Table S1. Ecological diversity indices obtained for this study. Sample names PIG, GRO, FIN, and SOW denote each growth stage of swine; piglet, grower, finisher, and sow, respectively. Numbers indicate replicates.

Sample / # of reads / Coverage / # of OTUs / Chao / Inverted
Simpson
PIG1 / 44,894 / 1.00 / 497 / 579 / 20.8
PIG2 / 35,263 / 1.00 / 532 / 607 / 19.7
PIG3 / 35,207 / 1.00 / 508 / 582 / 22.1
PIG4 / 40,080 / 0.99 / 603 / 689 / 24.6
PIG5 / 46,802 / 0.99 / 556 / 677 / 19.5
GRO1 / 41,213 / 0.99 / 795 / 939 / 23.1
GRO2 / 71,659 / 0.99 / 922 / 1178 / 40.2
GRO3 / 49,014 / 0.99 / 812 / 982 / 37.2
GRO4 / 39,715 / 0.99 / 838 / 973 / 31.0
GRO5 / 42,926 / 0.99 / 805 / 1029 / 34.9
FIN1 / 41,092 / 0.99 / 889 / 1072 / 57.1
FIN2 / 40,732 / 0.99 / 827 / 967 / 40.5
FIN3 / 43,765 / 0.99 / 739 / 928 / 39.3
FIN4 / 32,683 / 0.99 / 828 / 938 / 27.1
FIN5 / 46,987 / 0.99 / 770 / 926 / 44.8
SOW1 / 35,782 / 0.99 / 666 / 752 / 22.3
SOW2 / 39,235 / 0.99 / 650 / 763 / 8.7
SOW3 / 57,469 / 0.99 / 668 / 843 / 7.1
SOW4 / 34,447 / 0.99 / 727 / 861 / 35.4
SOW5 / 27,783 / 0.99 / 786 / 845 / 82.7

Table S2. Growth stage specific abundant genera defined by the Metastats(P<0.05)

Growth stage / Genus / P-value / Q-value
Piglet / Xylanibacter / 0.00 / 0.03
Lachnospiracea_incertae_sedis / 0.03 / 0.28
Erysipelotrichaceae_incertae_sedis / 0.02 / 0.24
Grower / Collinsella / 0.04 / 0.45
Clostridium_XVIII / 0.03 / 0.45
Pectinatus / 0.04 / 0.45
Bacteroides / 0.01 / 0.39
Sow / Anaerovibrio / 0.00 / 0.09
Acetanaerobacterium / 0.03 / 0.24
Erysipelothrix / 0.03 / 0.24
Tepidibacter / 0.01 / 0.18
Finisher / Clostridium_XI / 0.01 / 0.33

Table S3. Number of total, selected, and shared operational taxonomic units

OTUs / Total / Piglet / Growers / Finishers / Sow
All samples / 2,800 / 539 / 834 / 810 / 699
Common / 560 / 203 / 390 / 356 / 253
Commonly shared / 343 / 180 / 300 / 286 / 219