Bacteria	Firmicutes	Phylum	0.63	0.023	Solid v epithelial	Solid
ASV14	Bacteria	Fibrobacter	Phylum	1.95	0.023	Solid v epithelial	Solid
ASV81	Bacteria	Spirochaetes	Phylum	1.97	0.050	Solid v epithelial	Solid
ASV141	Bacteria	Campylobacteria	Class	5.51	0.000	Solid v epithelial	Epithelial
ASV141	Bacteria	Campylobacterales	Order	5.26	0.000	Solid v epithelial	Epithelial
ASV449	Bacteria	Desulfobacterales	Order	3.48	0.002	Solid v epithelial	Epithelial
ASV219	Bacteria	Betaproteobacteriales	Order	2.53	0.005	Solid v epithelial	Epithelial
ASV219	Bacteria	Neisseriaceae	Family	3.31	0.002	Liquid v epithelial	Epithelial
ASV141	Bacteria	Campylobacteraceae	Family	5.15	0.000	Solid v epithelial	Epithelial
ASV449	Bacteria	Desulfobulbaceae	Family	3.74	0.001	Solid v epithelial	Epithelial
ASV219	Bacteria	Neisseriaceae	Family	3.51	0.000	Solid v epithelial	Epithelial
ASV3	Bacteria	Acidaminococcaceae	Family	0.98	0.042	Solid v epithelial	Solid
ASV198	Bacteria	O_Coriobacteriales	Family	1.59	0.001	Solid v epithelial	Solid
ASV81	Bacteria	Spirochaetaceae	Family	2.12	0.042	Solid v epithelial	Solid
ASV198	Bacteria	O_Coriobacteriales	Family	1.57	0.005	Solid v liquid	Solid
ASV142	Bacteria	F_Erysipelotrichaceae UCG-004	Genus	3.50	0.025	Liquid v epithelial	Liq
ASV141	Bacteria	Campylobacter	Genus	5.70	0.000	Solid v epithelial	Epithelial
ASV254	Bacteria	Butyrivibrio_2	Genus	4.16	0.001	Solid v epithelial	Epithelial
ASV263	Bacteria	F_Burkholderiaceae	Genus	4.02	0.001	Solid v epithelial	Epithelial
ASV128	Bacteria	F_Lachnospiraceae UCG-008	Genus	3.73	0.018	Solid v epithelial	Epithelial
ASV199	Bacteria	Mogibacterium	Genus	3.70	0.002	Solid v epithelial	Epithelial
ASV449	Bacteria	Desulfobulbus	Genus	3.63	0.002	Solid v epithelial	Epithelial
ASV347	Bacteria	Family XIII AD3011 group	Genus	2.56	0.032	Solid v epithelial	Epithelial
ASV141	Bacteria	G_Campylobacter	ASV	6.15	0.001	Solid v epithelial	Epithelial
ASV263	Bacteria	F_Burkholderiaceae	ASV	4.32	0.006	Solid v epithelial	Epithelial
Lanark
ASV141	Bacteria	Epsilonbacteraeota	Phylum	4.09	0.023	Liquid v epithelial	Epithelial
ASV141	Bacteria	Epsilonbacteraeota	Phylum	5.88	0.000	Solid v epithelial	Epithelial
ASV41	Bacteria	Fibrobacter	Phylum	1.34	0.035	Solid v epithelial	Solid
ASV141	Bacteria	Campylobacteria	Class	5.68	0.001	Solid v epithelial	Epithelial
ASV421	Bacteria	Desulfobacterales	Order	4.57	0.001	Liquid v epithelial	Epithelial
ASV141	Bacteria	Campylobacterales	Order	4.39	0.011	Liquid v epithelial	Epithelial
ASV1	Bacteria	Bacteroidales	Order	0.63	0.021	liquid v epithelial	Liquid
ASV141	Bacteria	Campylobacterales	Order	5.76	0.000	Solid v epithelial	Epithelial
ASV421	Bacteria	Desulfobacterales	Order	5.63	0.000	Solid v epithelial	Epithelial
ASV41	Bacteria	Fibrobacterales	Order	1.55	0.011	Solid v epithelial	Solid
ASV421	Bacteria	Desulfobulbaceae	Family	4.45	0.001	Liquid v epithelial	Epithelial
ASV141	Bacteria	Campylobacteraceae	Family	4.20	0.024	Liquid v epithelial	Epithelial
ASV141	Bacteria	Campylobacteraceae	Family	5.77	0.000	Solid v epithelial	Epithelial
ASV421	Bacteria	Desulfobulbaceae	Family	5.77	0.000	Solid v epithelial	Epithelial
ASV219	Bacteria	Neisseriaceae	Family	4.38	0.005	Solid v epithelial	Epithelial
ASV41	Bacteria	Fibrobacteraceae	Family	1.49	0.019	Solid v epithelial	Solid
ASV239	Bacteria	Butyrivibrio 2	Genus	5.41	0.031	Liquid v epithelial	Epithelial
ASV421	Bacteria	Desulfobulbus	Genus	4.95	0.002	Liquid v epithelial	Epithelial
ASV391	Bacteria	Fretibacterium	Genus	4.78	0.014	Liquid v epithelial	Epithelial
ASV141	Bacteria	Campylobacter	Genus	4.73	0.014	Liquid v epithelial	Epithelial
ASV391	Bacteria	Fretibacterium	Genus	7.48	0.000	Solid v epithelial	Epithelial
ASV239	Bacteria	Butyrivibrio 2	Genus	7.07	0.001	Solid v epithelial	Epithelial
ASV141	Bacteria	Campylobacter	Genus	6.56	0.000	Solid v epithelial	Epithelial
ASV421	Bacteria	Desulfobulbus	Genus	6.37	0.000	Solid v epithelial	Epithelial
ASV219	Bacteria	F_Neisseriaceae	Genus	5.21	0.001	Solid v epithelial	Epithelial
ASV708	Bacteria	Bacteroides	Genus	3.70	0.020	Solid v epithelial	Epithelial
ASV568	Bacteria	Alistipes	Genus	3.39	0.016	Solid v epithelial	Epithelial
ASV846	Bacteria	Howardella	Genus	2.78	0.011	Solid v epithelial	Epithelial
ASV523	Bacteria	F_Eggerthellaceae	Genus	1.39	0.011	Solid v epithelial	Solid
ASV587	Bacteria	Shuttleworthia	Genus	2.49	0.005	Solid v epithelial	Solid
ASV406	Bacteria	Family XIII UCG-001	Genus	3.19	0.000	Solid v epithelial	Solid
ASV141	Bacteria	G_Campylobacter	ASV	5.02	0.017	Liquid v epithelial	Epithelial
ASV379	Bacteria	F_Family XIII	ASV	4.40	0.014	Liquid v epithelial	Epithelial
ASV379	Bacteria	F_Family XIII	ASV	7.53	0.000	Solid v epithelial	Epithelial
ASV141	Bacteria	G_Campylobacter	ASV	6.93	0.000	Solid v epithelial	Epithelial
ASV247	Bacteria	F_Family XIII	ASV	5.87	0.005	Solid v epithelial	Epithelial
ASV361	Bacteria	F_Family XIII AD3011 group	ASV	5.72	0.004	Solid v epithelial	Epithelial
ASV210	Bacteria	G_Mogibacterium	ASV	4.09	0.002	Solid v epithelial	Epithelial
Perth
ASV126	Bacteria	Tenericutes	Phylum	0.97	0.003	Liquid v epithelial	Liquid
ASV421	Bacteria	Desulfobacterales	Order	3.73	0.007	Solid v epithelial	Epithelial
ASV102	Bacteria	Family XIII	Family	1.27	0.050	Solid v liquid	Solid
ASV219	Bacteria	Neisseriaceae	Family	4.24	0.027	Solid v epithelial	Epithelial
ASV391	Bacteria	Fretibacterium	Genus	6.89	0.006	Solid v epithelial	Epithelial
ASV421	Bacteria	Desulfobulbus	Genus	4.25	0.006	Solid v epithelial	Epithelial
ASV276	Bacteria	O_Clostridiales	ASV	6.27	0.050	Solid v epithelial	Epithelial
ASV128	Bacteria	F_Lachnospiraceae UCG-008	ASV	4.63	0.036	Solid v epithelial	Epithelial

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 significant findings along with the log10 of normalised counts (Mean ± Sd), BH adjusted P values, Log2 fold change, taxonomic rank and classification, fractions compared, and the fraction the abundance was increased in. Cheviot (solid n = 7, liquid n = 7, epithelial n = 7), Lanark (solid n = 5, liquid n = 5, epithelial n = 5), Perth (solid n = 5, liquid n = 5, epithelial n = 5).

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Table 9 Differential abundance analysis investigating the pairwise differences in bacterial and archaeal abundances between each of the fractions (i.e. solid, liquid and epithelial) in the Cheviot, Lanark and Perth breeds.

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