Table 4. Functional genes with a MRA (%) > 0.5 and corresponding standard error in caeca and crops in at least one treatment (i.e., day 1, high dose (HD) 14 and 35 days, low dose (LD) 14 and 35 days, control (C) 14 and 35 days).

	Mean relative abundance (%) (standard error)
	Day 1	HD 14d	HD 35d	LD 14d	LD 35d	C 14d	C35 d
Caeca
Cell division protein FtsH EC.3.4.24	0.576 (0.038)	0.39 (0.016)	0.475 (0.011)	0.383 (0.012)	0.452 (0.013)	0.385 (0.026)	0.428 (0.009)
Copper translocating P type ATPase EC.3.6.3.4.	0.19 (0.033)	0.462 (0.018)	0.407 (0.009)	0.508 (0.022)	0.448 (0.017)	0.489 (0.016)	0.469 (0.014)
Decarboxylase	0.661 (0.167)	0.265 (0.006)	0.25 (0.008)	0.276 (0.014)	0.253 (0.011)	0.28 (0.011)	0.242 (0.008)
DNA directed RNA polymerase beta subunit EC.2.7.7.6.	0.31 (0.075)	0.467 (0.02)	0.576 (0.02)	0.45 (0.015)	0.573 (0.03)	0.439 (0.017)	0.542 (0.023)
DNA polymerase III alpha subunit EC.2.7.7.7.	0.273 (0.05)	0.572 (0.022)	0.752 (0.025)	0.577 (0.011)	0.74 (0.035)	0.576 (0.018)	0.699 (0.03)
DNA topoisomerase III EC.5.99.1.2.	0.164 (0.037)	0.728 (0.096)	0.586 (0.006)	0.747 (0.072)	0.617 (0.024)	0.755 (0.047)	0.563 (0.043)
Excinuclease ABC subunit A	0.352 (0.067)	0.583 (0.035)	0.635 (0.019)	0.643 (0.028)	0.672 (0.014)	0.652 (0.028)	0.695 (0.022)
GTP binding protein	1.057 (0.052)	0.274 (0.005)	0.293 (0.005)	0.28 (0.01)	0.29 (0.009)	0.295 (0.009)	0.304 (0.007)
Retron type reverse transcriptase	0.165 (0.025)	0.431 (0.033)	0.539 (0.022)	0.425 (0.034)	0.404 (0.027)	0.375 (0.058)	0.362 (0.047)
Site specific recombinase	0.188 (0.035)	0.733 (0.019)	0.681 (0.025)	0.815 (0.029)	0.712 (0.034)	0.658 (0.088)	0.518 (0.043)
Crops
Carbamoyl phosphate synthase large chain EC.6.3.5.5.	0.541 (0.03)	0.495 (0.049)	0.559 (0.038)	0.676 (0.166)	0.475 (0.065)	0.464 (0.069)	0.466 (0.015)
Decarboxylase	0.705 (0.063)	0.624 (0.052)	0.335 (0.019)	0.497 (0.095)	0.285 (0.013)	0.453 (0.014)	0.249 (0.016)
DNA directed RNA polymerase beta subunit EC.2.7.7.6.	0.199 (0.055)	0.342 (0.088)	0.555 (0.031)	0.339 (0.066)	0.508 (0.058)	0.436 (0.051)	0.565 (0.018)
DNA polymerase III alpha subunit EC.2.7.7.7.	0.208 (0.03)	0.415 (0.079)	0.663 (0.012)	0.382 (0.057)	0.576 (0.084)	0.435 (0.047)	0.632 (0.028)
Glycosyltransferase	0.532 (0.047)	0.525 (0.075)	0.427 (0.027)	0.511 (0.017)	0.452 (0.055)	0.527 (0.049)	0.437 (0.027)
GTP binding protein	1.491 (0.179)	1.059 (0.251)	0.334 (0.025)	1.054 (0.181)	0.358 (0.034)	0.716 (0.026)	0.309 (0.011)
Oligopeptide ABC transporter periplasmic oligopeptide binding protein OppA TC.3.A.1.5.1.	0.087 (0.029)	0.511 (0.109)	0.766 (0.071)	0.372 (0.078)	0.639 (0.093)	0.606 (0.067)	0.785 (0.059)
X6 phospho beta glucosidase EC.3.2.1.86.	0.153 (0.037)	0.403 (0.097)	0.512 (0.073)	0.349 (0.096)	0.51 (0.081)	0.589 (0.043)	0.484 (0.053)