| broad-scale environmental context | Pig digestive system |
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| collection date | not provided |
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| environmental medium | Feces |
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| geographic location | China |
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| investigation type | metagenome-assembled genome |
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| isolation source | pig gut metagenome |
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| project name | Lipid accumulation and high oxidative stress has become a serious health and economic problem in pig production. Fatness traits are very important in pig production since they are closely related to meat quality. Gut microbiome is generally recognized as a factor in fat deposition. However, the linkage of gut microbiota with fat accumulation in pigs remains elusive. To investigate the association among gut microbiome, lipogenic characteristics, and oxidative stress in Jinhua pigs, we selected 5 high-fat pigs and 5 low-fat pigs from 60 250-day-old Jinhua pigs in the present study and collected colon contents for metagenomic analysis, serum samples for the oxidative stress assay, and liver and abdominal fat tissues for RT-qPCR analysis.Collectively, this study would give a deep insight into how gut microbiome influence fat deposition in Jinhua pigs and would give a hint for improving growth performance and fatness traits by manipulating gut microbiome. |
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| sample name | SRR15725430_bin.17_metaWRAP_v1.3_MAG |
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| ENA-CHECKLIST | ERC000047 |
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| ENA-FIRST-PUBLIC | 2022-07-28 |
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| ENA-LAST-UPDATE | 2022-07-28 |
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| External Id | SAMEA110426385 |
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| INSDC center alias | EMG |
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| INSDC center name | EMG |
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| INSDC first public | 2022-07-28T16:25:47Z |
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| INSDC last update | 2022-07-28T16:25:47Z |
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| INSDC status | public |
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| Submitter Id | SRR15725430_bin.17_metaWRAP_v1.3_MAG |
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| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics |
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| assembly software | metaSPAdes v3.15.3 |
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| binning parameters | MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. |
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| binning software | metaWRAP v1.3 |
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| broker name | EMG broker account, EMBL-EBI |
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| completeness score | 73.72 |
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| completeness software | CheckM |
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| contamination score | 0.68 |
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| geographic location (latitude) | 29.12 |
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| geographic location (longitude) | 119.64 |
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| local environmental context | Intestine |
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| metagenomic source | pig gut metagenome |
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| sample derived from | SAMN21220124 |
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| sequencing method | Illumina HiSeq 2500 |
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| taxonomic classification | The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Subdoligranulum;s__Subdoligranulum variabile |
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| taxonomic identity marker | multi-marker approach |
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