TABLE A3.
Beta diversity based on different distance metrics
| n | Bray–Curtis | Jaccard | UF | WUF | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| R 2 (%) | p‐Value | R 2 (%) | p‐Value | R 2 (%) | p‐Value | R 2 (%) | p‐Value | |||
| Age | Farm 1 + 2 | 341 | 12.1 | 1.00e−04*** | 7.5 | 1.00e−04*** | 19.1 | 1.00e−04*** | 18.6 | 1.00e−04*** |
| Farm 1 | 179 | 14.4 | 1.00e−04*** | 9.1 | 1.00e−04*** | 21.4 | 1.00e−04*** | 20.6 | 1.00e−04*** | |
| Farm 2 | 162 | 12.8 | 1.00e−04*** | 8.3 | 1.00e−04*** | 20.1 | 1.00e−04*** | 18.7 | 1.00e−04*** | |
| Age | 21 + 28 + 35 | 107 | 2.7 | 1.00e−04*** | 2.1 | 1.00e−04*** | 4.5 | 1.00e−04*** | 4.2 | 1.00e−04*** |
| F1 vs F2 | All ages | 341 | 2.0 | 1.00e−04*** | 1.5 | 1.00e−04*** | 2.0 | 1.00e−04*** | 1.2 | 0.002** |
| Age 0 | 36 | 24.9 | 1.00e−04*** | 23.3 | 1.00e−04*** | 19.6 | 1.00e−04*** | 11.5 | 0.013* | |
| Age 2 | 36 | 22.8 | 1.00e−04*** | 14.9 | 1.00e−04*** | 17.1 | 1.00e−04*** | 12.3 | 0.002** | |
| Age 7 | 36 | 11.1 | 1.00e−04*** | 7.7 | 1.00e−04*** | 18.4 | 1.00e−04*** | 9.7 | 8.00e−04*** | |
| Age 14 | 36 | 6.1 | 3.00e−04*** | 4.9 | 1.00e−04*** | 13.6 | 1.00e−04*** | 7.1 | 0.026* | |
| Age 21 | 35 | 9.3 | 1.00e−04*** | 7.1 | 1.00e−04*** | 10.7 | 1.00e−04*** | 8.6 | 3.00e−04*** | |
| Age 28 | 36 | 8.3 | 1.00e−04*** | 6.3 | 1.00e−04*** | 10.9 | 1.00e−04*** | 10.7 | 1.00e−04*** | |
| Age 35 | 36 | 10.7 | 1.00e−04*** | 7.9 | 1.00e−04*** | 13.9 | 1.00e−04*** | 8.4 | 0.003** | |
| 21 + 28 + 35 | 107 | 5.2 | 1.00e−04*** | 3.7 | 1.00e−04*** | 7.0 | 1.00e−04*** | 6.2 | 1.00e−04*** | |
| F1; poultry house | All ages | 179 | 1.1 | 0.018* | 1.0 | 0.009** | 0.6 | 0.299 | 0.6 | 0.385 |
| Age 21 + 28 + 35 | 53 | 5.7 | 1.00e−04*** | 4.3 | 1.00e−04*** | 3.9 | 0.006** | 2.9 | 0.109 | |
| Age 35 | 18 | 8.8 | 0.048* | 7.9 | 0.040* | 6.0 | 0.376 | 4.2 | 0.649 | |
| F2; poultry house | All ages | 162 | 0.6 | 0.387 | 0.6 | 0.376 | 0.4 | 0.646 | 0.2 | 0.931 |
| Age 21 + 28 + 35 | 54 | 2.3 | 0.170 | 2.2 | 0.128 | 2.2 | 0.231 | 1.6 | 0.597 | |
| Age 35 | 18 | 6.1 | 0.375 | 6.1 | 0.338 | 6.9 | 0.238 | 5.2 | 0.491 | |
| Sex | All ages | 341 | 0.2 | 0.924 | 0.2 | 0.920 | 0.1 | 0.942 | 0.1 | 0.946 |
| Cecal foam | All ages | 340 | 1.9 | 1.00e−04*** | 1.3 | 1.00e−04*** | 3.8 | 1.00e−04*** | 3.4 | 1.00e−04*** |
| Age 21 + 28 + 35 | 107 | 1.8 | 0.0033** | 1.5 | 0.002** | 1.7 | 0.010* | 2.2 | 0.009** | |
| Cecal color | All ages | 340 | 3.7 | 1.00e−04*** | 2.5 | 1.00e−04*** | 5.4 | 1.00e−04*** | 5.5 | 1.00e−04*** |
| Age 21 + 28 + 35 | 107 | 4.0 | 1.00e−04*** | 3.1 | 1.00e−04*** | 4.8 | 1.00e−04*** | 5.6 | 1.00e−04*** | |
| GS | Age 21 + 28 + 35 | 81 | 4.7 | 0.639 | 4.8 | 0.665 | 5.1 | 0.348 | 5.1 | 0.365 |
| CLS | Age 21 + 28 + 35 | 81 | 6.2 | 0.060. | 5.6 | 0.076. | 7.2 | 0.048* | 12.4 | 0.045* |
| Footpad integrity | Age 21 + 28 + 35 | 107 | 1.3 | 0.064. | 1.2 | 0.048* | 1.5 | 0.015* | 1.1 | 0.290 |
R 2 = Percentage of the variation between chickens explained, p‐value = based on PERMANOVA test, GS = gut score (2), CLS = coccidiosis lesion score (18), ***p < 0.001, **p < 0.01, *p < 0.05. The age of the broilers explains 18.6% of the variation between all the cecal samples, while the farm just explained 1.2% (weighted UniFrac, WUF). When we stratified the data per age, around 10% (7%–12%) of the variation was explained by farm based on weighted UniFrac. Furthermore, unweighted UniFrac distance was slightly higher than the weighted UniFrac distance between the two farms, whereas the opposite trend was observed for corresponding Jaccard and Bray–Curtis distances that are not phylogenetically weighted. Taken together, this indicated that abundant taxa are more phylogenetically related compared with the less abundant taxa between the two farms.