Table 4.

Bacterial phyla that were differentially abundant within the faecal microbiota of pigs in the Control/Control group and all other treatment groups.

	Treatment					SEM1
Treatment day 0–28 PW	Con	Con	Pro	Pro	AB + ZnO
Treatment day 29–56 PW	Con	Pro	Con	Pro	Con
D13 PW
Bacteroidetes	32.092	32.76	34.22	34.56	51.66***	1.748
Epsilonbacteraeota	0.64	0.58	1.05	0.64	0.00***	0.189
Proteobacteria	1.72	2.08	2.77	2.02	0.51*	0.491
Spirochaetes	4.71	2.16	4.67	5.89	0.03***	0.814
Tenericutes	0.49	0.14	0.08***	0.26	0.00***	0.073
D27 PW
Bacteroidetes	31.66	30.81	30.63	31.95	53.51***	1.715
Chlamydiae	0.03	0.02	0.01	0.03	0.00*	0.010
Elusimicrobia	0.03	0.07*	0.26	0.24	0.00	0.078
Epsilonbacteraeota	0.60	0.73	0.42	0.65	0.08*	0.113
Kiritimatiellaeota	0.23	0.06	0.18	0.17	0.00***	0.046
Lentisphaerae	0.52	0.32	0.28	0.23	0.00***	0.090
Planctomycetes	0.09	0.05	0.11	0.05	0.00***	0.021
Proteobacteria	2.60	3.63	2.49	3.45	0.58**	0.543
Spirochaetes	7.35	5.02	5.15	6.83	0.28**	1.231
Synergistetes	0.02	0.01	0.02	0.02	0.00***	0.004
Tenericutes	0.18	0.11	0.20	0.14	0.00***	0.041
D35 PW
Actinobacteria	0.29	0.31	0.37	0.32	0.62**	0.046
Firmicutes	51.91	55.00	60.40	58.26	62.71*	2.066
Kiritimatiellaeota	0.35	0.30	0.24	0.27	0.00***	0.080
Lentisphaerae	0.33	0.32	0.23	0.20	0.01***	0.067
Patescibacteria	0.02	0.10*	0.03	0.03	0.00	0.018
Planctomycetes	0.24	0.24	0.12	0.14	0.00***	0.044
Spirochaetes	9.19	6.55	3.11**	3.99	0.23***	1.092
D55 PW
Fibrobacteres	0.13	0.61	0.73*	0.75	0.24	0.257

PW, post-weaning, Con, control; Pro, probiotic; AB + ZnO, antibiotic  + zinc oxide.

¹Pooled standard error of the mean (SEM).

²Relative abundances for each treatment are normalized with the total-sum scaling method.

Significant differences between treatment groups and the Con/Con group are indicated as: *** (P ≤ 0.001), ** (0.001 < P ≤ 0.01), and * (0.01 < P ≤ 0.05).

No significant differences were observed at D100 PW.

Statistical analysis of amplicon sequence variant (ASV) abundance was performed using DeSeq2²⁴ in R version 4.02²³, where low abundance ASVs were manually filtered and a false discovery rate (FDR) of < 0.05 was indicative of significant abundance difference between groups. For each taxon, differences between the median abundances of samples in each treatment group compared to the control group (Con/Con) were assessed using the Wilcoxon Rank Sum test of the R package Metacoder²⁵.