Table 2.
Average number of sequences (standard deviation) per taxon obtained from fecal samples of Holstein-Friesian heifers (HFH), Holstein-Friesian cows (HFC), Simmental heifers (SIH), and Simmental cows (SIC)
| HFH | HFC | SIH | SIC | |
|---|---|---|---|---|
| Archaea | 819 (371) | 2,289 (731) | 1,429 (503) | 1,557 (539) |
| Euryarchaeota | 819 (371) | 2,289 (731) | 1,429 (503) | 1,557 (539) |
| Methanobrevibacter | 700 (277) | 2,132 (663) | 1,200 (414) | 1,389 (532) |
| Methanocorpusculum | 73 (66) | 17 (18) | 77 (38) | 11 (10) |
| Methanosphaera | 22 (12) | 141 (64) | 74 (33) | 157 (34) |
| Unclassified Methanobacteriaceae | 13 (9) | - | 73 (25) | - |
| Uncultured Methanomethylophilaceae | 13 (7) | - | 6 (5) | - |
| Bacteria | 27,662 | 26,443 | 26,401 | 27,262 |
| Actinobacteria | 35 (16) | 1,265 (589) | 73 (41) | 594 (399) |
| Aeriscardovia | - | 14 (3) | - | 3 (4) |
| Arcanobacterium | 6 (7) | - | 1(2) | - |
| Atopobium | 3 (4) | 5 (1) | 3 (4) | 9 (8) |
| Bifidobacterium | - | 1,130 (565) | - | 28 (26) |
| Olsenella | - | 66 (42) | 25 (34) | 493 (357) |
| Raoultibacter | 2 (3) | - | 7 (5) | - |
| Eggerthellaceae DNF00809 | 10 (11) | 13 (6) | 22 (14) | 13 (10) |
| Uncultured Eggerthellaceae | 1 (2) | 5 (6) | 2 (3) | 13 (8) |
| Unclassified Actinobacteria | 12 (7) | 31 (16) | 14 (20) | 35 (20) |
| Bacteroidetes | 12,529 (610) | 10,308 (753) | 9,997 (586) | 10,019 (581) |
| Alistipes | 1,489 (181) | 866 (207) | 1,108 (248) | 709 (230) |
| Alloprevotella | 202 (72) | 198 (146) | 135 (86) | 780 (348) |
| Bacteroides | 1,715 (67) | 2,807 (151) | 1,759 (263) | 2,350 (230) |
| Odoribacter | 32 (8) | 16 (24) | 20 (11) | 35 (16) |
| Sanguibacteroides | 2 (4) | - | 7 (6) | - |
| Paludibacter | - | 15 (22) | - | - |
| Parabacteroides | 11 (6) | 37 (7) | 19 (10) | 103 (23) |
| Prevotella | 137 (39) | 479 (113) | 78 (29) | 193 (123) |
| Prevotellaceae UCG-001 | 82 (32) | 258 (50) | 74 (30) | 150 (58) |
| Prevotellaceae UCG-003 | 988 (76) | 1,908 (100) | 704 (160) | 1,172 (243) |
| Prevotellaceae UCG-004 | 1,168 (151) | 183 (147) | 1,308 (264) | 532 (81) |
| Prevotellaceae Ga6A1 group | 6 (7) | 25 (21) | 18 (14) | 33 (27) |
| Rikenellaceae RC9 gut group | 2,380 (158) | 2,015 (254) | 2,238 (313) | 1,918 (229) |
| Rikenellace dgA-11 gut group | 952 (183) | 70 (83) | 622 (88) | 132 (79) |
| Uncultured Bacteroidales F082 | 558 (120) | 8 (12) | 773 (117) | 87 (38) |
| Uncultured Bacteroidales gir-aah93h0 | 335 (116) | 235 (233) | 177 (32) | 335 (240) |
| Uncultured Bacteroidales M2PB4-65 termite group | 169 (183) | - | 234 (192) | - |
| Uncultured Bacteroidales p-251-o5 | 118 (65) | 21 (41) | 169 (81) | 125 (123) |
| Uncultured Bacteroidales p-2534-18B5 gut group | 398 (185) | - | - | 235 (216) |
| Uncultured Bacteroidales RF16 group Paludibacter sp. | 36 (20) | - | 30 (28) | 19 (6) |
| Uncultured Bacteroidales RF16 group Porphyromonadaceae bacterium | 225 (38) | 196 (102) | 259 (179) | 218 (167) |
| Uncultured Barnesiellaceae | 29 (11) | 46 (23) | 21 (7) | 61 (44) |
| Uncultured Bacteroidales RF16 group Uncultured bacterium | 43 (16) | 22 (22) | 165 (163) | 35 (23) |
| Uncultured Bacteroidales UCG-001 | 49 (10) | - | 76 (17) | 25 (9) |
| Uncultured Bacteroidales | - | - | 31 (8) | 11 (14) |
| Uncultured Dysgonomonadaceae | 149 (65) | 82 (95) | 316 (208) | 198 (129) |
| Uncultured Flavobacteriaceae | 702 (130) | 394 (77) | 163 (53) | 332 (106) |
| Uncultured Muribaculaceae | 213 (139) | 60 (34) | 31 (9) | 17 (11) |
| Unclassified Bacteroidetes | 341 (91) | 367 (326) | 166 (93) | 195 (106) |
| Chloroflexi | 3 (4) | 34 (12) | ||
| Flexilinea | 3 (4) | - | 34 (12) | - |
| Cyanobacteria | 396 (174) | 147 (212) | 439 (146) | 140 (84) |
| Uncultured Cyanobacteria | 371 (162) | 147 (212) | 423 (162) | 140 (84) |
| Unclassified Cyanobacteria | 24 (25) | - | 16 (18) | - |
| Elusimicrobia | 32 (20) | 3 (6) | 39 (31) | 2 (4) |
| Eluisimicrobium | 32 (20) | 3 (6) | 39 (31) | 2 (4) |
| Epsilonbacteraeota | 7 (16) | 1 (1) | 2 (4) | 1 (3) |
| Campylobacter | 7 (16) | 1 (1) | 2 (4) | 1 (3) |
| Fibrobacteres | 156 (51) | - | 511 (149) | 71 (70) |
| Fibrobacter | 156 (51) | - | 511 (149) | 71 (70) |
| Firmicutes | 13,285 (1130) | 13,568 (546) | 13,216 (869) | 15,380 (1022) |
| Acetitomaculum | 17 (14) | 47 (21) | 65 (12) | 65 (10) |
| Aerococcus | 6 (7) | 3 (8) | - | - |
| Agathobacter | 10 (14) | 170 (78) | - | 77 (70) |
| Anaerorhabdus furcosa group | 28 (14) | 25 (13) | 17 (10) | 20 (7) |
| Anaerosporobacter | 51 (21) | 18 (17) | 71 (98) | 20 (31) |
| Anaerostipes | - | 22 (27) | - | - |
| Anaerovibrio | - | 97 (107) | - | 29 (30) |
| Anaerovorax | 30 (11) | 16 (14) | 42 (8) | 200 (52) |
| Angelakisella | 19 (4) | - | 8 (3) | - |
| Blautia | 7 (10) | 137 (59) | 24 (14) | 104 (37) |
| Breznakia | 1 (2) | 21 (16) | 1 (1) | 3 (3) |
| Butyricicoccus | 5 (12) | 7 (4) | - | 6 (4) |
| Butyrivibrio | 8 (8) | 19 (12) | 2 (3) | 12 (12) |
| Candidatus Soleaferrea | 107 (20) | 42 (14) | 138 (29) | 90 (10) |
| Candidatus Stoquefichus | - | 149 (121) | - | - |
| Caproiciproducens | 7 (9) | 1 (1) | 11 (10) | 8 (8) |
| Cellulosilyticum | 52 (69) | 31 (23) | 5 (4) | 64 (33) |
| Christensenellaceae R-7 group | 498 (134) | 765 (213) | 797 (156) | 905 (403) |
| Clostridium | 173 (11) | 307 (271) | 41 (14) | 482 (262) |
| Coprobacillus | 1 (3) | 42 (9) | 8 (3) | 6 (8) |
| Coprococcus | 17 (14) | 121 (53) | 37 (40) | 122 (61) |
| Defluvitaleaceae UCG-011 | 22 (9) | 14 (8) | 8 (9) | 13(11) |
| Dielma | 7 (5) | 13 (8) | 12 (7) | 15 (3) |
| Dorea | 56 (30) | 90 (34) | 71 (23) | 78 (39) |
| Eisenbergiella | - | 4 (5) | 1 (1) | 2 (5) |
| Erysipelatoclostridium | 1 (3) | 42 (9) | 8 (3) | 42 (12) |
| Erysipelotrichaceae UCG-002 | - | 12 (16) | - | - |
| Erysipelotrichaceae UCG-004 | 10 (14) | 104 (41) | - | 24 (30) |
| Erysipelotrichaceae UCG-006 | - | - | - | 16 (17) |
| Erysipelotrichaceae UCG-007 | - | - | - | 27 (18) |
| Erysipelotrichaceae UCG-009 | - | 4 (3) | - | - |
| Eubacterium brachy group | 56 (31) | 66 (10) | 72 (8) | 80 (21) |
| Eubacterium halii group | 7 (7) | 1 (1) | 22 (5) | 37 (33) |
| Eubacterium nodatum group | 42 (35) | 31 (10) | 80 (22) | 71 (43) |
| Eubacteriu ruminantium group | 2 (4) | 23 (22) | 11 (11) | 32 (22) |
| Eubacterium ventriosum group | 2 (2) | - | 11 (8) | - |
| Fecalibacterium | - | 5 (2) | - | 4 (2) |
| Fecalitalea | 9 (8) | 65 (51) | 2 (3) | 7 (7) |
| Family XIII AD3011 | 273 (50) | 140 (18) | 273 (26) | 200 (52) |
| Family XIII UCG-001 | 3(4) | 6 (2) | 3 (4) | 10 (2) |
| Flavonifractor | 14 (32) | 66 (36) | 30 (19) | 57 (21) |
| Fourneriella | - | 13 (10) | - | 12 (3) |
| Howardella | 4 (6) | 20 (8) | 18 (10) | 45 (33) |
| Intestinimonas | 3 (7) | - | 6 (6) | - |
| Lachnoclostridium | 51 (35) | 24 (29) | 55 (16) | 44 (24) |
| Lachnospira | 8 (19) | - | - | - |
| Lachnospiraceae AC2044 group | 48 (20) | 274 (118) | 44 (18) | 68 (70) |
| Lachnospiraceae FCS020 group | 5 (5) | 5 (7) | 7 (8) | - |
| Lachnospiraceae FE2018 group | - | 4 (3) | 2 (3) | 2 (2) |
| Lachnospiraceae NK3A20 group | 67 (32) | 149 (52) | 87 (29) | 154 (53) |
| Lachnospiracea NK4A136 group | 9 (13) | 175 (133) | 184 (105) | 228 (133) |
| Lachnospiraceae UCG-001 | 36 (16) | 62 (51) | 35 (12) | 46 (11) |
| Lachnospiraceae UCG-002 | - | - | - | 5 (4) |
| Lachnospiraceae UCG-007 | - | - | - | 9 (13) |
| Lachnospiraceae UCG-010 | 106 (29) | 58 (18) | 101 (29) | 154 (68) |
| Lysinibacillus | 2 (4) | - | 3 (7) | 11 (1) |
| Marvinbryantia | 16 (10) | 157 (54) | 27 (11) | 158 (44) |
| Mitsuokella | - | 10 (10) | - | - |
| Mogibacterium | 9 (6) | 3 (7) | 12 (8) | 4 (8) |
| Moryella | 4 (4) | 7 (4) | 7 (5) | 10 (5) |
| Negativibacillus | 24 (13) | 51 (12) | 30 (10) | 66 (15) |
| Oscillibacter | 112 (26) | 148 (25) | 86 (15) | 110 (22) |
| Oscillospira | 66 (28) | 1 (2) | 14 (5) | 1 (2) |
| Paeniclostridium | 1,543 (261) | 433 (191) | 705 (472) | 370 (174) |
| Papillibacter | 11 (11) | 4 (0) | 14 (5) | 3 (0) |
| Phascolarctobacterium | 114 (41) | 155 (31) | 107 (18) | 136 (42) |
| Pseudobutyrivibrio | 9 (20) | - | - | - |
| Pygmaiobacter | 29 (17) | 69 (39) | 10 (6) | 56 (28) |
| Romboutsia | 1,119 (206) | 514 (370) | 902 (462) | 952 (423) |
| Roseburia | 17 (10) | 202 (257) | 10 (8) | 71 (91) |
| Ruminiclostridium | 72 (29) | 15 (10) | 75 (28) | 7 (2) |
| Ruminococcaceae Eubacterium coprostanoligenes group | 795 (141) | 535 (250) | 880 (109) | 928 (214) |
| Ruminococcace GCA-90066225 | 8 (4) | 17 (10) | 10 (6) | 13 (6) |
| Ruminococcace NK4A214 group | 217 (49) | 123 (38) | 275 (33) | 187 (33) |
| Ruminococcaceae UCG-002 | 91 (25) | 18 (13) | 104 (29) | 34 (20) |
| Ruminococcaceae UCG-004 | 58 (15) | 45 (12) | 59 (15) | 60 (20) |
| Ruminococcaceae UCG-005 | 2,144 (288) | 2,913 (396) | 2,214 (395) | 3,114 (387) |
| Ruminococcaceae UCG-009 | 209 (39) | 84 (38) | 238 (55) | 122 (22) |
| Ruminococcaceae UCG-010 | 1,881 (181) | 978 (439) | 1,736 (192) | 1,044 (525) |
| Ruminococcaceae UCG-011 | 26 (17) | - | 110 (12) | - |
| Ruminococcaceae UCG-013 | 1,156 (150) | 543 (274) | 822 (83) | 941 (218) |
| Ruminococcaceae UCG-014 | 302 (83) | 343 (347) | 360 (44) | 363 (76) |
| Ruminococcu gauvreauii group | 2 (5) | 30 (24) | 7 (9) | 77 (27) |
| Saccharofermentans | 10 (10) | 3 (2) | 36 (7) | 11 (6) |
| Sharpea | - | 16 (17) | - | 18 (9) |
| Solobacterium | - | - | 11 (8) | - |
| Streptococcus | 1 (3) | 2 (2) | 4 (4) | 1 (1) |
| Syntrophococcus | 2 (4) | 4 (10) | 11 (12) | 288 (229) |
| Terrisporobacter | 39 (17) | 18 (0) | 18 (7) | - |
| Turicibacter | 141 (19) | 254 (273) | 166 (70) | 117 (100) |
| Tyzzerella 4 | 29 (17) | 107 (87) | 67 (21) | 116 (32) |
| XBB1006 | - | - | 7 (8) | - |
| Uncultured Christensenellaceae | - | - | 8 (6) | - |
| Uncultured Clostridiales vadinBB60 group | 99 (26) | 188 (202) | 69 (37) | 179 (108) |
| Uncultured Erysipelotrichaceae | 12 (9) | 25 (33) | - | 16 (11) |
| Uncultured Lachnospiraceae | 42 (18) | 92 (47) | 62 (12) | 42 (6) |
| Uncultured Peptococcaceae | 150 (20) | 64 (13) | 150 (55) | 48 (16) |
| Uncultured Ruminococcaceae | 239 (35) | 92 (23) | 252 (48) | 115 (40) |
| Uncultured Veillonellaceae | - | - | - | 14 (7) |
| Unclassified Firmicutes | 1,019 (296) | 2,092 (722) | 1,128 (302) | 1,882 (953) |
| Patescibacteria | 62 (7) | 37 (13) | 83 (23) | 113 (40) |
| Candidatus Saccharimonas | 62 (7) | 37 (13) | 83 (23) | 113 (40) |
| Proteobacteria | 351 (108) | 760 (456) | 566 (197) | 216 (144) |
| Escherichia-Shigella | - | 39 (24) | - | 6 (9) |
| Kingella | 3 (5) | 6 (13) | - | - |
| Mailhella | 178 (60) | 19 (9) | 279 (47) | 20 (13) |
| Parasutterella | 47 (16) | 52 (24) | 23 (9) | 28 (11) |
| Ruminobacter | 3 (4) | 54 (27) | 25 (37) | 16 (28) |
| Succinivibrio | 9 (21) | 512 (446) | 1 (1) | 117 (93) |
| Succinivibrionaceae UCG-001 | - | 5 (4) | - | - |
| Sutterella | - | 9 (4) | - | 3 (8) |
| Uncultured Paracaedibacteraceae | 6 (2) | - | - | - |
| Uncultured Rhodospirillales | 63 (33) | - | 168 (133) | 16 (24) |
| Uncultured Rickettsiales | 6 (4) | 7 (2) | - | - |
| Unclassified Proteobacteria | 36 (24) | - | 70 (80) | 10 (14) |
| Spirochaetes | 197 (44) | 133 (89) | 143 (35) | 263 (129) |
| Sediminisprirochaeta | 10 (8) | - | - | - |
| Spirochaetaceae GWE-31-10 | 20 (13) | 9 (15) | 14 (6) | 37(9) |
| Treponema | 167 (32) | 124 (75) | 129 (29) | 226 (126) |
| Tenericutes | 128 (45) | 139 (19) | 88 (37) | 84 (26) |
| Anaeroplasma | - | 40 (15) | - | 9 (10) |
| Uncultured Tenericutes | 113 (53) | 82 (70) | 70 (67) | 58 (39) |
| Unclassified Tenericutes | 15 (10) | 17 (20) | 18 (24) | 17 (17) |
| Verrucomicrobia | 481 (96) | 82 (113) | 850 (195) | 379 (122) |
| Akkermansia | 481 (96) | 82 (113) | 850 (195) | 379 (122) |