title: Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome.
abstract: Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species' evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts.
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America.
authors.forename: Kema
authors.initials: K
authors.lastname: Malki
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America.|Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Shapiro
authors.affiliation: Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America.
authors.forename: Travis K
authors.initials: TK
authors.lastname: Price
authors.affiliation: Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America.
authors.forename: Evann E
authors.initials: EE
authors.lastname: Hilt
authors.affiliation: Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America.
authors.forename: Krystal
authors.initials: K
authors.lastname: Thomas-White
authors.affiliation: Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America.
authors.forename: Trina
authors.initials: T
authors.lastname: Sircar
authors.affiliation: Center for Biomedical Informatics, Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, United States of America.
authors.forename: Amy B
authors.initials: AB
authors.lastname: Rosenfeld
authors.affiliation: Center for Biomedical Informatics, Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, United States of America.
authors.forename: Gina
authors.initials: G
authors.lastname: Kuffel
authors.affiliation: Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Zilliox
authors.affiliation: Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America.
authors.forename: Alan J
authors.initials: AJ
authors.lastname: Wolfe
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America.|Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America.|Department of Computer Science, Loyola University Chicago, Chicago, Illinois, United States of America.
authors.forename: Catherine
authors.initials: C
authors.lastname: Putonti
mesh_terms: D000328:Adult; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D005260:Female; D016975:Gardnerella / Q000235:genetics* / Q000821:virology; D005814:Genes, Viral; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064307:Microbiota; D016366:Open Reading Frames; D010802:Phylogeny; D039002:Prophages / Q000235:genetics*; D001743:Urinary Bladder / Q000382:microbiology*
chemical_list: D004251:DNA Transposable Elements