Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd

Table 1 Effects of different factors on the beta diversity of dairy cow microbiota

	Jaccard^a		Bray–Curtis^a		UniFrac^a		wUniFrac^a
	R2^b	P value	R2^b	P value	R2^b	P value	R2^b	P value
Group of animals	0.0047^b	0.001***	0.0053	0.001***	0.0046	0.001***	0.0045	0.002**
Site	0.0484	0.001***	0.0768	0.001***	0.1119	0.001***	0.1324	0.001***
Time	0.0242	0.001***	0.0266	0.001***	0.0663	0.001***	0.0375	0.001***
SM_score	0.0012	0.061.	0.0010	0.423	0.0017	0.035*	0.0006	0.786
BC_score	0.0011	0.206	0.0012	0.122	0.0009	0.433	0.0007	0.716
Animal	0.0411	0.166	0.0449	0.001	0.0381	0.129	0.0400	0.054.

^aSummary of the effects (P values) (as determined using Jaccard, Bray–Curtis, UniFrac and wUnifrac distances) of different factors on the beta diversity of the oral, nasal, vaginal and milk microbiota. ***P value < 0.001; **P value < 0.01; *P value < 0.05; “.” P value < 0.1
^bR2 indicates the contribution of each factor to the beta-diversity. A R2 of 0.0047 indicates a contribution of the “group of animals” factor to the beta-diversity of 0.47% with the Jaccard distance

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