Genomic analysis of uncultured marine viral communities

Breitbart, Mya; Salamon, Peter; Andresen, Bjarne; Mahaffy, Joseph M.; Segall, Anca M.; Mead, David A.; Azam, Farooq; Rohwer, Forest

doi:10.1073/pnas.202488399

Cited by 855 publications

(891 citation statements)

References 18 publications

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“…While the roles of viruses in microbial food webs were the focus of most studies during the 1990's, the dawning of the "omics" era in the 2000's widened the scope of their study (Breitbart et al, 2002;Culley et al, 2006;Martínez et al, 2014;Hurwitz et al, 2016). Viral metagenomics has not only confirmed what was previously known about viruses, but it also shed new light on topics such as geographical patterns (Angly et al, 2006;De Corte et al, 2016), and the relationship between their diversity and abundance with biotic and abiotic variables (Breitbart et al, 2004;Dunigan et al, 2006).…”

Section: Introductionmentioning

confidence: 97%

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Mateus

2017

Front. Mar. Sci.

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Viruses are the most abundant biological entities in the world's oceans. Their potential control on the dynamics and diversity of bacterioplankton and some phytoplankton groups, and consequent effect on the flow of energy and matter in food webs, may be argued as beyond dispute. Paradoxically, their importance seems to be persistently underestimated by marine modelers, frequently by exclusion, despite the uninterrupted volume of knowledge advanced during the past decades. Bridging the gap between knowing and modeling the role of viruses is, undoubtedly, one of the upcoming frontiers to be crossed in modeling the plankton. This paper has a two-fold objective: (1) review the knowledge on the roles of viruses in marine systems that has been put forward over the past decades, and (2) see how viruses have been incorporated into marine ecosystem models, along with the factors that are limiting their inclusion.

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Section: Introductionmentioning

confidence: 97%

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Mateus

2017

Front. Mar. Sci.

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“…Viruses are the most abundant (Suttle, 2005) and genetically diverse (Breitbart et al, 2002;Angly et al, 2006) life forms in the biosphere; yet, little is known about the diversity of ssDNA viruses in natural systems, the evolutionary relationships among them and with characterized viruses, and the role they have in ecosystems. Sequences with similarity to ssDNA viruses have been found in metagenomic data from multiple environments (reviewed in Rosario and Breitbart, 2011;Rosario et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Previously unknown and highly divergent ssDNA viruses populate the oceans

2013

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Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.

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“…The phage population is very dynamic, with rapid population turnover occurring within a relatively short period of time (7). They represent a rich and unique source of genetic and protein diversity, since less than 0.0002% of the global phage metagenome has been sampled (65) and a majority of genes have no assigned functions or matches in GenBank (6,62). Bacteriophages also confer novel biological and physiological traits allowing host strains to adapt to new environments or obtain virulence determinants, thereby driving bacterial speciation and adaptation.…”

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confidence: 99%

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Daniel¹,

Bonnen

Fischetti³

2007

J Bacteriol

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Staphylococcus epidermidis is an important opportunistic pathogen causing nosocomial infections and is often associated with infections in patients with implanted prosthetic devices. A number of virulence determinants have been identified in S. epidermidis, which are typically acquired through horizontal gene transfer. Due to the high recombination potential, bacteriophages play an important role in these transfer events. Knowledge of phage genome sequences provides insights into phage-host biology and evolution. We present the complete genome sequence and a molecular characterization of two S. epidermidis phages, PH15 (PH15) and CNPH82 (CNPH82). Both phages belonged to the Siphoviridae family and produced stable lysogens. The PH15 and CNPH82 genomes displayed high sequence homology; however, our analyses also revealed important functional differences. The PH15 genome contained two introns, and in vivo splicing of phage mRNAs was demonstrated for both introns. Secondary structures for both introns were also predicted and showed high similarity to those of Streptococcus thermophilus phage 2972 introns. An additional finding was differential superinfection inhibition between the two phages that corresponded with differences in nucleotide sequence and overall gene content within the lysogeny module. We conducted phylogenetic analyses on all known Siphoviridae, which showed PH15 and CNPH82 clustering with Staphylococcus aureus, creating a novel clade within the S. aureus group and providing a higher overall resolution of the siphophage branch of the phage proteomic tree than previous studies. Until now, no S. epidermidis phage genome sequences have been reported in the literature, and thus this study represents the first complete genomic and molecular description of two S. epidermidis phages.Staphylococcus epidermidis, a member of the novobiocin-susceptible coagulase-negative staphylococci, is an important opportunistic pathogen and a major cause of nosocomial infections (42, 55). S. epidermidis predominantly colonizes the mucous membranes, groin, and axillar areas, as well as the cutaneous system of human body, with bacterial counts of up to 10 to 10 3 CFU/cm 2 (26). S. epidermidis is usually considered a harmless commensal microorganism; however, infections can occur in immunocompromised individuals and in patients with indwelling or implanted medical devices such as prosthetic heart valves and joint prostheses, where the staphylococci penetrate cutaneous and mucosal barriers (79). With the increasing use of such devices in medical practice, several million people are affected by complications arising from S. epidermidis infections (49). The widespread use of various antimicrobial agents, including penicillins, macrolides, aminoglycosides, and semisynthetic penicillins such as methicillin, has now led to the emergence of multiple-drug-resistant S. epidermidis strains (21, 72).Two S. epidermidis genomes have been sequenced: those of the non-biofilm-forming, non-infection-associated strain ATCC 12228 and the infecti...

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Genomic analysis of uncultured marine viral communities

Cited by 855 publications

References 18 publications

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Previously unknown and highly divergent ssDNA viruses populate the oceans

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

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