Lactobacillus Metabolite-Mediated Induction of Bacteriophage

Once considered sterile in the absence of an infection, the female urinary tract is home to a diverse community (microbiota) of bacterial species and bacteriophage (phage), viruses that infect bacteria A dominant member of the female urinary microbiota is the bacterial genus Lactobacillus. Several Lactobacillus species are even associated with urinary health. Phage infectious of bacteria in the urinary tract tend to replicate through one of two life cycles: the lytic (active) life cycle or the lysogenic (dormant) life cycle. Temperate phage can switch from the lysogenic life cycle to the lytic life cycle in the presence of an environmental cue. This process is called induction. Within the urinary tract, Lactobacillus species naturally produce several of the inducing agents used in the lab; they release lactic acid, reducing the pH of their environment, and hydrogen peroxide as part of the glycolytic pathway. This observation motivated the investigation into how Lactobacillus metabolites induce phage in other urinary bacteria species. Eight communities, each containing either a Lactobacillus jensenii or Lactobacillus mulieris strain and at least two other community members, were selected for analysis. The genomes of all community members were sequenced and screened for the presence of phage. The pH and hydrogen peroxide outputs were measured for each of the L. jensenii and L. mulieris isolates. Other taxa in the community were grown in media adjusted to Lactobacillus-relevant pH levels based up on the Lactobacillus strain in their community. These cultures were screened for the presence of induced phage. Finally, community members were grown with varying concentrations of their community\u27s Lactobacillus strain\u27s spent media. These cultures were sequenced, and the sequences were screened for the presence of induced phage. 106 individual phage were induced during this process. These results suggest that Lactobacillus is inducing phages in other community members in the urinary tract. Thus, the beneficial effects of Lactobacilli in the urinary tract and/or the dominance of Lactobacillus in the female urinary tract may be a result of induction and lysis of other bacterial taxa

Draft Genome Sequence of Lactobacillus jensenii Strain UMB7766, Isolated from the Female Bladder

Lactobacillus jensenii is a beneficial and prominent community member within both the vaginal and female urinary microbiota. As more genomes for L. jensenii strains are made publicly available, we gain more knowledge about this beneficial community member. Here, we present the draft genome sequence of L. jensenii UMB7766, which was isolated from a urine specimen from a catheterized female patient with recurrent urinary tract infections

When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages

High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages

Draft Genome Sequence of Streptococcus anginosus UMB7768, Isolated from a Woman with Recurrent UTI Symptoms

Streptococcus anginosus recently was implicated as a pathogen involved in urinary tract infections. A strain of S. anginosus was isolated from the female urogenital tract. Here, we present the draft genome sequence of S. anginosus strain UMB7768

Bacteriophages of the Lower Urinary Tract

Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections

Draft Genome Sequence of Streptococcus anginosus UMB1296, Isolated from the Female Urinary Tract

We present the draft genome sequence of a Streptococcus anginosus strain isolated from the female urinary tract. The S. anginosus UMB1296 draft genome has a size of 1,924,009 bp assembled into 35 contigs with a GC content of 38.69%. Genome annotation revealed 1,775 protein-coding genes, including several known virulence factors

Draft Genome Sequence of Streptococcus anginosus UMB0839, Isolated from the Female Urinary Tract

Here, we present the draft genome sequence of Streptococcus anginosus UMB0839, isolated from the female urinary tract. The total size of the genome is 2,104,786 bp assembled into 42 contigs with a GC content of 38.8% and 284× genome coverage

Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract

Here, we introduce the 2.8-Mbp draft genome of Enterococcus faecalis strain UMB0843, isolated from the female urinary tract. E. faecalis is a leading cause of nosocomial infections, and many strains are often resistant to multiple antibiotics. We focus our genome analysis on the multiple genes involved in antibiotic resistance in this strain

Draft Genome Sequence of Corynebacterium aurimucosum UMB7769, Isolated from the Female Urinary Tract

Here, we present the draft genome sequence of Corynebacterium aurimucosum UMB7769, isolated from the female urinary tract. The size of the genome is 2,731,818 bp, assembled in 50 contigs, with an observed GC content of 60.9% and an N50 score of 129,518 bp. Annotation revealed 31 antibiotic resistance genes

Draft Genome Sequence of Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection

Escherichia coli is a Gram-negative, motile, rod-shaped bacterium that causes the majority of uncomplicated urinary tract infections (UTIs). Here, we report the draft genome of E. coli strain UMB9246, an isolate from a woman with recurrent UTI