characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR19149278 of study SRP295918.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Ralstonia sp.

characteristic: organism

text: uncultured Ralstonia sp.

text: NextSeq 2000

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR19149278_bin.1_MetaWRAP_v1.3_MAG

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaspades v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: uncultured Burkholderia sp.

text: Metagenomes of the bacterial and viral constituents of the lower urinary tract.

characteristic: project name

characteristic: sample derived from

text: uncultured Burkholderia sp.

text: NextSeq 2000

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR19149278_bin.2_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR19149280 of study SRP295918.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Lactobacillus gasseri

characteristic: organism

text: Lactobacillus gasseri

text: NextSeq 2000

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus gasseri

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR19149280_bin.1_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Gardnerella vaginalis

characteristic: project name

characteristic: sample derived from

text: Gardnerella vaginalis

text: NextSeq 2000

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Gardnerella;s__Gardnerella vaginalis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR19149280_bin.2_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR19149281 of study SRP295918.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Lactobacillus jensenii

characteristic: organism

text: Lactobacillus jensenii

text: NextSeq 2000

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus jensenii

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR19149281_bin.1_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Lactobacillus iners

characteristic: project name

characteristic: sample derived from

text: Lactobacillus iners

text: NextSeq 2000

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus iners

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR19149281_bin.2_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR22733260 of study SRP295918.

text: urine

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

text: not provided

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Enterococcus faecalis

characteristic: organism

text: Enterococcus faecalis

text: NextSeq 2000

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__Enterococcus faecalis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR22733260_bin.1_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaspades v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

text: not provided

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: not provided

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Proteus mirabilis

characteristic: project name

characteristic: sample derived from

text: Proteus mirabilis

text: NextSeq 2000

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Morganellaceae;g__Proteus;s__Proteus mirabilis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR22733260_bin.2_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR22733261 of study SRP295918.

text: urine

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

text: not provided

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Staphylococcus epidermidis

characteristic: organism

text: Metagenomes of the bacterial and viral constituents of the lower urinary tract.

text: Staphylococcus epidermidis

text: NextSeq 2000

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus epidermidis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR22733261_bin.4_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798694 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Staphylococcus simulans

text: Community-acquired urinary tract infection (UTI) is among the most common bacterial infections. When a patient suffers 3 UTIs per year, it is defined as recurrent UTI (rUTI). Postmenopausal (PM) women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options after each episode. The majority of rUTIs develop in women with a history of UTI, suggesting that changes in the urogenital (UG) environment after UTI predispose women to rUTI. Although much is known about the microbiomes of the gut, skin and mouth, the urobiome is poorly understood. Here, we characterize the urobiome of PM women by metagenomic analysis of three human cohorts: 1) PM women with no UTI history (n=25), 2) remittent rUTI (recent history of rUTI but currently no UTI, n=25), and 3) relapsed rUTI (recent history of rUTI with current UTI, n=25). We have employed a hybrid approach, combining advanced urine culture with culture-independent shotgun metagenomic sequencing to generate an unbiased, metagenome-wide analysis of the taxonomic and functional genomic ecology of the PM urobiome in health and rUTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We find that there may be a robust protective commensal population within the urobiome of women who do not experience UTI, which is depleted or absent in patients with rUTI history. Integration of clinical metadata has detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). However, our data suggests that the modality of EHT may strongly affect urobiome Lactobacillus enrichment. We have used functional metagenomic profiling to identify microbial metabolic pathways, and antimicrobial resistance genes (ARGs) enriched between cohorts. Our data suggest distinct metabolic and ARG signatures of the urobiome between cohorts. When completed, this project will significantly advance our understanding of the relationship of the urobiome to rUTI pathogenesis and will lay the framework for future, targeted research endeavors towards the development of novel antibiotic and probiotic therapies for rUTI.

characteristic: project name

characteristic: sample derived from

text: Staphylococcus simulans

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus simulans

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798694_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Corynebacterium sp.

characteristic: organism

text: uncultured Corynebacterium sp.

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798694_bin.6_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798697 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Peptoniphilus harei

characteristic: project name

characteristic: sample derived from

text: Peptoniphilus harei

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus;s__Peptoniphilus harei

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798697_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Actinomycetaceae bacterium

characteristic: organism

text: uncultured Actinomycetaceae bacterium

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798697_bin.5_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798698 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Streptococcus agalactiae

characteristic: project name

characteristic: sample derived from

text: Streptococcus agalactiae

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus agalactiae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798698_bin.2_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798702 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Corynebacterium kroppenstedtii

characteristic: organism

text: Corynebacterium kroppenstedtii

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__Corynebacterium kroppenstedtii

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798702_bin.4_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798703 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Aerococcus urinae

text: Community-acquired urinary tract infection (UTI) is among the most common bacterial infections. When a patient suffers 3 UTIs per year, it is defined as recurrent UTI (rUTI). Postmenopausal (PM) women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options after each episode. The majority of rUTIs develop in women with a history of UTI, suggesting that changes in the urogenital (UG) environment after UTI predispose women to rUTI. Although much is known about the microbiomes of the gut, skin and mouth, the urobiome is poorly understood. Here, we characterize the urobiome of PM women by metagenomic analysis of three human cohorts: 1) PM women with no UTI history (n=25), 2) remittent rUTI (recent history of rUTI but currently no UTI, n=25), and 3) relapsed rUTI (recent history of rUTI with current UTI, n=25). We have employed a hybrid approach, combining advanced urine culture with culture-independent shotgun metagenomic sequencing to generate an unbiased, metagenome-wide analysis of the taxonomic and functional genomic ecology of the PM urobiome in health and rUTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We find that there may be a robust protective commensal population within the urobiome of women who do not experience UTI, which is depleted or absent in patients with rUTI history. Integration of clinical metadata has detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). However, our data suggests that the modality of EHT may strongly affect urobiome Lactobacillus enrichment. We have used functional metagenomic profiling to identify microbial metabolic pathways, and antimicrobial resistance genes (ARGs) enriched between cohorts. Our data suggest distinct metabolic and ARG signatures of the urobiome between cohorts. When completed, this project will significantly advance our understanding of the relationship of the urobiome to rUTI pathogenesis and will lay the framework for future, targeted research endeavors towards the development of novel antibiotic and probiotic therapies for rUTI.

characteristic: project name

characteristic: sample derived from

text: Aerococcus urinae

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus;s__Aerococcus urinae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798703_bin.14_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Schaalia turicensis

characteristic: organism

text: Schaalia turicensis

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Schaalia;s__Schaalia turicensis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798703_bin.2_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Gardnerella vaginalis

characteristic: project name

characteristic: sample derived from

text: Gardnerella vaginalis

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Gardnerella;s__Gardnerella vaginalis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798703_bin.7_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Peptoniphilus duerdenii

characteristic: organism

text: Peptoniphilus duerdenii

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus;s__Peptoniphilus duerdenii

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798703_bin.9_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798707 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Escherichia coli

characteristic: project name

characteristic: sample derived from

text: Escherichia coli

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798707_bin.1_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798708 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Ezakiella coagulans

characteristic: organism

text: Ezakiella coagulans

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__;f__;g__Ezakiella;s__Ezakiella coagulans

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798708_bin.1_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798709 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Prevotella disiens

text: Community-acquired urinary tract infection (UTI) is among the most common bacterial infections. When a patient suffers 3 UTIs per year, it is defined as recurrent UTI (rUTI). Postmenopausal (PM) women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options after each episode. The majority of rUTIs develop in women with a history of UTI, suggesting that changes in the urogenital (UG) environment after UTI predispose women to rUTI. Although much is known about the microbiomes of the gut, skin and mouth, the urobiome is poorly understood. Here, we characterize the urobiome of PM women by metagenomic analysis of three human cohorts: 1) PM women with no UTI history (n=25), 2) remittent rUTI (recent history of rUTI but currently no UTI, n=25), and 3) relapsed rUTI (recent history of rUTI with current UTI, n=25). We have employed a hybrid approach, combining advanced urine culture with culture-independent shotgun metagenomic sequencing to generate an unbiased, metagenome-wide analysis of the taxonomic and functional genomic ecology of the PM urobiome in health and rUTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We find that there may be a robust protective commensal population within the urobiome of women who do not experience UTI, which is depleted or absent in patients with rUTI history. Integration of clinical metadata has detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). However, our data suggests that the modality of EHT may strongly affect urobiome Lactobacillus enrichment. We have used functional metagenomic profiling to identify microbial metabolic pathways, and antimicrobial resistance genes (ARGs) enriched between cohorts. Our data suggest distinct metabolic and ARG signatures of the urobiome between cohorts. When completed, this project will significantly advance our understanding of the relationship of the urobiome to rUTI pathogenesis and will lay the framework for future, targeted research endeavors towards the development of novel antibiotic and probiotic therapies for rUTI.

characteristic: project name

characteristic: sample derived from

text: Prevotella disiens

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__Prevotella disiens

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798709_bin.2_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798710 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Lactobacillus iners

characteristic: organism

text: Lactobacillus iners

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus iners

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798710_bin.7_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798713 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Allobacillus halotolerans

characteristic: project name

characteristic: sample derived from

text: Allobacillus halotolerans

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Allobacillus;s__Allobacillus halotolerans

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798713_bin.1_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798714 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Campylobacter ureolyticus

characteristic: organism

text: Campylobacter ureolyticus

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter;s__Campylobacter ureolyticus

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798714_bin.10_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: uncultured Actinomyces sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Actinomyces sp.

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798714_bin.13_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Bifidobacterium scardovii

characteristic: organism

text: Bifidobacterium scardovii

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium scardovii

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798714_bin.14_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Aerococcus sanguinicola

text: Community-acquired urinary tract infection (UTI) is among the most common bacterial infections. When a patient suffers 3 UTIs per year, it is defined as recurrent UTI (rUTI). Postmenopausal (PM) women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options after each episode. The majority of rUTIs develop in women with a history of UTI, suggesting that changes in the urogenital (UG) environment after UTI predispose women to rUTI. Although much is known about the microbiomes of the gut, skin and mouth, the urobiome is poorly understood. Here, we characterize the urobiome of PM women by metagenomic analysis of three human cohorts: 1) PM women with no UTI history (n=25), 2) remittent rUTI (recent history of rUTI but currently no UTI, n=25), and 3) relapsed rUTI (recent history of rUTI with current UTI, n=25). We have employed a hybrid approach, combining advanced urine culture with culture-independent shotgun metagenomic sequencing to generate an unbiased, metagenome-wide analysis of the taxonomic and functional genomic ecology of the PM urobiome in health and rUTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We find that there may be a robust protective commensal population within the urobiome of women who do not experience UTI, which is depleted or absent in patients with rUTI history. Integration of clinical metadata has detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). However, our data suggests that the modality of EHT may strongly affect urobiome Lactobacillus enrichment. We have used functional metagenomic profiling to identify microbial metabolic pathways, and antimicrobial resistance genes (ARGs) enriched between cohorts. Our data suggest distinct metabolic and ARG signatures of the urobiome between cohorts. When completed, this project will significantly advance our understanding of the relationship of the urobiome to rUTI pathogenesis and will lay the framework for future, targeted research endeavors towards the development of novel antibiotic and probiotic therapies for rUTI.

characteristic: project name

characteristic: sample derived from

text: Aerococcus sanguinicola

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus;s__Aerococcus sanguinicola

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798714_bin.2_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Anaerococcus sp.

characteristic: organism

text: uncultured Anaerococcus sp.

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798714_bin.20_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Fastidiosipila sanguinis

characteristic: project name

characteristic: sample derived from

text: Fastidiosipila sanguinis

text: NextSeq 500

characteristic: sequencing method

text: 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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798714_bin.6_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Helcococcus sp.

characteristic: organism

text: uncultured Helcococcus sp.

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798714_bin.8_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798714 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: uncultured Anaerococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Anaerococcus sp.

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798714_bin.9_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798717 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798717_bin.1_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798718 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Aerococcus urinae

characteristic: project name

characteristic: sample derived from

text: Aerococcus urinae

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus;s__Aerococcus urinae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798718_bin.3_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798720 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Eubacteriales bacterium

characteristic: organism

text: Community-acquired urinary tract infection (UTI) is among the most common bacterial infections. When a patient suffers 3 UTIs per year, it is defined as recurrent UTI (rUTI). Postmenopausal (PM) women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options after each episode. The majority of rUTIs develop in women with a history of UTI, suggesting that changes in the urogenital (UG) environment after UTI predispose women to rUTI. Although much is known about the microbiomes of the gut, skin and mouth, the urobiome is poorly understood. Here, we characterize the urobiome of PM women by metagenomic analysis of three human cohorts: 1) PM women with no UTI history (n=25), 2) remittent rUTI (recent history of rUTI but currently no UTI, n=25), and 3) relapsed rUTI (recent history of rUTI with current UTI, n=25). We have employed a hybrid approach, combining advanced urine culture with culture-independent shotgun metagenomic sequencing to generate an unbiased, metagenome-wide analysis of the taxonomic and functional genomic ecology of the PM urobiome in health and rUTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We find that there may be a robust protective commensal population within the urobiome of women who do not experience UTI, which is depleted or absent in patients with rUTI history. Integration of clinical metadata has detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). However, our data suggests that the modality of EHT may strongly affect urobiome Lactobacillus enrichment. We have used functional metagenomic profiling to identify microbial metabolic pathways, and antimicrobial resistance genes (ARGs) enriched between cohorts. Our data suggest distinct metabolic and ARG signatures of the urobiome between cohorts. When completed, this project will significantly advance our understanding of the relationship of the urobiome to rUTI pathogenesis and will lay the framework for future, targeted research endeavors towards the development of novel antibiotic and probiotic therapies for rUTI.

text: uncultured Eubacteriales bacterium

text: NextSeq 500

text: 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__;g__;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798720_bin.10_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Klebsiella oxytoca

characteristic: project name

characteristic: sample derived from

text: Klebsiella oxytoca

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella oxytoca

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798720_bin.11_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Propionimicrobium sp.

characteristic: organism

text: uncultured Propionimicrobium sp.

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionimicrobium;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798720_bin.13_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: uncultured Ezakiella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Ezakiella sp.

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__;f__;g__Ezakiella;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798720_bin.15_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Porphyromonas sp.

characteristic: organism

text: uncultured Porphyromonas sp.

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798720_bin.18_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Corynebacterium riegelii

characteristic: project name

characteristic: sample derived from

text: Corynebacterium riegelii

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__Corynebacterium riegelii

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798720_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798721 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Actinotignum schaalii

characteristic: organism

text: Actinotignum schaalii

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum;s__Actinotignum schaalii

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798721_bin.2_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Propionimicrobium lymphophilum

text: Community-acquired urinary tract infection (UTI) is among the most common bacterial infections. When a patient suffers 3 UTIs per year, it is defined as recurrent UTI (rUTI). Postmenopausal (PM) women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options after each episode. The majority of rUTIs develop in women with a history of UTI, suggesting that changes in the urogenital (UG) environment after UTI predispose women to rUTI. Although much is known about the microbiomes of the gut, skin and mouth, the urobiome is poorly understood. Here, we characterize the urobiome of PM women by metagenomic analysis of three human cohorts: 1) PM women with no UTI history (n=25), 2) remittent rUTI (recent history of rUTI but currently no UTI, n=25), and 3) relapsed rUTI (recent history of rUTI with current UTI, n=25). We have employed a hybrid approach, combining advanced urine culture with culture-independent shotgun metagenomic sequencing to generate an unbiased, metagenome-wide analysis of the taxonomic and functional genomic ecology of the PM urobiome in health and rUTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We find that there may be a robust protective commensal population within the urobiome of women who do not experience UTI, which is depleted or absent in patients with rUTI history. Integration of clinical metadata has detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). However, our data suggests that the modality of EHT may strongly affect urobiome Lactobacillus enrichment. We have used functional metagenomic profiling to identify microbial metabolic pathways, and antimicrobial resistance genes (ARGs) enriched between cohorts. Our data suggest distinct metabolic and ARG signatures of the urobiome between cohorts. When completed, this project will significantly advance our understanding of the relationship of the urobiome to rUTI pathogenesis and will lay the framework for future, targeted research endeavors towards the development of novel antibiotic and probiotic therapies for rUTI.

characteristic: project name

characteristic: sample derived from

text: Propionimicrobium lymphophilum

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionimicrobium;s__Propionimicrobium lymphophilum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798721_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798722 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Campylobacter ureolyticus

characteristic: organism

text: Campylobacter ureolyticus

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter;s__Campylobacter ureolyticus

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798722_bin.4_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Actinotignum sanguinis

characteristic: project name

characteristic: sample derived from

text: Actinotignum sanguinis

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum;s__Actinotignum sanguinis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798722_bin.6_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798724 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Imtechella halotolerans

characteristic: organism

text: Imtechella halotolerans

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae;g__Imtechella;s__Imtechella halotolerans

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798724_bin.2_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Corynebacterium striatum

characteristic: project name

characteristic: sample derived from

text: Corynebacterium striatum

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__Corynebacterium striatum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798724_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798728 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Porphyromonas uenonis

characteristic: organism

text: Porphyromonas uenonis

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas;s__Porphyromonas uenonis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798728_bin.12_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Actinotignum sanguinis

text: Community-acquired urinary tract infection (UTI) is among the most common bacterial infections. When a patient suffers 3 UTIs per year, it is defined as recurrent UTI (rUTI). Postmenopausal (PM) women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options after each episode. The majority of rUTIs develop in women with a history of UTI, suggesting that changes in the urogenital (UG) environment after UTI predispose women to rUTI. Although much is known about the microbiomes of the gut, skin and mouth, the urobiome is poorly understood. Here, we characterize the urobiome of PM women by metagenomic analysis of three human cohorts: 1) PM women with no UTI history (n=25), 2) remittent rUTI (recent history of rUTI but currently no UTI, n=25), and 3) relapsed rUTI (recent history of rUTI with current UTI, n=25). We have employed a hybrid approach, combining advanced urine culture with culture-independent shotgun metagenomic sequencing to generate an unbiased, metagenome-wide analysis of the taxonomic and functional genomic ecology of the PM urobiome in health and rUTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We find that there may be a robust protective commensal population within the urobiome of women who do not experience UTI, which is depleted or absent in patients with rUTI history. Integration of clinical metadata has detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). However, our data suggests that the modality of EHT may strongly affect urobiome Lactobacillus enrichment. We have used functional metagenomic profiling to identify microbial metabolic pathways, and antimicrobial resistance genes (ARGs) enriched between cohorts. Our data suggest distinct metabolic and ARG signatures of the urobiome between cohorts. When completed, this project will significantly advance our understanding of the relationship of the urobiome to rUTI pathogenesis and will lay the framework for future, targeted research endeavors towards the development of novel antibiotic and probiotic therapies for rUTI.

characteristic: project name

characteristic: sample derived from

text: Actinotignum sanguinis

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798728_bin.16_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Finegoldia magna

characteristic: organism

text: Finegoldia magna

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia;s__Finegoldia magna

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798728_bin.3_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Prevotella bivia

characteristic: project name

characteristic: sample derived from

text: Prevotella bivia

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__Prevotella bivia

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798728_bin.9_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798731 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Anaerococcus sp.

characteristic: organism

text: uncultured Anaerococcus sp.

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Tissierellia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798731_bin.4_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: uncultured Corynebacterium sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Corynebacterium sp.

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798731_bin.5_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Ureaplasma parvum

characteristic: organism

text: Ureaplasma parvum

text: NextSeq 500

text: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Tenericutes;c__Mollicutes;o__Mycoplasmatales;f__Mycoplasmataceae;g__Ureaplasma;s__Ureaplasma parvum

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798731_bin.7_MetaWRAP_v1.3_MAG

characteristic: title