Kema Malki

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

BackgroundThe 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.FindingsFour 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.ConclusionsThe 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.

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 generally.

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.

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.

Seven Bacteriophages Isolated from the Female Urinary Microbiota

ABSTRACT 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.

Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches.

In comparison to the oceans, freshwater environments represent a more diverse community of microorganisms, exhibiting comparatively high levels of variability both temporally and spatially Maranger and Bird, Microb. Ecol. 31 (1996) 141–151. This level of variability is likely to extend to the world of viruses as well, in particular bacteria-infecting viruses (bacteriophages). Phages are known to influence bacterial diversity, and therefore key processes, in environmental niches across the globe Clokie et al., Bacteriophage 1 (2011) 31–45; Jacquet et al., Adv. Ocean Limn. 1 (2010) 97–141; Wilhelm and Suttle, Bioscience 49 (1999) 781–788; Bratback et al., Microb. Ecol. 28 (1994) 209–221. Despite their prevalence and likely critical role in freshwater environments, very few viral species have been characterized. Metagenomic approaches, however, have allowed for a glimpse into phage diversity. We collected surface water samples from four Chicago area beaches – Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach – every two weeks from May 13 through August 5, 2014. Sampling was conducted with four biological replicates for each sampling date and location, resulting in 112 samples. DNA isolated from each of the individual samples for a given collection date/location was pooled together, with one exception – Calumet Beach on August 5, 2014 – in which each biological replicate was sequenced individually. Raw sequence data is available via NCBI’s SRA database (part of BioProject PRJNA248239).

Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches

Lake Michigan is a critical resource for the residents of Chicago, providing drinking water to its 9+ million area residents. Along Chicago׳s 26 miles of public beaches the populous urban environment and this freshwater environment meet. While city-led monitoring initiatives investigate pathogenic bacteria in these nearshore waters, very little is known about other microbial species present. We collected surface water samples from two Chicago public beaches – Montrose Beach and 57th Street Beach – every ten days from June 5 through August 4, 2013 as well as once in early Fall (October 4, 2013). Sixteen bacterial communities in total were surveyed through targeted sequencing of the V4 16S rRNA gene. Taxa were identified using Mothur. Raw sequence data is available via NCBI׳s SRA database (part of BioProject PRJNA245802). OTU calls for each read are also available at our online repository: www.lakemichiganmicrobes.com/bacteria/.

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.

Assessment of microbial populations within Chicago area nearshore waters and interfaces with river systems.

The Chicago area locks separate and control water flow between the freshwaters of Lake Michigan and the network of Illinois waterways. Under extreme storm conditions, however, the locks are opened and storm waters, untreated waste, and runoff are released directly into the lake. These combined sewer overflow (CSO) events introduce microbes, viruses, and nutrients such as nitrogen and phosphorous into nearshore waters which likely affect the native species. We collected surface water samples from four Chicago area beaches – Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach – every two weeks from May 13 through August 5, 2014. Sampling was conducted with four biological replicates for each sampling date and location, resulting in 112 samples. Each community was surveyed through targeted sequencing of the V4 16S rRNA gene. Technical replicates were also sequenced and are included in this dataset. Taxa were identified using Mothur. Raw sequence data is available via NCBI׳s SRA database (part of BioProject PRJNA245802).

Draft Genome Sequence of a Urinary Isolate of Lactobacillus crispatus

ABSTRACT 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.