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 Eubacteriales bacterium

characteristic: organism

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: SRR17798750_bin.19_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

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798750 of study SRP357142.

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 Corynebacterium sp.

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: 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: SRR17798750_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: Staphylococcus hominis

characteristic: organism

text: Staphylococcus hominis

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__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus hominis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798750_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: 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: Staphylococcus epidermidis

characteristic: project name

characteristic: sample derived from

text: Staphylococcus epidermidis

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 epidermidis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798750_bin.23_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: Corynebacterium haemomassiliense

characteristic: organism

text: Corynebacterium haemomassiliense

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 haemomassiliense

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798750_bin.24_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: Facklamia hominis

characteristic: project name

characteristic: sample derived from

text: Facklamia hominis

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__Facklamia;s__Facklamia hominis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798750_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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Dialister invisus

characteristic: organism

text: Dialister invisus

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__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Dialister;s__Dialister invisus

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798750_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 Peptoniphilaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Peptoniphilaceae bacterium

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__Lagierella;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798750_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

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

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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Peptoniphilus grossensis

characteristic: organism

text: Peptoniphilus grossensis

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 grossensis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798750_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 SRR17798750 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: Lactobacillus crispatus

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: Lactobacillus crispatus

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__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus crispatus

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798750_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

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 harei

characteristic: organism

text: Peptoniphilus harei

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 harei

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798750_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: 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 SRR17798751 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: Brevibacterium ravenspurgense

characteristic: project name

characteristic: sample derived from

text: Brevibacterium ravenspurgense

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__Micrococcales;f__Brevibacteriaceae;g__Brevibacterium;s__Brevibacterium ravenspurgense

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798751_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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Corynebacterium imitans

characteristic: organism

text: Corynebacterium imitans

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 imitans

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798751_bin.11_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 Anaerococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Anaerococcus 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__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798751_bin.12_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: Streptococcus oralis

characteristic: organism

text: Streptococcus oralis

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__Streptococcaceae;g__Streptococcus;s__Streptococcus oralis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798751_bin.17_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: Sneathia sanguinegens

characteristic: project name

characteristic: sample derived from

text: Sneathia sanguinegens

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__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Sneathia;s__Sneathia sanguinegens

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798751_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: uncultured Corynebacterium sp.

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 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: SRR17798751_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 SRR17798752 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 Coprobacillus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Coprobacillus 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__Erysipelotrichia;o__Erysipelotrichales;f__Coprobacillaceae;g__Coprobacillus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798752_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 Subdoligranulum sp.

characteristic: organism

text: uncultured Subdoligranulum 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__Clostridia;o__Eubacteriales;f__Oscillospiraceae;g__Subdoligranulum;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798752_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: uncultured Collinsella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Collinsella 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__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798752_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: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798755 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: SRR17798755_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: 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: uncultured Fastidiosipila sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Fastidiosipila 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__Clostridia;o__Eubacteriales;f__Oscillospiraceae;g__Fastidiosipila;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798755_bin.18_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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Aerococcus urinae

characteristic: organism

text: Aerococcus urinae

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__Aerococcaceae;g__Aerococcus;s__Aerococcus urinae

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798755_bin.19_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 Prevotella sp.

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: uncultured Prevotella 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__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798755_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: Varibaculum massiliense

characteristic: organism

text: Varibaculum massiliense

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__Varibaculum;s__Varibaculum massiliense

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798755_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: 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: Actinobaculum massiliense

characteristic: project name

characteristic: sample derived from

text: Actinobaculum massiliense

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__Actinobaculum;s__Actinobaculum massiliense

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798755_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 SRR17798756 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 Mobiluncus sp.

characteristic: organism

text: uncultured Mobiluncus 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__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798756_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: Corynebacterium pyruviciproducens

characteristic: project name

characteristic: sample derived from

text: Corynebacterium pyruviciproducens

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 pyruviciproducens

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798756_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

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: SRR17798756_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: 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 SRR17798757 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 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: SRR17798757_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: uncultured Anaerococcus sp.

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 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: SRR17798757_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: 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 SRR17798758 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 Propionimicrobium sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Propionimicrobium 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__Propionibacteriales;f__Propionibacteriaceae;g__Propionimicrobium;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798758_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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Peptoniphilus coxii

characteristic: organism

text: Peptoniphilus coxii

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 coxii

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798758_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 Dialister sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Dialister 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__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Dialister;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798758_bin.12_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 Anaerococcus sp.

characteristic: organism

text: uncultured Anaerococcus sp.

text: NextSeq 500

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798758_bin.17_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 Actinomycetaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Actinomycetaceae bacterium

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__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798758_bin.19_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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Gardnerella vaginalis

characteristic: organism

text: Gardnerella vaginalis

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__Gardnerella;s__Gardnerella vaginalis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798758_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: 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 SRR17798759 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: Bifidobacterium longum

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: Bifidobacterium longum

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__Bifidobacterium;s__Bifidobacterium longum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798759_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: Streptococcus anginosus

characteristic: organism

text: Streptococcus anginosus

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__Streptococcaceae;g__Streptococcus;s__Streptococcus anginosus

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798759_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 SRR17798760 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: Bifidobacterium dentium

characteristic: project name

characteristic: sample derived from

text: Bifidobacterium dentium

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__Bifidobacterium;s__Bifidobacterium dentium

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798760_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 SRR17798761 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 Mobiluncus sp.

characteristic: organism

text: uncultured Mobiluncus 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__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798761_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: uncultured Anaerococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Anaerococcus 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__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798761_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

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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Aerococcus sp.

characteristic: organism

text: uncultured Aerococcus 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__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798761_bin.15_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 Streptococcus sp.

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: uncultured Streptococcus 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__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798761_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 Streptococcus sp.

characteristic: organism

text: uncultured Streptococcus sp.

text: NextSeq 500

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798761_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: 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 SRR17798763 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: Lactobacillus gasseri

characteristic: project name

characteristic: sample derived from

text: Lactobacillus gasseri

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__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus gasseri

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798763_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: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Limosilactobacillus vaginalis

characteristic: organism

text: Limosilactobacillus vaginalis

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__Limosilactobacillus;s__Limosilactobacillus vaginalis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798763_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

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798766 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: Corynebacterium aurimucosum

characteristic: project name

characteristic: sample derived from

text: Corynebacterium aurimucosum

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 aurimucosum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798766_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

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 SRR17798767 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 Megasphaera sp.

characteristic: organism

text: uncultured Megasphaera 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__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Megasphaera;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798767_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: 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: SRR17798767_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

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 SRR17798768 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 bennonis

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: Porphyromonas bennonis

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 bennonis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798768_bin.11_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 Corynebacteriales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Corynebacteriales bacterium

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__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798768_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: Varibaculum cambriense

characteristic: organism

text: Varibaculum cambriense

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__Varibaculum;s__Varibaculum cambriense

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798768_bin.5_MetaWRAP_v1.3_MAG

characteristic: title