Table 2.
Good's coverage indices (estimated sequencing coverage) and alpha diversity indices of bacterial taxonomic profiles by 16S rRNA gene sequences at the (a) genus and (b) species levels.
| Fecal manure | Sample ID | Raw reads | Quality reads | OTUs | Good’s coverage | Chao | Shannon |
|---|---|---|---|---|---|---|---|
| (a) | |||||||
| E | E_1 | 49,832 | 18,613 | 261 | 0.98930 | 380 | 3.16098 |
| E_2 | 33,624 | 12,371 | 309 | 0.98754 | 406.02 | 3.39099 | |
| E_3 | 28,559 | 10,894 | 310 | 0.98628 | 437.95652 | 3.47094 | |
| PC1 | PC1_1 | 301,641 | 196,013 | 148 | 0.99584 | 174.4 | 3.59382 |
| PC1_2 | 464,643 | 299,411 | 168 | 0.99484 | 198.37037 | 3.20792 | |
| PC1_3 | 372,058 | 246,862 | 106 | 0.99648 | 129.625 | 2.38559 | |
| PC2 | PC2_1 | 243,712 | 159,192 | 144 | 0.99509 | 218.1 | 2.66204 |
| PC2_2 | 270,242 | 176,288 | 155 | 0.99332 | 280.27272 | 3.02093 | |
| PC2_3 | 276,023 | 178,737 | 127 | 0.99597 | 154.55555 | 2.76922 | |
| PC3 | PC3_1 | 317,279 | 206,799 | 107 | 0.99672 | 132 | 3.19780 |
| PC3_2 | 371,787 | 237,351 | 116 | 0.99648 | 145.07692 | 3.27428 | |
| PC3_3 | 275,511 | 183,585 | 107 | 0.99584 | 147.61538 | 2.07227 | |
| PCO | PCO_1 | 209,667 | 108,003 | 104 | 0.99698 | 134.66666 | 3.20418 |
| PCO_2 | 279,425 | 168,142 | 115 | 0.99622 | 140.58823 | 2.78577 | |
| PCO_3 | 172,991 | 100,335 | 101 | 0.99761 | 109.55 | 2.89678 | |
| S | S_1 | 161,937 | 107,210 | 91 | 0.99622 | 163.5 | 2.80794 |
| S_2 | 320,353 | 205,017 | 83 | 0.99761 | 97.25 | 2.62696 | |
| S_3 | 218,944 | 198,614 | 88 | 0.99648 | 135.25 | 2.66646 | |
| R | R_1 | 98,546 | 93,085 | 120 | 0.99610 | 153.21428 | 3.21580 |
| R_2 | 136,011 | 127,435 | 165 | 0.99383 | 234.17647 | 2.51931 | |
| R_3 | 272,892 | 255,428 | 115 | 0.99622 | 146.07142 | 3.01602 | |
| G1 | G1_1 | 127,942 | 112,607 | 99 | 0.99786 | 112.6 | 2.87956 |
| G1_2 | 44,671 | 16,998 | 84 | 0.99711 | 109.3 | 2.17222 | |
| G1_3 | 82,404 | 29,752 | 92 | 0.99799 | 100 | 2.51211 | |
| G2 | G2_1 | 24,100 | 8,688 | 93 | 0.99748 | 108.83333 | 2.38991 |
| G2_2 | 22,265 | 8,204 | 86 | 0.99786 | 105.42857 | 2.23782 | |
| G2_3 | 20,917 | 7,945 | 100 | 0.99685 | 127.27272 | 2.57821 | |
| DC | DC_1 | 119,376 | 114,228 | 130 | 0.99560 | 165 | 2.37328 |
| DC_2 | 112,197 | 40,854 | 100 | 0.99685 | 142.85714 | 2.00946 | |
| DC_3 | 148,943 | 137,401 | 105 | 0.99698 | 151.5 | 2.82303 | |
| D | D_1 | 154,153 | 97,954 | 136 | 0.99585 | 165.33333 | 3.21510 |
| D_2 | 201,247 | 117,168 | 141 | 0.99610 | 162.13636 | 3.25661 | |
| D_3 | 211,853 | 115,864 | 150 | 0.99371 | 222.05882 | 3.29154 | |
| MB | MB_1 | 146,008 | 135,114 | 126 | 0.99484 | 189.07692 | 2.82331 |
| MB_2 | 134,925 | 128,005 | 146 | 0.99585 | 173.78947 | 3.04006 | |
| MB_3 | 132,775 | 125,347 | 124 | 0.99622 | 157.46153 | 2.68982 | |
| CC | CC_1 | 186,002 | 173,315 | 182 | 0.99396 | 225.38461 | 3.39068 |
| CC_2 | 130,352 | 122,980 | 121 | 0.99597 | 148.55555 | 2.07403 | |
| CC_3 | 180,039 | 171,258 | 119 | 0.99610 | 161.27272 | 2.81354 | |
| Fecal manure | Sample ID | OTUs | Good’s coverage | Chao | Shannon | ||
|---|---|---|---|---|---|---|---|
| (b) | |||||||
| E | E_1 | 293 | 0.98754 | 396.2128 | 3.21184 | ||
| E_2 | 332 | 0.98351 | 521.2222 | 3.38902 | |||
| E_3 | 325 | 0.98540 | 496.0256 | 3.46138 | |||
| PC1 | PC1_1 | 175 | 0.99358 | 230.4348 | 3.66648 | ||
| PC1_2 | 185 | 0.99446 | 230.0476 | 3.34555 | |||
| PC1_3 | 123 | 0.99534 | 174.2308 | 2.44652 | |||
| PC2 | PC2_1 | 162 | 0.99421 | 211.2857 | 2.68645 | ||
| PC2_2 | 167 | 0.99308 | 249.5 | 3.02509 | |||
| PC2_3 | 145 | 0.99421 | 214 | 2.92657 | |||
| PC3 | PC3_1 | 131 | 0.99459 | 195.5 | 3.31345 | ||
| PC3_2 | 130 | 0.99622 | 163.4615 | 3.39241 | |||
| PC3_3 | 114 | 0.99522 | 177.9091 | 2.26757 | |||
| PCO | PCO_1 | 140 | 0.99408 | 200.0556 | 3.37754 | ||
| PCO_2 | 139 | 0.99471 | 200.5 | 2.94793 | |||
| PCO_3 | 122 | 0.99534 | 182.5455 | 3.09510 | |||
| S | S_1 | 115 | 0.99522 | 193.1111 | 2.84378 | ||
| S_2 | 109 | 0.99585 | 157 | 2.77461 | |||
| S_3 | 98 | 0.99610 | 140.2727 | 2.74297 | |||
| R | R_1 | 132 | 0.99610 | 157.8333 | 3.30997 | ||
| R_2 | 189 | 0.99295 | 248.2308 | 2.78897 | |||
| R_3 | 127 | 0.99597 | 165.1538 | 3.10773 | |||
| G1 | G1_1 | 130 | 0.99559 | 172.5 | 2.93511 | ||
| G1_2 | 92 | 0.99698 | 126.5 | 2.22541 | |||
| G1_3 | 112 | 0.99648 | 146.3636 | 2.523160 | |||
| G2 | G2_1 | 106 | 0.99660 | 129.4 | 2.40532 | ||
| G2_2 | 96 | 0.99736 | 115.0909 | 2.25199 | |||
| G2_3 | 119 | 0.99509 | 180.75 | 2.59913 | |||
| DC | DC_1 | 134 | 0.99534 | 185.2308 | 2.49933 | ||
| DC_2 | 118 | 0.99547 | 163 | 2.06601 | |||
| DC_3 | 109 | 0.99723 | 120 | 2.82375 | |||
| D | D_1 | 165 | 0.99396 | 210.12 | 3.28698 | ||
| D_2 | 178 | 0.99245 | 266.5 | 3.32280 | |||
| D_3 | 166 | 0.99320 | 237.55 | 3.34855 | |||
| MB | MB_1 | 126 | 0.99660 | 140.04 | 2.89128 | ||
| MB_2 | 176 | 0.99358 | 217.129 | 3.06995 | |||
| MB_3 | 161 | 0.99383 | 217 | 2.82487 | |||
| CC | CC_1 | 199 | 0.99333 | 258.913 | 3.49072 | ||
| CC_2 | 131 | 0.99547 | 166 | 2.33934 | |||
| CC_3 | 142 | 0.99534 | 177.0526 | 2.91837 | |||