Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

Table 1 Statistics for PERMANOVA against performance parameters when using different dissimilarity measures on microbiome data. R² represents the proportion of variability explained, for example, using ‘Days’ and ‘Bray-Curtis’ dissimilarity, the days explain 21.2% variability in microbial community structure

Predictors	Df	SumsOfSqs	MeanSqs	F.Model	R²	p
Bray-Curtis distance
Days	1	4.9513	4.9513	26.8712	0.21163***	< 0.001
No. of parent flocks used	1	1.065	1.065	5.7796	0.04552***	< 0.001
Birds placed	1	1.0209	1.0209	5.5407	0.04364***	< 0.001
log CFU/g Campylobacter	1	0.9606	0.9606	5.2131	0.04106***	< 0.001
Protein (% of ration)	1	0.2729	0.2729	1.4813	0.01167^.	< 0.1
Energy of ration (Kcal/lb AME)	1	0.9375	0.9375	5.088	0.04007***	< 0.001
Residuals	77	14.1881	0.1843	0.60642
Total	83	23.3964	1
Unweighted UniFrac distance
Days	1	4.2369	4.2369	46.886	0.32727***	< 0.001
No. of parent flocks used	1	0.3242	0.3242	3.588	0.02504**	< 0.01
Birds placed	1	0.6806	0.6806	7.532	0.05258***	< 0.001
log CFU/g Campylobacter	1	0.386	0.386	4.272	0.02982***	< 0.001
Protein (% of ration)	1	0.1251	0.1251	1.385	0.00966	0.1744
Energy of ration (Kcal/lb AME)	1	0.235	0.235	2.601	0.01816*	0.0165
Residuals	77	6.9582	0.0904	0.53747
Total	83	12.9461	1
Weighted UniFrac distance
Days	1	0.055783	0.055783	76.574	0.43079***	< 0.001
No. of parent flocks used	1	0.001894	0.001894	2.6	0.01463^.	0.0509
Birds placed	1	0.005532	0.005532	7.594	0.04272***	< 0.001
log CFU/g Campylobacter	1	0.00484	0.00484	6.644	0.03738***	< 0.001
Protein (% of ration)	1	0.00092	0.00092	1.262	0.0071	0.2534
Energy of ration (Kcal/lb AME)	1	0.004429	0.004429	6.08	0.0342**	< 0.01
Residuals	77	0.056093	0.000728	0.43318
Total	83	0.129491	1

ISSN: 2049-2618