broad-scale environmental context | human excretory system |
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collection date | 2013-03-27 |
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environmental medium | urine |
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geographic location | not provided |
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investigation type | metagenome-assembled genome |
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isolation source | urine metagenome |
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project name | Urinary tract infection is thought to result from the growth of a limited number of uropathogenic organisms in an otherwise sterile environment. We revisited this concept by analyzing clean-catch urine samples representing a spectrum of clinical laboratory profiles. Whole genome shotgun sequencing was served to described the microbial metagenome. Infection was associated with dominant organisms in the metagenome as well as novel potential pathogens that are difficult to grow in routine cultures. |
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sample name | SRR5535749_bin.3_MetaWRAP_v1.3_MAG |
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ENA-CHECKLIST | ERC000047 |
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INSDC center name | EMG |
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Submitter Id | SRR5535749_bin.3_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 | EBI-EMG |
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completeness score | 80.5 |
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completeness software | CheckM |
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contamination score | 0.0 |
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geographic location (latitude) | not provided |
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geographic location (longitude) | not provided |
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local environmental context | urethra |
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metagenomic source | urine metagenome |
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sample derived from | SAMN06899163 |
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scientific_name | Fastidiosipila sanguinis |
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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__Eubacteriales;f__Oscillospiraceae;g__Fastidiosipila;s__Fastidiosipila sanguinis |
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taxonomic identity marker | multi-marker approach |
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