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 SRR17798732 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 Eubacteriales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Eubacteriales 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__Clostridia;o__Eubacteriales;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798732_bin.1_MetaWRAP_v1.3_MAG


status: PUBLIC

tag: attribute

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)

unit: DD

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Hoylesella timonensis

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: Hoylesella timonensis

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__Prevotellaceae;g__Prevotella;s__Prevotella timonensis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798732_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

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 Bradyrhizobium sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Bradyrhizobium 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__Proteobacteria;c__Alphaproteobacteria;o__Hyphomicrobiales;f__Bradyrhizobiaceae;g__Bradyrhizobium;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798732_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 lacrimalis

characteristic: organism

text: Peptoniphilus lacrimalis

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 lacrimalis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798732_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 SRR17798734 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Staphylococcus haemolyticus

characteristic: project name

characteristic: sample derived from

text: Staphylococcus haemolyticus

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 haemolyticus

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798734_bin.17_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 Facklamia sp.

characteristic: organism

text: uncultured Facklamia 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__Facklamia;s__Facklamia ignava

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798734_bin.2_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: 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: SRR17798734_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: Facklamia hominis

characteristic: organism

text: Facklamia 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__Lactobacillales;f__Aerococcaceae;g__Facklamia;s__Facklamia hominis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798734_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: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaspades v3.15.3

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

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798734_bin.8_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 Varibaculum 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 Varibaculum 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__Varibaculum;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798734_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 SRR17798735 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: Alloscardovia omnicolens

characteristic: project name

characteristic: sample derived from

text: Alloscardovia omnicolens

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__Alloscardovia;s__Alloscardovia omnicolens

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798735_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798737 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: Facklamia languida

characteristic: organism

text: Facklamia languida

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__Facklamia;s__Facklamia languida

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798737_bin.12_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Corynebacterium glucuronolyticum

characteristic: project name

characteristic: sample derived from

text: Corynebacterium glucuronolyticum

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 glucuronolyticum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798737_bin.13_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Corynebacterium sp.

characteristic: organism

text: uncultured Corynebacterium sp.

text: NextSeq 500

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

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798737_bin.2_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Hoylesella timonensis

characteristic: project name

characteristic: sample derived from

text: Hoylesella timonensis

text: NextSeq 500

characteristic: sequencing method

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798737_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: Streptococcus parasanguinis

characteristic: organism

text: Streptococcus parasanguinis

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 parasanguinis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798737_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

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: Trueperella bernardiae

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: Trueperella bernardiae

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__Trueperella;s__Trueperella bernardiae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798737_bin.9_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798738 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 Micrococcaceae bacterium

characteristic: organism

text: uncultured Micrococcaceae bacterium

text: NextSeq 500

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

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798738_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: uncultured Arthrobacter sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Arthrobacter 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__Micrococcales;f__Micrococcaceae;g__Arthrobacter;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798738_bin.10_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 Brevibacterium sp.

characteristic: organism

text: uncultured Brevibacterium 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__Micrococcales;f__Brevibacteriaceae;g__Brevibacterium;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798738_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: Corynebacterium tuscaniense

characteristic: project name

characteristic: sample derived from

text: Corynebacterium tuscaniense

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 tuscaniense

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798738_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Corynebacterium sp.

characteristic: organism

text: uncultured Corynebacterium sp.

text: NextSeq 500

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

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798738_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: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaspades v3.15.3

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

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

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: Fannyhessea vaginae

characteristic: project name

characteristic: sample derived from

text: Fannyhessea vaginae

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__Fannyhessea;s__Fannyhessea vaginae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798738_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 Gulosibacter 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 Gulosibacter 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__Micrococcales;f__Microbacteriaceae;g__Gulosibacter;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798738_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 SRR17798738 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Aerococcus christensenii

characteristic: project name

characteristic: sample derived from

text: Aerococcus christensenii

text: NextSeq 500

characteristic: sequencing method

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798738_bin.9_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798739 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: Enterococcus faecalis

characteristic: organism

text: Enterococcus faecalis

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__Enterococcaceae;g__Enterococcus;s__Enterococcus faecalis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798739_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: Bifidobacterium breve

characteristic: project name

characteristic: sample derived from

text: Bifidobacterium breve

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 breve

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798739_bin.4_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798740 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Actinotignum timonense

characteristic: organism

text: Actinotignum timonense

text: NextSeq 500

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

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798740_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: 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 SRR17798741 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 jensenii

characteristic: project name

characteristic: sample derived from

text: Lactobacillus jensenii

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 jensenii

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798741_bin.13_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Levyella massiliensis

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: Levyella massiliensis

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__Levyella;s__Levyella massiliensis

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798741_bin.16_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: SRR17798741_bin.22_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: 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: SRR17798741_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

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: Anaerococcus hydrogenalis

characteristic: project name

characteristic: sample derived from

text: Anaerococcus hydrogenalis

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__Anaerococcus hydrogenalis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798741_bin.8_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: Prevotella histicola

characteristic: organism

text: Prevotella histicola

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__Prevotellaceae;g__Prevotella;s__Prevotella histicola

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798741_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 SRR17798742 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: uncultured Anaerococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Anaerococcus sp.

text: NextSeq 500

characteristic: sequencing method

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: SRR17798742_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: Campylobacter ureolyticus

characteristic: organism

text: Campylobacter ureolyticus

text: NextSeq 500

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

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798742_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

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: Hallella colorans

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: Hallella colorans

text: NextSeq 500

characteristic: sequencing method

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798742_bin.8_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 SRR17798743 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 Streptococcus sp.

characteristic: organism

text: uncultured Streptococcus 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__Streptococcaceae;g__Streptococcus;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798743_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: Anaerococcus prevotii

characteristic: project name

characteristic: sample derived from

text: Anaerococcus prevotii

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__Anaerococcus prevotii

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798743_bin.9_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798744 of study SRP357142.

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: Lactobacillus delbrueckii

characteristic: organism

text: Lactobacillus delbrueckii

text: NextSeq 500

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

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798744_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: 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: SRR17798744_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

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 SRR17798746 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: 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: SRR17798746_bin.5_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

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

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798747 of study SRP357142.

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Prevotella corporis

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

characteristic: project name

characteristic: sample derived from

text: Prevotella corporis

text: NextSeq 500

characteristic: sequencing method

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798747_bin.13_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: urine

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: urine metagenome

text: urethra

text: urine metagenome

text: uncultured Dialister sp.

characteristic: organism

text: uncultured Dialister 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__Dialister;s__

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798747_bin.16_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: Anaerococcus vaginalis

characteristic: project name

characteristic: sample derived from

text: Anaerococcus vaginalis

text: NextSeq 500

characteristic: sequencing method

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798747_bin.17_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: Gardnerella vaginalis

characteristic: organism

text: Gardnerella vaginalis

text: NextSeq 500

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798747_bin.18_MetaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: metaspades v3.15.3

text: MetaWRAP v1.3

text: human excretory system

text: EBI-EMG

characteristic: common name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: urine

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: urine metagenome

text: urethra

characteristic: local environmental context

text: urine metagenome

characteristic: metagenomic source

text: Peptoniphilus duerdenii

characteristic: project name

characteristic: sample derived from

text: Peptoniphilus duerdenii

text: NextSeq 500

characteristic: sequencing method

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798747_bin.22_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: Lactobacillus gasseri

characteristic: organism

text: Lactobacillus gasseri

text: NextSeq 500

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

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798747_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: 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: Atopobium deltae

characteristic: project name

characteristic: sample derived from

text: Atopobium deltae

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__Atopobiaceae;g__Atopobium;s__Atopobium deltae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798747_bin.8_MetaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaspades v3.15.3

characteristic: assembly software

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

characteristic: binning parameters

text: MetaWRAP v1.3

characteristic: binning software

text: human excretory system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR17798749 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: Prevotella denticola

characteristic: organism

text: Prevotella denticola

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__Prevotellaceae;g__Prevotella;s__Prevotella denticola

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798749_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: Lancefieldella parvula

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: Lancefieldella parvula

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__Atopobiaceae;g__Lancefieldella;s__Lancefieldella parvula

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-Assembled Genome: SRR17798749_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: Lancefieldella rimae

characteristic: organism

text: Lancefieldella rimae

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__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella;s__Lancefieldella rimae

text: multi-marker approach

text: Metagenome-Assembled Genome: SRR17798749_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 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: 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: SRR17798750_bin.12_MetaWRAP_v1.3_MAG