Table 1.
Description of six MAG datasets used in this study.
| Dataset name | Number of genomesa | Taxonomic annotation | Assembly | Binning | Quality check | Reference |
|---|---|---|---|---|---|---|
| Seawater MAGs | Short-read: 47,120 | GTDB-Tk v1.3.0 | MEGAHIT v1.1.4 |
MaxBin v2.2.6 MetaBAT v2.12.1 CONCOCT v1.0.0 Ensembled using MetaWRAP v1.2.1 |
CheckM v1.0.13 | [7] |
| Human gut MAGs | Short-read: 90,301 | GTDB-Tk v2.1.0b | MEGAHIT v1.1.3 |
MaxBin v2.2.4 MetaBAT v2.12.1 MetaBAT1 Ensembled using MetaWRAP v1.0 |
CheckM v1.0.7 | [8] |
| Chicken gut MAGs | Short-read: 12,232 | GTDB-Tk; version not disclosed | MEGAHIT v1.1.3 |
MaxBin v2.2.6 MetaBAT v2.12.1 CONCOCT v1.1.0 Ensembled using MetaWRAP v1.2.1 |
CheckM v1.0.12 | [19] |
| Rice phyllosphere MAGs | Short-read: 503 | GTDB-Tk v1.4.1 | MEGAHIT; version not disclosed |
MaxBin v2.2.7 MetaBAT v2.12.1 Vamb v3.0.2 Ensembled using DASTool v1.1.1 |
CheckM v1.0.13 | [20] |
| Genomic catalog of Earth’s Microbiomes (GEM) |
Short-read: 45,695 Long-read or hybrid: 369 |
GTDB-Tk; version not disclosed | Not standardized | MetaBAT v0.32.4/5 | CheckM v1.0.11 | [21] |
| Wastewater long-read MAGs | Hybrid: 1080 | GTDB-Tk v1.0.2 | CANU v1.8 |
MetaBAT v2.12.1 MaxBin v2.2.7 Ensembled using DASTool v1.1.1 |
CheckM v1.0.11 | [22] |
aNumber of bacterial MAGs.
bAnnotated in this study.