Seven Bacteriophages Isolated from the Female Urinary Microbiota

Recent research has debunked the myth that urine is sterile, having uncovered bacteria within the bladders of healthy individuals. However, the identity, diversity, and putative roles of bacteriophages in the bladder are unknown. We report the draft genome sequences of seven bacteriophages isolated from microbial communities from adult female bladders

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

BACKGROUND: The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples. FINDINGS: Four phages were extracted from Lake Michigan on the same bacterial host, exhibiting similar morphological characteristics as shown under transmission electron microscopy. Growth characteristics of the phages were unique to each isolate. Each phage demonstrated a host-range spanning several phyla of bacteria - to date, such a broad host-range is yet to be reported. Genomic data reveals genomes of a similar size, and close similarities between the Lake Michigan phages and the Pseudomonas phage PB1, however, the majority of annotated genes present were ORFans and little insight was offered into mechanisms for host-range. CONCLUSIONS: The phages isolated from Lake Michigan are capable of infecting several bacterial phyla, and demonstrate varied phenotypic characteristics despite similarities in host preference, and at the genomic level. We propose that such a broad host-range is likely related to the oligotrophic nature of Lake Michigan, and the competitive benefit that this characteristic may lend to phages in nature

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations

Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida)

How from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities.IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes

Genome Sequences and Annotation of Two Urinary Isolates of E. Coli

The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not have symptoms of cystitis. Whereas strain E75 is most closely related to an avian extraintestinal pathogen, strain E78 is a member of a clade that includes extraintestinal strains often found in the human bladder. Both genomes are uncommonly rich in prophages

Draft Genome for a Urinary Isolate of Lactobacillus crispatus

While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms

Assessment of a Metaviromic Dataset Generated from Nearshore Lake Michigan

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse similar data. Our results revealed a diverse community of DNA phages, largely comprising the order Caudovirales. Within the scope of the current study, the Lake Michigan virome demonstrates a distinct community. Although several phages appeared to hold dominance, further examination highlighted the importance of interrogating metagenomic data at the genome level. We present our study as baseline information for further examination of the ecology of the lake. In the current study we discuss our results and highlight issues of data analysis which may be important for freshwater studies particularly, in light of the complexities associated with examining phage ecology generall

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 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

Exploring Prokaryotic and Viral Communities within Florida’s Freshwater Springs

Florida’s freshwater springs serve as a crucial ecosystem for the state, having both ecological and economic importance. Springs occur where there is an opening where aquifers discharge groundwater. Florida’s springs are fed by the Floridan aquifer system (FAS), which underlies the entire state and extends into several neighboring states. The FAS provides potable water to over 10 million people. The constant flow of groundwater through the springs feeds major river systems and creates unique freshwater systems that support numerous plants and animals. The combination of natural beauty and charismatic fauna attract tourism and generate millions of dollars in revenue for the state. However, due to anthropogenic influences the health of the FAS and Florida’s springs have declined. Despite these challenges and the importance of the springs, little is known about the composition and dynamics of prokaryotic and viral communities living in the water. Prokaryotic and viral communities play a large role in maintaining the health of aquatic ecosystems. Microbial communities in the springs are a useful tool for monitoring ecosystem health; however, prior to this dissertation, there were no baseline data available. This dissertation explores both the spatial (Appendix A) and temporal (Appendix B) variation of prokaryotic and viral communities within the springs through the use of 16S ribosomal RNA gene sequencing and viral metagenomics. The spatial investigation generated snapshots of prokaryotic and viral communities within five first magnitude springs, demonstrating that these communities are unique to each site. The temporal investigation revealed spatial and temporal variability with a single spring system. These findings are supported when looking at the diversity and distribution of single-stranded DNA phage within these viral communities (Appendix C). This doctoral work provides the first descriptions of the prokaryotic and viral communities of Florida’s springs and a foundational understanding of the spatial and temporal dynamics of these communities for monitoring future changes

Exploring Prokaryotic and Viral Communities within Florida’s Freshwater Springs

Florida’s freshwater springs serve as a crucial ecosystem for the state, having both ecological and economic importance. Springs occur where there is an opening where aquifers discharge groundwater. Florida’s springs are fed by the Floridan aquifer system (FAS), which underlies the entire state and extends into several neighboring states. The FAS provides potable water to over 10 million people. The constant flow of groundwater through the springs feeds major river systems and creates unique freshwater systems that support numerous plants and animals. The combination of natural beauty and charismatic fauna attract tourism and generate millions of dollars in revenue for the state. However, due to anthropogenic influences the health of the FAS and Florida’s springs have declined. Despite these challenges and the importance of the springs, little is known about the composition and dynamics of prokaryotic and viral communities living in the water. Prokaryotic and viral communities play a large role in maintaining the health of aquatic ecosystems. Microbial communities in the springs are a useful tool for monitoring ecosystem health; however, prior to this dissertation, there were no baseline data available. This dissertation explores both the spatial (Appendix A) and temporal (Appendix B) variation of prokaryotic and viral communities within the springs through the use of 16S ribosomal RNA gene sequencing and viral metagenomics. The spatial investigation generated snapshots of prokaryotic and viral communities within five first magnitude springs, demonstrating that these communities are unique to each site. The temporal investigation revealed spatial and temporal variability with a single spring system. These findings are supported when looking at the diversity and distribution of single-stranded DNA phage within these viral communities (Appendix C). This doctoral work provides the first descriptions of the prokaryotic and viral communities of Florida’s springs and a foundational understanding of the spatial and temporal dynamics of these communities for monitoring future changes