scholarly journals A new family of “megaphages” abundant in the marine environment

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Slawomir Michniewski ◽  
Branko Rihtman ◽  
Ryan Cook ◽  
Michael A. Jones ◽  
William H. Wilson ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
English Channel ◽  
Nucleotide Biosynthesis ◽  
Viral Genomes ◽  
Channel One ◽  
New Family ◽  
Metabolic Genes ◽  
Long Read ◽  
Network Approaches ◽  
Auxiliary Metabolic Genes

AbstractMegaphages, bacteriophages harbouring extremely large genomes, have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of megaphages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other megaphages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including a NADP-dependent isocitrate dehydrogenase [Idh] and nicotinamide-nucleotide amidohydrolase [PncC], which have not previously been identified in megaphages. Mar_Mega_1 was abundant in a marine virome sample and related phages are widely prevalent in the oceans.

scholarly journals Identification of a new family of "megaphages" that are abundant in the marine environment

2021 ◽  
Author(s):  
Slawomir Michniewski ◽  
Branko Rihtman ◽  
Ryan Cook ◽  
Michael Jones ◽  
William Wilson ◽  
...  
Keyword(s):  
Marine Environment ◽  
Genomic Analysis ◽  
Nucleotide Biosynthesis ◽  
Viral Genomes ◽  
Channel One ◽  
New Family ◽  
Long Read ◽  
Network Approaches ◽  
Auxiliary Metabolic Genes ◽  
Large Genomes

Megaphages - bacteriophages harbouring extremely large genomes - have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of bacteriophages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other mega-phages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including isocitrate dehydrogenase [NADP] and nicotinamide-nucleotide amidohydrolase [PncC] which have not previously been identified in megaphages. The results of this study indicate that phages containing extremely large genomes can be found in abundance in the marine environment and augment host metabolism by mechanisms not previously described.

scholarly journals RaFAH: A superior method for virus-host prediction

2020 ◽  
Author(s):  
FH Coutinho ◽  
A Zaragoza-Solas ◽  
M López-Pérez ◽  
J Barylski ◽  
A Zielezinski ◽  
...  
Keyword(s):  
Viral Genomes ◽  
Metabolic Genes ◽  
Archaeal Viruses ◽  
Machine Learning Approach ◽  
Culture Independent ◽  
Molecular Machinery ◽  
Biological Entities ◽  
Auxiliary Metabolic Genes ◽  
Shed Light ◽  
Diverse Culture

AbstractViruses of prokaryotes are extremely abundant and diverse. Culture-independent approaches have recently shed light on the biodiversity these biological entities1,2. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), based on the analysis of nearly 200,000 viral genomes. RaFAH outperformed other methods for virus-host prediction (F1-score = 0.97 at the level of phylum). RaFAH was applied to diverse datasets encompassing genomes of uncultured viruses derived from eight different biomes of medical, biotechnological, and environmental relevance, and was capable of accurately describing these viromes. This led to the discovery of 537 genomic sequences of archaeal viruses. These viruses represent previously unknown lineages and their genomes encode novel auxiliary metabolic genes, which shed light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.

scholarly journals Optimization and Ev a Luation of Viral Metagenomic Amplification and Sequencing Methods Toward a Genome -le Vel Resolution of the Human Fecal DNA Virome

2021 ◽  
Author(s):  
Guangyang Wang ◽  
Shenghui Li ◽  
Qiulong Yan ◽  
Ruochun Guo ◽  
Yue Zhang ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Pcr Amplification ◽  
Genomic Analysis ◽  
Optimal Number ◽  
Future Research ◽  
Metagenomic Sequencing ◽  
Optimal Method ◽  
Viral Genomes ◽  
A Genome ◽  
Long Read

Abstract Background: Viruses in the human gut have been linked to health and disease. Deciphering of the gut virome is dependent on metagenomic sequencing of the virus-like particles purified from the fecal specimens. A major limitation of conventional viral metagenomic sequencing is the low recoverability of viral genomes from the metagenomic dataset. Results: Herein, we developed an optimal method for viral amplification and metagenomic sequencing to maximize the recovery of viral genomes. Using 5 fecal specimens with multiple repetitions, we revealed the optimal number of PCR cycles of high-fidelity enzyme-based amplification and the reliability of multiple displacement amplification in virome DNA preparation, verified the reproducibility of the optimally whole viral metagenomic experimental process, and tested the capability of long-read sequencing for improving viral metagenomic assembly. Based on our optimized results, we generated 151 high-quality viruses using the data combined from short-read (15 cycles for PCR amplification) and long-read sequencing. Genomic analysis of these viruses found that most (60.3%) of them were previously unknown and showed a remarkable diversity of viral functions, especially the existence of 206 viral auxiliary metabolic genes. Finally, we compared the viral metagenomic and bulk metagenomic sequencing approaches and revealed significant differences in the efficiency and coverage of viral identification between them. Conclusions: Our study demonstrates the potential of optimized experiment and sequencing strategies in uncovering viral genomes from fecal specimens, which will facilitate future research about genome-level characterization of complex viral communities.

scholarly journals CheckV assesses the quality and completeness of metagenome-assembled viral genomes

2020 ◽  
Author(s):  
Stephen Nayfach ◽  
Antonio Pedro Camargo ◽  
Frederik Schulz ◽  
Emiley Eloe-Fadrosh ◽  
Simon Roux ◽  
...  
Keyword(s):  
Global Ocean ◽  
Large Database ◽  
High Quality ◽  
Accurate Identification ◽  
Short Read ◽  
Viral Genomes ◽  
Metabolic Genes ◽  
Automated Pipeline ◽  
Auxiliary Metabolic Genes ◽  
Viral Sequences

AbstractMillions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

scholarly journals Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 800
Author(s):  
Tong Jiang ◽  
Cui Guo ◽  
Min Wang ◽  
Meiwen Wang ◽  
Xinran Zhang ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Open Reading Frames ◽  
The Yellow Sea ◽  
Comparative Genomic ◽  
Genomic Context ◽  
Phytoplankton Primary Production ◽  
Metabolic Genes ◽  
Ecological Features ◽  
Auxiliary Metabolic Genes ◽  
Reading Frames

The abundant and widespread unicellular cyanobacteria Synechococcus plays an important role in contributing to global phytoplankton primary production. In the present study, two novel cyanomyoviruses, S-N03 and S-H34 that infected Synechococcus MW02, were isolated from the coastal waters of the Yellow Sea. S-N03 contained a 167,069-bp genome comprising double-stranded DNA with a G + C content of 50.1%, 247 potential open reading frames and 1 tRNA; S-H34 contained a 167,040-bp genome with a G + C content of 50.1%, 246 potential open reading frames and 5 tRNAs. These two cyanophages contain fewer auxiliary metabolic genes (AMGs) than other previously isolated cyanophages. S-H34 in particular, is currently the only known cyanomyovirus that does not contain any AMGs related to photosynthesis. The absence of such common AMGs in S-N03 and S-H34, their distinct evolutionary history and ecological features imply that the energy for phage production might be obtained from other sources rather than being strictly dependent on the maintenance of photochemical ATP under high light. Phylogenetic analysis showed that the two isolated cyanophages clustered together and had a close relationship with two other cyanophages of low AMG content. Comparative genomic analysis, habitats and hosts across 81 representative cyanomyovirus showed that cyanomyovirus with less AMGs content all belonged to Synechococcus phages isolated from eutrophic waters. The relatively small genome size and high G + C content may also relate to the lower AMG content, as suggested by the significant correlation between the number of AMGs and G + C%. Therefore, the lower content of AMG in S-N03 and S-H34 might be a result of viral evolution that was likely shaped by habitat, host, and their genomic context. The genomic content of AMGs in cyanophages may have adaptive significance and provide clues to their evolution.

scholarly journals CheckV: assessing the quality of metagenome-assembled viral genomes

2020 ◽  
Author(s):  
Stephen Nayfach ◽  
Antonio Pedro Camargo ◽  
Emiley Eloe-Fadrosh ◽  
Simon Roux ◽  
Nikos Kyrpides
Keyword(s):  
Viral Genome ◽  
Global Ocean ◽  
High Quality ◽  
Viral Genomes ◽  
Metabolic Genes ◽  
Complete Genomes ◽  
Automated Pipeline ◽  
Auxiliary Metabolic Genes ◽  
Viral Sequences

AbstractOver the last several years, metagenomics has enabled the assembly of millions of new viral sequences that have vastly expanded our knowledge of Earth’s viral diversity. However, these sequences range from small fragments to complete genomes and no tools currently exist for estimating their quality. To address this problem, we developed CheckV, which is an automated pipeline for estimating the completeness of viral genomes as well as the identification and removal of non-viral regions found on integrated proviruses. After validating the approach on mock datasets, CheckV was applied to large and diverse viral genome collections, including IMG/VR and the Global Ocean Virome, revealing that the majority of viral sequences were small fragments, with just 3.6% classified as high-quality (i.e. > 90% completeness) or complete genomes. Additionally, we found that removal of host contamination significantly improved identification of auxiliary metabolic genes and interpretation of viral-encoded functions. We expect CheckV will be broadly useful for all researchers studying and reporting viral genomes assembled from metagenomes. CheckV is freely available at: http://bitbucket.org/berkeleylab/CheckV.

Fatal Respiratory Diphtheria Caused by ß-Lactam–Resistant Corynebacterium diphtheriae

2020 ◽  
Author(s):  
Brian M Forde ◽  
Andrew Henderson ◽  
Elliott G Playford ◽  
David Looke ◽  
Belinda C Henderson ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genomic Analysis ◽  
Carbapenem Resistance ◽  
Corynebacterium Diphtheriae ◽  
Penicillin Binding Protein ◽  
Long Read ◽  
Amoxicillin Clavulanic Acid ◽  
Resistance To Penicillin ◽  
High Level

Abstract Background Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Although resistance to erythromycin has been recognized, β-lactam resistance in toxigenic diphtheria has not been described. Here, we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and all other β-lactam antibiotics, and describe a novel mechanism of inducible carbapenem resistance associated with the acquisition of a mobile resistance element. Methods Long-read whole-genome sequencing was performed using Pacific Biosciences Single Molecule Real-Time sequencing to determine the genome sequence of C. diphtheriae BQ11 and the mechanism of β-lactam resistance. To investigate the phenotypic inducibility of meropenem resistance, short-read sequencing was performed using an Illumina NextSeq500 sequencer on the strain both with and without exposure to meropenem. Results BQ11 demonstrated high-level resistance to penicillin (benzylpenicillin minimum inhibitory concentration [MIC] ≥ 256 μg/ml), β-lactam/β-lactamase inhibitors and cephalosporins (amoxicillin/clavulanic acid MIC ≥ 256 μg/mL; ceftriaxone MIC ≥ 8 μg/L). Genomic analysis of BQ11 identified acquisition of a novel transposon carrying the penicillin-binding protein (PBP) Pbp2c, responsible for resistance to penicillin and cephalosporins. When strain BQ11 was exposed to meropenem, selective pressure drove amplification of the transposon in a tandem array and led to a corresponding change from a low-level to a high-level meropenem-resistant phenotype. Conclusions We have identified a novel mechanism of inducible antibiotic resistance whereby isolates that appear to be carbapenem susceptible on initial testing can develop in vivo resistance to carbapenems with repeated exposure. This phenomenon could have significant implications for the treatment of C. diphtheriae infection, and may lead to clinical failure.

scholarly journals Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family

2006 ◽  
Vol 87 (10) ◽  
pp. 3045-3051 ◽  
Author(s):  
Mazen S. Habayeb ◽  
Sophia K. Ekengren ◽  
Dan Hultmark
Keyword(s):  
Persistent Infection ◽  
Open Reading Frames ◽  
Close Relative ◽  
Virus Family ◽  
Viral Genomes ◽  
Persistent Infections ◽  
New Family ◽  
Nora Virus ◽  
Persistent Virus ◽  
Viral Sequences

Several viruses, including picornaviruses, are known to establish persistent infections, but the mechanisms involved are poorly understood. Here, a novel picorna-like virus, Nora virus, which causes a persistent infection in Drosophila melanogaster, is described. It has a single-stranded, positive-sense genomic RNA of 11879 nt, followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RNA-dependent RNA polymerase and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viral sequences. The unusual sequence and genome organization in Nora virus suggest that it belongs to a new family of picorna-like viruses. Surprisingly, Nora virus could be detected in all tested D. melanogaster laboratory stocks, as well as in wild-caught material. The viral titres varied enormously, between 104 and 1010 viral genomes per fly in different stocks, without causing obvious pathological effects. The virus was also found in Drosophila simulans, a close relative of D. melanogaster, but not in more distantly related Drosophila species. It will now be possible to use Drosophila genetics to study the factors that control this persistent infection.

scholarly journals Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

2021 ◽  
Author(s):  
Mihnea R. Mangalea ◽  
David Paez-Espino ◽  
Kristopher Kieft ◽  
Anushila Chatterjee ◽  
Jennifer A. Seifert ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
At Risk ◽  
Autoimmune Disease ◽  
Intestinal Microbiota ◽  
Disease Development ◽  
Metabolic Potential ◽  
Metabolic Genes ◽  
Auxiliary Metabolic Genes ◽  
Citrullinated Protein ◽  
Insight Into

SUMMARYRheumatoid arthritis (RA) is an autoimmune disease characterized in seropositive individuals by the presence of anti-cyclic citrullinated protein (CCP) antibodies. RA is linked to the intestinal microbiota, yet the association of microbes with CCP serology and their contribution to RA is unclear. We describe intestinal phage communities of individuals at risk for developing RA, with or without anti-CCP antibodies, whose first degree relatives have been diagnosed with RA. We show that at-risk individuals harbor intestinal phage compositions that diverge based on CCP serology, are dominated by Lachnospiraceae phages, and originate from disparate ecosystems. These phages encode unique repertoires of auxiliary metabolic genes (AMGs) which associate with anti-CCP status, suggesting that these phages directly influence the metabolic and immunomodulatory capability of the microbiota. This work sets the stage for the use of phages as preclinical biomarkers and provides insight into a possible microbial-based causation of RA disease development.

scholarly journals Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies

2021 ◽  
Vol 10 (46) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Natsuko Tokito
Keyword(s):  
Complete Genome ◽  
Thermus Thermophilus ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Hybrid Assembly ◽  
Genome Resequencing ◽  
Short Read ◽  
Content Type ◽  
Sequencing Technologies ◽  
Long Read

Complete genome resequencing was conducted for Thermus thermophilus strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related T. thermophilus genomes.

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