Uncovering the Fecal Bacterial Communities of Sympatric Sika Deer (Cervus nippon) and Wapiti (Cervus canadensis)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. DNA Extraction and Sequencing
2.2. Quality Control of the Raw Sequences
2.3. OTU Clustering and Species Classification Analysis
2.4. Complexity Analysis
2.5. Comparative Analysis
3. Results
3.1. Sequence Data Processing
3.2. OTU Clustering and Species Annotation
3.3. Distribution of Fecal Microbiota
3.4. Alpha Diversity
3.5. Beta Diversity
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample Name | Species | Sex | Raw PE | Raw Tags | Effective Tags | Base (nt) | Q20 (%) |
---|---|---|---|---|---|---|---|
CE.F1 | Wapiti | Female | 215,245 | 141,222 | 134,475 | 60,715,588 | 97.58 |
CE.F2 | Wapiti | Female | 312,835 | 198,233 | 187,510 | 84,818,640 | 97.52 |
CE.F3 | Wapiti | Female | 166,116 | 90,359 | 84,310 | 38,127,557 | 97.19 |
CE.M1 | Wapiti | Male | 405,347 | 259,034 | 243,872 | 110,341,845 | 97.53 |
CE.M2 | Wapiti | Male | 259,462 | 161,632 | 152,476 | 68,796,462 | 97.5 |
CE.M3 | Wapiti | Male | 372,031 | 231,191 | 216,808 | 98,053,905 | 97.53 |
CE.M4 | Wapiti | Male | 253,677 | 164,855 | 156,897 | 70,878,325 | 97.56 |
CN.F1 | Sika | Female | 262,154 | 169,901 | 158,383 | 71,622,503 | 97.6 |
CN.F2 | Sika | Female | 268,349 | 157,103 | 149,495 | 67,308,187 | 97.43 |
CN.F3 | Sika | Female | 182,780 | 91,628 | 85,071 | 38,336,278 | 97.14 |
CN.F4 | Sika | Female | 223,971 | 128,275 | 116,926 | 52,878,708 | 97.28 |
CN.F5 | Sika | Female | 127,220 | 66,761 | 62,767 | 28,159,699 | 97.12 |
CN.M1 | Sika | Male | 133,959 | 69,757 | 64,502 | 29,144,342 | 97.15 |
CN.M2 | Sika | Male | 162,926 | 89,577 | 82,270 | 37,163,066 | 97.2 |
Sample | Species | Sex | Observed_Species | Shannon | Simpson | Chao1 | ACE | Goods_Coverage |
---|---|---|---|---|---|---|---|---|
CN.F1 | Wapiti | Female | 1084 | 7.974 | 0.991 | 1148.024 | 1156.249 | 0.998 |
CN.F2 | Wapiti | Female | 970 | 7.703 | 0.99 | 1044.882 | 1059.369 | 0.998 |
CN.F3 | Wapiti | Female | 1046 | 8.227 | 0.993 | 1100.301 | 1103.797 | 0.998 |
CN.F4 | Wapiti | Male | 1087 | 7.675 | 0.986 | 1190.5 | 1195.605 | 0.997 |
CN.F5 | Wapiti | Male | 1202 | 8.526 | 0.994 | 1251.5 | 1249.636 | 0.998 |
CN.M1 | Wapiti | Male | 1160 | 8.172 | 0.992 | 1294.384 | 1287.833 | 0.997 |
CN.M2 | Wapiti | Male | 1060 | 7.686 | 0.986 | 1113.509 | 1118.624 | 0.998 |
CE.F1 | Sika | Female | 1255 | 8.313 | 0.993 | 1325.522 | 1334.977 | 0.998 |
CE.F2 | Sika | Female | 1233 | 8.168 | 0.992 | 1365.026 | 1340.944 | 0.997 |
CE.F3 | Sika | Female | 1170 | 8.053 | 0.99 | 1232.046 | 1236.775 | 0.998 |
CE.M1 | Sika | Female | 1240 | 8.201 | 0.993 | 1390.976 | 1369.852 | 0.997 |
CE.M2 | Sika | Female | 1263 | 8.408 | 0.993 | 1322.049 | 1335.561 | 0.998 |
CE.M3 | Sika | Male | 1245 | 8.328 | 0.993 | 1319.773 | 1321.592 | 0.998 |
CE.M4 | Sika | Male | 1210 | 8.27 | 0.993 | 1331.454 | 1298.882 | 0.997 |
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Yan, J.; Wu, X.; Wang, X.; Shang, Y.; Zhang, H. Uncovering the Fecal Bacterial Communities of Sympatric Sika Deer (Cervus nippon) and Wapiti (Cervus canadensis). Animals 2022, 12, 2468. https://doi.org/10.3390/ani12182468
Yan J, Wu X, Wang X, Shang Y, Zhang H. Uncovering the Fecal Bacterial Communities of Sympatric Sika Deer (Cervus nippon) and Wapiti (Cervus canadensis). Animals. 2022; 12(18):2468. https://doi.org/10.3390/ani12182468
Chicago/Turabian StyleYan, Jiakuo, Xiaoyang Wu, Xibao Wang, Yongquan Shang, and Honghai Zhang. 2022. "Uncovering the Fecal Bacterial Communities of Sympatric Sika Deer (Cervus nippon) and Wapiti (Cervus canadensis)" Animals 12, no. 18: 2468. https://doi.org/10.3390/ani12182468
APA StyleYan, J., Wu, X., Wang, X., Shang, Y., & Zhang, H. (2022). Uncovering the Fecal Bacterial Communities of Sympatric Sika Deer (Cervus nippon) and Wapiti (Cervus canadensis). Animals, 12(18), 2468. https://doi.org/10.3390/ani12182468