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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

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

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   
  1. .p < 0.1, *p < 0.05, **p < 0.01, ***p < 0.001
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