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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162471
mra00498-24
10.1128/mra.00498-24
mra.00498-24
Genome Sequences
genomics-and-proteomicsGenomics and ProteomicsDraft genomes of Neisseria perflava UMB0578, Proteus mirabilis UMB8339, and Enterococcus faecalis UMB7967 isolated from urine samples
Kula Alex 1 2
Khan Ali 1 2 3
Martinez Megan 2
Terry Jevan 1
Appleberry Helen 1
https://orcid.org/0000-0003-4532-0545
Wolfe Alan J. 4
https://orcid.org/0000-0003-3049-5991
Putonti Catherine 1 2 4 cputonti@luc.edu

1 Department of Biology, Loyola University , Chicago, Illinois, USA
2 Bioinformatics Program, Loyola University , Chicago, Illinois, USA
3 Department of Chemistry and Biochemistry, Loyola University , Chicago, Illinois, USA
4 Department of Microbiology and Immunology, Loyola University Chicago , Maywood, Illinois, USA
Editor Rasko David University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Catherine Putonti, cputonti@luc.edu
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00498-2411 5 2024
08 7 2024
Copyright © 2024 Kula et al.
2024
Kula et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

The urinary tract of females harbors a variety of microorganisms, both for those with and without symptoms. Here, we present the draft genome sequences of three isolates from urine samples—Neisseria perflava UMB0578, Proteus mirabilis UMB8339, and Enterococcus faecalis UMB7967.

KEYWORDS

Neisseria perflava
Proteus mirabilis
Enterococcus faecalis
urinary microbiome
urobiome
SUI
rUTI
Loyola University Chicago (LUC) Mulcahy Scholars Program Appleberry Helen cover-dateSeptember 2024
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pmcANNOUNCEMENT

Recent efforts have been focused on cataloging the bacterial species of the urinary microbiota (1), and research has found that many species within the female urinary microbiota also inhabit the vaginal microbiota (2–4). As the most recent catalog of bacterial species diversity in the urinary tract shows, numerous taxa can be found in this ecological niche (1). While some are considered “commensal” or “transient,” those taxa associated with symptoms/diseases are significantly better studied. In our group’s continued effort to characterize and sequence strains from the urinary microbiota, here, we present the draft genome assemblies of three species: Neisseria perflava, Proteus mirabilis, and Enterococcus faecalis. While N. perflava is not associated with urinary tract infections, both P. mirabilis and E. faecalis are known causes of both uncomplicated and complicated urinary tract infections (UTIs) (5).

N. perflava UMB0578 was isolated from a catheterized urine sample from a female with stress urinary incontinence [IRB: LU204133, LU 204658, and LU206449 (Loyola University Chicago) (6)]. Both P. mirabilis UMB8339 and E. faecalis UMB7967 were isolated from voided urine samples from two different females diagnosed with recurrent UTI [IRB: 170077AW (University of California, San Diego) (7, 8)]. These strains were isolated using the expanded quantitative urine culture method (9); the taxonomy of these isolates was determined via matrix-assisted laser desorption ionization-time of flight, as previously described (10), and stored at −80°C in the Loyola Urinary Education and Research Collaborative (LUEREC) collection. We obtained samples from this collection and streaked the N. perflava isolate onto a nutrient broth (NB) agar plate and the P. mirabilis and E. faecalis isolates onto brain heart infusion agar plates. The N. perflava NB plate was incubated at 37°C for 48 hours; the other two plates were incubated at 35°C in 5% CO2 for 24 hours. For each, a single colony was selected and grown in their respective culture media under the above culture conditions. DNA extraction was performed using the DNeasy Blood and Tissue Kit (Qiagen), following the protocol for Gram-positive organisms, and sent to SeqCoast Genomics (Portsmouth, NH) for library construction, using the Illumina DNA Prep tagmentation kit, and sequencing on the Illumina NextSeq2000 platform. Raw reads (2 × 150 bp reads) were assembled using BV-BRC v3.35.5 (11) with the “auto” parameter. The raw reads were first trimmed using Trim Galore v0.6.5 (https://github.com/FelixKrueger/TrimGalore) and then assembled using Unicycler v0.4.8 (12). Assemblies were next polished with Pilon v1.23 (13). BV-BRC also was used to calculate genome coverage, completeness, and contamination. Genome annotations were produced using the NCBI Prokaryotic Genome Annotation Pipeline v6.7 (14). Unless otherwise specified, default parameters were used for all software tools.

Genome assembly statistics are provided in Table 1. Continued efforts to sequence both commensal and pathogenic species of the urinary microbiota are needed to better understand this community, both for symptomatic and asymptomatic individuals.

TABLE 1 Genome assembly statistics

Strain	UMB0578	UMB8339	UMB7967	
Species	N. perflava	P. mirabilis	E. faecalis	
SRA accession no.	SRR28710915	SRR28710898	SRR28710894	
Assembly accession no.	JBCGFA000000000	JBCGEX000000000	JBCGEU000000000	
No. raw reads	1,699,568	1,535,364	3,035,810	
Assembly length (bp)	2,273,827	3,722,531	2,908,311	
G+C (%)	48.98	38.49	37.3	
No. contigs	42	62	43	
Contigs N50 (bp)	232,257	217,641	603,203	
Coverage (×)	106.01	51.49	140.04	
Completeness (%)	100	100	100	
Contamination (%)	0.2	0	0	

ACKNOWLEDGMENTS

We wish to acknowledge the study participants who consented to donate urine, the clinical members of LUEREC who recruited those participants and collected their urine, and members of the Wolfe lab who processed the samples. This work was part of a course-based undergraduate research experience at Loyola University Chicago through the support of the College of Arts and Sciences.

DATA AVAILABILITY

Table 1 lists the SRA accession numbers and assembly accession numbers for the three strains.
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