Complete Genome Sequences of Three Lactobacillus Gasseri Urine Isolates Obtained from Postmenopausal Women

Overview

Journal Microbiol Resour Announc

Publisher American Society for Microbiology

Specialty Microbiology

Date 2022 Aug 8

PMID 35938830

Authors

Braden M Shipman

Amber Nguyen

Belle M Sharon

Philippe E Zimmern

Nicole J De Nisco

Affiliations

Soon will be listed here.

Abstract

Lactobacillus gasseri frequently colonizes the lower urinary tract of healthy women. However, the role of L. gasseri in urinary tract health and the genes required for urinary tract colonization are poorly understood. Herein, we announce the complete genome sequences of three Lactobacillus gasseri isolates collected from the urine of postmenopausal women.

Citing Articles

Synthesis of current pediatric urinary microbiome research.

Jeries L, Sysoeva T, Karstens L, Kelly M Front Pediatr. 2024; 12:1396408.

PMID: 38957777 PMC: 11217333. DOI: 10.3389/fped.2024.1396408.

References

Wick R, Schultz M, Zobel J, Holt K . Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015; 31(20):3350-2. PMC: 4595904. DOI: 10.1093/bioinformatics/btv383. View

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki E, Zaslavsky L . NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016; 44(14):6614-24. PMC: 5001611. DOI: 10.1093/nar/gkw569. View

Haft D, DiCuccio M, Badretdin A, Brover V, Chetvernin V, ONeill K . RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res. 2017; 46(D1):D851-D860. PMC: 5753331. DOI: 10.1093/nar/gkx1068. View

Nishimura O, Hara Y, Kuraku S . gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics. 2017; 33(22):3635-3637. PMC: 5870689. DOI: 10.1093/bioinformatics/btx445. View

Vaser R, Sovic I, Nagarajan N, Sikic M . Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017; 27(5):737-746. PMC: 5411768. DOI: 10.1101/gr.214270.116. View

De Coster W, DHert S, Schultz D, Cruts M, Van Broeckhoven C . NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018; 34(15):2666-2669. PMC: 6061794. DOI: 10.1093/bioinformatics/bty149. View

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

Gurevich A, Saveliev V, Vyahhi N, Tesler G . QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29(8):1072-5. PMC: 3624806. DOI: 10.1093/bioinformatics/btt086. View

Selle K, Klaenhammer T . Genomic and phenotypic evidence for probiotic influences of Lactobacillus gasseri on human health. FEMS Microbiol Rev. 2013; 37(6):915-35. DOI: 10.1111/1574-6976.12021. View

10.

De Nisco N, Neugent M, Mull J, Chen L, Kuprasertkul A, Santos M . Direct Detection of Tissue-Resident Bacteria and Chronic Inflammation in the Bladder Wall of Postmenopausal Women with Recurrent Urinary Tract Infection. J Mol Biol. 2019; 431(21):4368-4379. PMC: 6801050. DOI: 10.1016/j.jmb.2019.04.008. View

11.

Wick R, Judd L, Gorrie C, Holt K . Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017; 13(6):e1005595. PMC: 5481147. DOI: 10.1371/journal.pcbi.1005595. View

12.

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

13.

Sharon B, Hulyalkar N, Nguyen V, Zimmern P, Palmer K, De Nisco N . Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies. J Vis Exp. 2021; (174). DOI: 10.3791/62872. View

14.

Pearce M, Hilt E, Rosenfeld A, Zilliox M, Thomas-White K, Fok C . The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. mBio. 2014; 5(4):e01283-14. PMC: 4161260. DOI: 10.1128/mBio.01283-14. View

15.

Zhang Z, Schwartz S, Wagner L, Miller W . A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000; 7(1-2):203-14. DOI: 10.1089/10665270050081478. View

16.

Walker B, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S . Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9(11):e112963. PMC: 4237348. DOI: 10.1371/journal.pone.0112963. View