Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome

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 s...

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Bibliographic Details
Published in:PloS one 2016-11, Vol.11 (11), p.e0166757-e0166757
Main Authors: Malki, Kema, Shapiro, Jason W, Price, Travis K, Hilt, Evann E, Thomas-White, Krystal, Sircar, Trina, Rosenfeld, Amy B, Kuffel, Gina, Zilliox, Michael J, Wolfe, Alan J, Putonti, Catherine
Format: Article
Language:English
Subjects:
Abundance
Adult
Bioinformatics
Biological evolution
Biology
Biology and Life Sciences
Bladder
Computational Biology - methods
DNA Transposable Elements
Endometrium
Female
Gardnerella
Gardnerella - genetics
Gardnerella - virology
Gardnerella vaginalis
Gene sequencing
Gene transfer
Genes
Genes, Viral
Genetic aspects
Genome, Bacterial
Genomes
Genomics
Health care
High-Throughput Nucleotide Sequencing
Homology
Humans
Immunology
Informatics
Medicine
Medicine and Health Sciences
Microbiomes
Microbiota
Microbiota (Symbiotic organisms)
Nucleotide sequence
Open Reading Frames
Phages
Phylogeny
Prophages
Prophages - genetics
Reproductive system
Research and Analysis Methods
Strains (organisms)
Surveys
Urinary Bladder - microbiology
Urinary incontinence
Urine
Vagina
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0166757