Bacteriophage play an important role in host-driven biological processes by controlling bacterial population size, horizontally transferring genes between hosts, and expressing host-derived genes to alter host metabolism. Metagenomics provides the genetic basis for understanding the interplay between uncultured bacteria, their phage, and the environment. In particular, viral metagenomes (viromes) are providing new insight into phage-encoded host genes (i.e., auxiliary metabolic genes; AMGs) that reprogram host metabolism during infection. Yet, despite deep sequencing efforts of viral communities, the majority of sequences have no match to known proteins. Reference-independent computational techniques, such as protein clustering, contig spectra, and ecological profiling are overcoming these barriers to examine both the known and unknown components of viromes. As the field of viral metagenomics progresses, a critical assessment of tools is required as the majority of algorithms have been developed for analyzing bacteria. The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes. Additionally, we present methods to carefully validate AMGs from host contamination. Despite computational challenges, these new methods offer novel insights into the diversity and functional roles of phage in diverse environments.
Viruses are leading causes of different types of human cancers, accounting for about 20% of total cases. Seven viruses are currently considered oncogenic viruses, including hepatitis B virus (HBV), hepatitis C virus (HCV), human papillomavirus (HPV), Epstein Barr virus (EBV), human herpes virus 8 (HHP8), Merkel cell polyomavirus (MCPyV), and human T-lymphotropic virus type 1 (HTLV-1). The molecular mechanisms of viral oncogenesis are complex and may involve the induction of chronic inflammation, disruption of host genetic and epigenetic integrity and homeostasis, interference with cellular DNA repair mechanisms resulting in genome instability and cell cycle dysregulation. Genetic and epigenetic alterations induced by infection and replication of oncogenic viruses may lead to the appearance and proliferation of cancer stem cells, which are important for the initiation, progression, metastasis, relapse, and chemotherapy resistance of cancers. The cover illustrates the seven oncoviruses that could lead to human cancer.
Here, we address this challenge and quantify algal blooms’ turnover using a combination of satellite and in situ data, which allows identification of a relatively stable oceanic patch that is subject to little mixing with its surroundings. Using a newly developed multisatellite Lagrangian diagnostic, we decouple the contributions of physical and biological processes, allowing quantification of a complete life cycle of a mesoscale (∼10–100 km) bloom of coccolithophores in the North Atlantic, from exponential growth to its rapid demise. We estimate the amount of organic carbon produced during the bloom to be in the order of 24,000 tons, of which two-thirds were turned over within 1 week. Complimentary in situ measurements of the same patch area revealed high levels of specific viruses infecting coccolithophore cells, therefore pointing at the importance of viral infection as a possible mortality agent. Application of the newly developed satellite-based approaches opens the way for large-scale quantification of the impact of diverse environmental stresses on the fate of phytoplankton blooms and derived carbon in the ocean.
Research into viruses associated with coral reefs is a newly emerging field. Corals form an important symbiotic relationship with the dinoflagellate species Symbiodinium, which the coral relies heavily upon for nutrients and calcification. Coral bleaching is the result of disruption of this symbiosis when the algae and/or its photosynthetic pigments are lost from the coral tissues. Environmental stressors, including elevated sea surface temperatures and increased UV light exposure, have been implicated in coral bleaching. We set out to test the hypothesis thatSymbiodinium in culture plays host to a latent virus that switches to a lytic infection under stress, such as UV exposure or elevated temperature. Analysis of Symbiodinium cultures (isolated from corals on the Great Barrier Reef) using flow cytometry and transmission electron microscopy (TEM), revealed an active viral infection was ongoing, regardless of experimental conditions. Morphological analysis using TEM revealed filamentous and icosahedral virus-like particles associated with Symbiodiniumcultures. We present genomic data of the virus assemblages isolated from cultured Symbiodinium cells that indicate this dinoflagellate is targeted by both a dsDNA virus, related to members of the Nucleo-Cytoplasmic Large dsDNA Virus family (NCLDV), and a novel ssRNA virus related to the Orthoretrovirinae. Further investigations are underway to detect viruses in freshly isolated Symbiodinium from reef corals and to compare these with viruses observed in laboratory cultures of this symbiotic alga. We aim to develop molecular diagnostic probes to detect viruses in field samples to help monitor and assess the impact of viruses in coral bleaching and other climate change-related events, which have huge implications for the health of coral reefs to future global climate scenarios.
Researchers from Maryland and New York have identified a novel herpes virus in cells taken from a bat. The work, published this week in mSphere, the American Society for Microbiology's new open access journal, could lead ...
Ed Rybicki's insight:
Bats. Carry everything. The furry cockroaches of the air...
CORVALLIS, Ore. A study at Oregon State University has concluded that significant outbreaks of viruses may be associated with coral bleaching events, especially as a result of multiple environmental stresses.One such event was documented even as it happen
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications.
The virus may also infect humans and affect the brain.
It’s relatively uncommon for viruses to infect organisms from different kingdoms of life. But now, scientists have determined that a particular virus known to infect green algae can also infect mouse macrophages, a type of immune cell. University of Nebraska-Lincoln researcher David Dunigan says that it’s the only known virus to be able to infect algal and mammalian cells.
In a study published this month in the Journal of Virology, Dunigan and his colleagues found that the virus, ATCV-1, was capable of entering and infecting mouse macrophages, and increasing in mass, suggesting that it was making copies of itself. Following introduction of the virus, the scientists witnessed other cellular changes consistent with infection including cell death, Dunigan says.
Ed Rybicki's insight:
Apparently Vincent Racaniello says "...finding a virus that can infect organisms in different kingdoms is quite unusual and not something you see every day, though it’s not unheard of.”
I think it is seriously unheard of: apart from reports implicating amoebae-infecting mimiviruses in pneumonia, which is not as great a phylogenetic divide as green algae and humans, I can't think of anything infecting organisms that are so diverse, UNLESS one of them preys on the other.
Like insects and plants, for example: there are insect- and plant-infecting rhabdoviruses and reoviruses and bunyaviruses. However, these viruses infect insects and plants that have been bound up in a predator-prey relationship for many millions of years, and which have consequently shared their nanobiota.
This does NOT apply to this case, where there is no obvious link between free-living green algae and humans - as in, the algae do not colonise human skin or internal organs.
Just more proof - if we needed any - that viruses are awesome B-)
Viral ecology is a rapidly progressing area of research, as molecular methods have improved significantly for targeted research on specific populations and whole communities. To interpret and synthesize global viral diversity and distribution, it is feasible to assess whether macroecology concepts can apply to marine viruses. We review how viral and host life history and physical properties can influence viral distribution in light of biogeography and meta-community ecology paradigms. We highlight analytical approaches that can be applied to emerging global data sets and meta-analyses to identify individual taxa with global influence and drivers of emergent properties that influence microbial community structure by drawing on examples across the spectrum of viral taxa, from RNA to ssDNA and dsDNA viruses.
Ed Rybicki's insight:
Excellent! Just when we needed one B-) Thanks, Flavia!
Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterise holobiont viral communities across species, environments, or experiments.
In this study, which was carried out within the ChEsSO consortium project (Chemosynthetically driven ecosystems south of the Polar Front), we sampled two hydrothermal vent sites on the East Scotia Ridge, Scotia Sea, one in the Kemp Caldera, South Sandwich Arc and one in the Bransfield Strait, north-west of the Antarctic Peninsula, which exhibit strong differences in their chemical characteristics. We compared a subset of their bacteriophage population by Sanger- and 454-sequencing of g23, which codes for the major capsid protein of T4likeviruses. We found that the sites differ vastly in their bacteriophage diversity, which reflects the differences in the chemical conditions and therefore putatively the differences in microbial hosts living at these sites. Comparing phage diversity in the vent samples to other aquatic samples, the vent samples formed a distinct separate cluster, which also included the non-vent control samples that were taken several hundred meters above the vent chimneys. This indicates that the influence of the vents on the microbial population and therefore also the bacteriophage population extends much further than anticipated.
The Kutch Desert (Great Rann of Kutch, Gujarat, India) is a unique ecosystem: in the larger part of the year it is a hot, salty desert that is flooded regularly in the Indian monsoon season. In the dry season, the crystallized salt deposits form the “white desert” in large regions. The first metagenomic analysis of the soil samples of Kutch was published in 2013, and the data were deposited in the NCBI Sequence Read Archive. At the same time, the sequences were analyzed phylogenetically for prokaryotes, especially for bacteria. In the present work, we identified DNA sequences of recently discovered giant viruses in the soil samples from the Kutch Desert. Since most giant viruses have been discovered in biofilms in industrial cooling towers, ocean water, and freshwater ponds, we were surprised to find their DNA sequences in soil samples from a seasonally very hot and arid, salty environment.
Electron microscopy images of three types of cyanophages: 1) upper left: AsGV-L cyanophage particles, showing geminivirus-like morphology with two incomplete icosahedra joined together; 2) lower left: MaCV-L cyanophage particles,showing corticovirus-like and round shape with icosahedral symmetry and a non-enveloped capsid; 3) right: cyanophage PP virions , with short and stubby tail structures. Images painted with pseudo-colors. (Cover designed by Meng Wang, Wuhan IOV.)
Ed Rybicki's insight:
Another useful resource - also a couple of years old
Environmental genomics can describe all forms of organisms—cellular and viral—present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts.
There are over 1,000,000,000,000,000,000,000,000,000,000 viruses in the ocean. This dashboard allows users to explore the relationship between microbial cells and viruses through data sampled around the world.
Ed Rybicki's insight:
Looks cool to me...! But needs updating - hey, Flavia??
The deadly virus affecting oysters in Tasmania's south-east is detected in a population of wild oysters in the Derwent estuary
Pacific Oyster Mortality Syndrome, or POMS, has been detected in six Tasmanian commercial growing regions — Lower Pittwater, Upper Pittwater, Pipe Clay Lagoon, Blackman Bay, Little Swanport and Dunalley Bay.
It is also believed the infection has hit oyster leases at Bruny Island's Great Bay, but that will not be confirmed until further testing is carried out.
The Environment Department has now confirmed the disease has affected a population of wild oysters in the Derwent estuary.
Tasmania's Chief Veterinary Officer Rod Andrewartha said the finding could be a positive aspect to the outbreak since wild oysters were considered pests.
The abundance of viruses in the world’s oceans varies wildly, regardless of the available ‘prey’, according to new research published by an international team that includes (UBC) University of British Columbia microbiologists. Marine viruses kill roughly 20 per cent of the oceans’ living matter by weight every day, so it’s vital that we get a better understanding of what is driving these variations from system to system.
The findings published in Nature Microbiology turn previous estimates on their heads, and inject a new source of variability into climate models and other biogeochemical measures.
“What was surprising was that there was not a constant relationship, as researchers had assumed, between the number of microbial cells available to infect, and the number of viruses,” said Joshua Weitz, an associate professor at the Georgia Institute of Technology and one of the paper’s two senior co-authors.
“A marine environment with 100-fold more viruses than microbes may have very different rates of microbial recycling than an environment with far fewer viruses. Our study begins to challenge the notion of a uniform ecosystem role for viruses.”
The researchers found the ratio of viruses to microbes varied from approximately 1 to 1 and 150 to 1 in surface waters, and from 5 to 1 and 75 to 1 in the deeper ocean. For years, scientists had used a baseline of 10 to 1 – ten times more viruses than microbes – which may not adequately represent conditions in many marine ecosystems.
The deep sea microbiology workshop series aimed to gather international experts in the field, and give them the opportunity to present up to date scientific research, and to discuss future cooperative works, in a friendly atmosphere. The idea of a series of workshops dedicated to deep sea microbiology was conceived first during the Extremophiles Conference held in Brest in September 2006. Prof. Dr. Xiao Xiang (University of Shanghai, China) has organized the first edition in Xiamen (China) in November 2008, where he was settled at that time. This meeting was very successful and a second edition has been organized by Prof Daniel Prieur and Prof Mohamed Jebbar in 2010 in Brest, France. Again, the 3rd edition was organized by Prof Xiao Xiang in Shanghai in October 2012 and in September 2014 Prof Mohamed Jebbar has organized the 4th edition in Brest.
New research led by the University of Nebraska-Lincoln has provided the first direct evidence that an algae-infecting virus can invade and potentially replicate within some mammalian cells.
Known as Acanthocystis turfacea chlorella virus 1, or ATCV-1, the pathogen is among a class of chloroviruses long believed to take up residence only in green algae. That thinking changed with a 2014 study from Johns Hopkins University and UNL that found gene sequences resembling those of ATCV-1 in throat swabs of human participants.
The new study, published in the Journal of Virology, introduced ATCV-1 to macrophage cells that serve critical functions in the immune responses of mice, humans and other mammals. By tagging the virus with fluorescent dye and assembling three-dimensional images of mouse cells, the authors determined that ATCV-1 successfully infiltrated them.
Ed Rybicki's insight:
Right up there with evidence that mimiviruses may be implicated in pneumonia - we are nowhere near determining how many viruses are actually involved in human disease.
Coral foe becomes a friend Nature.com Seaweed often inhibits the growth of corals, but it can help them when they are faced with a coral-eating starfish. Seaweed can suppress coral growth by shading it from sunlight and by releasing toxic chemicals.
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