Phage genomes and metagenomes. Medical search. Frequent questions

This is critical because, while individual genes or genome fragments provide useful information on the metabolic potential of a community, in practice most biochemical transformations take place inside a cell, involving sets of genes structured in controlled pathways. (biomedcentral.com)
Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. (biomedcentral.com)
Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. (aber.ac.uk)
These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage. (aber.ac.uk)
Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans. (biomedcentral.com)
A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. (biomedcentral.com)
A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. (biomedcentral.com)
Some "Quimbyviridae" phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. (biomedcentral.com)
A metagenome are all the genes and genomes of the microbiota, including plasmids (Berg et al. (goldbio.com)
Aziz, Breitbart, and Edwards examined some 10 million genes from 2137 sequenced genomes (47 archaeal, 725 bacterial, 29 eukaryotic and 1336 viral) plus 187 metagenomes, in search of. (asmblog.org)
and transplantation of these phages from humans to mice and Drosophila showed increased memory scores and upregulation of memory-involved brain genes. (metabiom.org)
treatment with HiAlc Kpn-specific phage was able to alleviate steatohepatitis caused by HiAlc Kpn, including hepatic dysfunction and expression of cytokines and lipogenic genes. (metabiom.org)
Genomics and model-systems-based experimentation revealed that cyanobacterial phages often contain host photosynthesis genes, which are expressed during infection and act as a diversity generator for their numerically-dominant, globally-distributed photosynthetic hosts. (appliedmicrobiology.org)
However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. (osti.gov)
Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the "diametric ratio" method. (osti.gov)
Horizontal gene transfer between strains is mediated by mobile genetic elements (such as plasmids, integrons, phages, transposons, etc.) of various drug-resistant genes that can be passed between bacterial strains of the same and different species, thus allowing rapid transmission of bacterial resistance, with recipient bacteria exhibiting multi-drug resistance. (cd-genomics.com)
The 3C technology, the predecessor of Hi-C technology, Meta 3C can also be used to associate mobile genetic elements (resistance genes, plasmids and integrons) with the host genome. (cd-genomics.com)
2. Associating mobile genetic elements (resistance genes, plasmids, and integrons) with the host genome. (cd-genomics.com)
7 ] undertook the first metagenome-based community characterization on amplified 16S rRNA genes. (biomedcentral.com)

In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs (Eukaryotic Viruses and Phages Orthologous Groups). (mdpi.com)
The most significant concerns focus on the fact that FastViromeExplorer is a tool for detecting viruses with some degree of similarity to known viruses given that it is dependent on using a reference database of known virus sequences in order to determine that reads originated from a virus genome. (peerj.com)
In this manuscript, the authors present a new tool (named FastViromeExplorer) destined to help detect and quantify known viruses in metagenome dataset. (peerj.com)
The authors could also test / illustrate this database bias by generating simulated metagenomes including new viral genomes published since they created their database, and observe the maximum "distance" at which FastViromeExplorer is able to identify these viruses (i.e. how different from the database genomes a new virus genome can be), although I don't see this additional benchmark as absolutely essential. (peerj.com)
Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. (peerj.com)
1 terabase each) were screened for viruses, resulting in 2,631 viral contigs, including 14 complete viral genomes. (pnnl.gov)
Identified soil viruses were primarily bacteriophages targeting dominant bacterial taxa and observed phage diversity correlated with host diversity. (pnnl.gov)
iPHoP: A Matchmaker for Phages and their Hosts Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts. (doe.gov)
Phages are back in the news, and there are lots of great conferences about phage biology including the Keystone Symposium on Global Virome in Health Disease , the International Viruses of Microbes Meeting , and more. (edu.au)
It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hosts must share a common genetic code ( 6 ). (scienceintheclassroom.org)
Notably, PD patients had fewer gut viruses, including bacterial and archaeal phages. (alzforum.org)
Although the human gut offers a rich source of phage genomic diversity, the virome so far has been explored to a much lesser extent than the whole community (metagenome), composed of viruses, bacteria, and archaea. (biomedcentral.com)
One of the most influential techniques is metagenomics, which allows researchers to sample the genomes in an environment without having to culture individual viruses. (ojcius.net)
This proliferation of genomes prompted virologists to rethink the way they classify viruses and helped to clarify their evolution. (ojcius.net)
All viruses have two things in common: each encases its genome in a protein-based shell, and each relies on its host - be it a person, spider or plant - to reproduce itself. (ojcius.net)

The sequences retrieved were remarkably similar to the existing genome of P. marinus subsp. (nih.gov)
The high abundance of phage sequences in the cellular size fraction indicated a remarkably high proportion of cells suffering phage lytic attack. (nih.gov)
The last decade's revolution in DNA sequencing throughput and cost has provided researchers with the unprecedented possibility of obtaining sequences from thousands of genomes at a time in natural samples. (biomedcentral.com)
Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. (microbial-ecology.net)
Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. (biomedcentral.com)
The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. (biomedcentral.com)
A key step in genome recovery from metagenomic sequence data is the classification of sequences assembled from metagenomic reads into discrete units, referred to as bins. (biomedcentral.com)
This is due to our limited access to genome sequences from uncultivated organisms, which are estimated to account for 99% in prokaryotes ( 11 ). (scienceintheclassroom.org)
To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber , TGA opal , and TAA ochre codons in assembled metagenomes and metatranscriptomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of viral sequences ( Fig. 1A ) ( 15 ). (scienceintheclassroom.org)
Global distribution of nearly identical phage-encoded DNA sequences. (academicinfluence.com)
A metagenome analysis recovered the genome sequences of Candidatus Wolbachia bourtzisii wDacA (supergroup A) and Candidatus Wolbachia pipientis wDacB (supergroup B). Genome read coverage, as well as 16S rRNA clone sequencing, revealed that wDacB was more abundant than wDacA. (uibk.ac.at)
This work will result in genome sequences, annotations, and metabolic models for ~100 microorganisms, with potential for propagation to all sequenced microbial genomes. (edu.au)
We will generate new draft genome sequences and transcriptomes, and create new web resources for querying, comparing, sharing, and analyzing growth phenotype data for microbial genomes. (edu.au)
The viral dark matter is all the sequences that we find in metagenomes that we don't know what to do with. (edu.au)
2020) introduce a genome-clustering method based on the number of shared identical DNA sequences of length k (or k -mers). (peercommunityin.org)
This is important because increasing the number of genome sequences in a reference database - without consistent taxonomic annotation of these genomes - paradoxically leads to fewer classified metagenomic reads. (peercommunityin.org)

Together with the Eisen and Facciotti labs at UC Davis, we sequenced and annotated the genomes of eight Halophilic Archaea. (edu.au)

This is specifically geared towards the bioinformaticians and practitioners who are the world experts on phage genome annotation and are working day-to-day on improving and enhancing those annotations. (edu.au)
The lack of high-throughput phenotypic data is hindering our ability to describe the metabolic potential of microbes based on their genome annotation and our ability to predict gene complements from phenotypic analyses. (edu.au)
December 11 Webinar: Running the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) on your own data (webinar) NCBI, Wed Dec 11, 12:00-12:45pm. (cdc.gov)

The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. (peerj.com)
SDSU is proud to host the 2020 phage genome and metagenomics conference from May 19th to 22nd, 2020. (edu.au)
vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. (biomedcentral.com)
We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies. (biomedcentral.com)
According to the Genomes OnLine Database (GOLD) [ 17 ] until January 2009, 137 metagenomics projects were in various stages of sequencing, 72% of which were derived from environmental samples, 23% from endobiotic samples, along with 5% synthetic metagenomes. (biomedcentral.com)

Through the process of binning, contigs or scaffolds derived from the same lineage can be clustered and genomes reconstructed. (biomedcentral.com)

Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. (biomedcentral.com)
Java ST28 with samples originating from poultry with whole-genome sequence (WGS) data ( 22 ). (cdc.gov)
As of now, the only mention of this bias is in the Conclusion section l. 354 ", the limitation of FastViromeExplorer is that it cannot identify a virus or phage if a similar sequence is not present in the reference database. (peerj.com)
The availability of a whole-genome sequence for AciHV-2 and a highly specific and sensitive qPCR assay for detection of AciHV-2 in white sturgeon lays a foundation for further studies on host-pathogen interactions while providing a specific and rapid test for AciHV-2 in captive and wild populations. (bvsalud.org)
This appears to be due to false constructive misassembly calls resulting from real variations between the reference genome sequence and the genomes of the isolates. (rorek.org)
Zhang YZ, Liu Y, Bai Z, Fujimoto K, Uematsu S, Imoto S . Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning. (google.com)
Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut. (biomedcentral.com)
In order to understand evolutionary adaptive dynamics, including the nature and fitness spectrum of mutations and their temporal dynamics, the fate of such low-frequency variants is increasingly studied by ultra-deep DNA sequencing of genome and meta-genome (=mixed microbial) samples that yield billions of short sequence reads. (mardata.de)
Using the cross-linking relationship, the sequence from the same cell is determined, and the genome of a single bacteria is constructed. (cd-genomics.com)
In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. (biomedcentral.com)
In parallel to such theoretical considerations, several research groups have taken more pragmatic approaches to defining bacterial species based on sequence similarity cutoffs, such as genome-wide average nucleotide identity (ANI). (peercommunityin.org)
Briand M, Bouzid M, Hunault G, Legeay M, Saux MF-L, Barret M (2020) A rapid and simple method for assessing and representing genome sequence relatedness. (peercommunityin.org)
A guide to machine learning for bacterial host attribution using genome sequence data. (cdc.gov)

Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages ( 12 - 14 ) and the discovery of a previously unknown reassignment of TGA opal stop codons to glycine ( 4 , 5 , 14 ). (scienceintheclassroom.org)

They report the ability of hyphal-riding bacteria to transport lytic phages and utilize them as 'weapons' during colonization of new water-unsaturated habitats. (phagedirectory.com)
These small, phage-encoded proteins time the length of lytic infections of some phages. (asmblog.org)

The efficacy of pSelAct-KO was demonstrated in C. michiganensis and confirmed using whole genome sequencing. (biorxiv.org)
However, single-cell sequencing requires a highly specialized laboratory facility, and single amplified genomes (SAGs) typically have fairly low genome coverage, due to the small amount of DNA in each cell and associated whole-genome amplification biases [ 9 ]. (biomedcentral.com)
MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. (biomedcentral.com)
The development of high-throughput genomic sequencing technologies has enabled the recovery of genomes directly from microbial communities in natural and engineered environments [ 1 ]. (biomedcentral.com)
They systematically assessed phage resistance evolution and bacterial fitness in Pseudomonas , including sequencing more than 250 mutant strains! (phagedirectory.com)
Anyone can post a message to the phage community - and it could be anything from collaboration requests, post-doc searches, sequencing help - just ask! (phagedirectory.com)
Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases. (embl.de)
In this study, DNA methylation patterns are analyzed in 8848 metagenome-assembled high-quality phages from 104 fecal samples using single-molecule real-time sequencing. (embl.de)
From Bacterial and Fungal genome sequencing to human Whole Genome Sequencing (WGS), MR DNA has you covered! (scotedowd.com)
Shotgun sequencing and de novo assembly of genomes at MR DNA. (scotedowd.com)
Whole genome sequencing allows scientists to elucidate the entirety of the genome of a specific organism. (scotedowd.com)
As the cost of DNA sequencing continues to decrease, due in large part to Next Generation Sequencing, the more affordable and cost effective whole genome sequencing becomes for researchers everywhere. (scotedowd.com)
Our experience in whole genome sequencing, paired with a comprehensive portfolio of sequencing platforms, allows us to provide you with the proper work flow for any project. (scotedowd.com)
From bacterial genomes to the human genome, we are dedicated to providing our customers with the most reliable and affordable sequencing solution possible. (scotedowd.com)
Why Should I Choose Whole Genome Sequencing? (scotedowd.com)
Ten years ago this would have been a valid question, and to some regard still is, but a more fitting question for the age of technology we find ourselves in today is, 'Why NOT choose whole genome sequencing? (scotedowd.com)
The a hundred pattern four hundred GB strain madness dataset accommodates 408 newly-sequencing genomes, of which ninety seven had a carefully related pressure. (rorek.org)
Specifically, we are sequencing the genomes of microbes and assaying their growth in 96-well microtiter plates. (edu.au)
We use high-resolution techniques, such as the sequencing of complete genomes of Brucella , combined with molecular and cell biology approaches, in order to understand how specificity is stablished in different animal species. (appliedmicrobiology.org)

Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. (biomedcentral.com)
Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CAMP, Dagan T (2018) Rates of mutation and recombination in Siphoviridae phage genome evolution over three decades. (mardata.de)

Novel eukaryotic genomes can be analyzed by the self-training GeneMark-ES . (gatech.edu)
Similar to the principle of Hi-C technology applied to eukaryotic chromosome-level reference genome-assisted assembly, Hi-C/3C technology can be applied to the assembly of metagenomes to improve the results of metagenome assembly. (cd-genomics.com)

Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. (biomedcentral.com)

In both methods, individual bins are tested for completeness (is it a complete genome? (biomedcentral.com)
We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)

Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. (biomedcentral.com)
yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. (biomedcentral.com)
The third proposed family, "Gratiaviridae," consists of less abundant phages that are distantly related to the families Autographiviridae , Drexlerviridae , and Chaseviridae . (biomedcentral.com)
whereas less abundant species included #Lactococcus phages ul36 and #Streptococcus phage Abc2. (metabiom.org)

While many bacteria have intrinsic, chromosomally encoded ARDs and the capability of increasing resistance through mutation, they can also enrich their resistance capabilities through the acquisition of exogenous ARDs located on mobile genetic elements (MGEs) such as plasmids, transposons or phages. (nature.com)
Hi-C not only clusters metagenomic results to species and strain levels, but also associates plasmids, phages and host bacteria in microbial communities. (cd-genomics.com)

Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)

Thus a rapid, automated taxonomy such as the one proposed here offers an opportunity to more fully harness the information from metagenomes. (peercommunityin.org)

Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. (biomedcentral.com)
These bins represent composite genomes of individual populations that comprise the microbial community. (biomedcentral.com)
Dr. Matthew B. Sullivan's research focus is on the co-evolution of microbe and virus (phage) in environmental populations, as well as the impact of marine phages on microbe-mediated global biogeochemistry. (appliedmicrobiology.org)

Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. (biomedcentral.com)
Bacteria of the genus Brucella share 96-98% similarity at genome level, despite infecting different species of animals. (appliedmicrobiology.org)
At a cutoff above 95% ANI, genomes are considered to come from the same species. (peercommunityin.org)

Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. (biomedcentral.com)
Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. (biomedcentral.com)
Thus, circularity can be used as one feature to identify putative complete phage genomes in viromes and metagenomes. (biomedcentral.com)

Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. (doe.gov)
DNA methylation plays a crucial role in the survival of bacteriophages (phages), yet the understanding of their genome methylation remains limited. (embl.de)
Our data indicate that bacteriophages can infect hosts with a different genetic code and demonstrate phage-host antagonism based on code differences. (scienceintheclassroom.org)

One copy of IS1A in the Illumina read set relocated to a position 105 kbp away from the reference genome, when an meeting spanned this area, QUAST recognized the distinction as a misassembly, lowering the NGA50. (rorek.org)

The c4 antisense RNA is a non-coding RNA used by certain phages that infect bacteria. (wikipedia.org)
There are lunar-lander-looking phage that infect bacteria and, of course, the killer spiky balls the world is now painfully familiar with. (ojcius.net)

Using a test dataset of Pseudomona s genomes, they find that 95% ANI corresponds to approximately 50% of shared 15-mers. (peercommunityin.org)

It is unknown how this expression pattern might relate to the phage biology. (wikipedia.org)

Since the discovery of the genetic code and protein translation mechanisms ( 1 ), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages ( 2 - 7 ). (scienceintheclassroom.org)
Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and noncanonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. (scienceintheclassroom.org)
Question: How much alternative genetic coding of uncultivated bacteria and phage genomes can be detected in all the metagenome data sets found in JGI's IMG database? (scienceintheclassroom.org)
there's even a phage that uses an alternative genetic alphabet, replacing the chemical base A in the standard ACGT system with a different molecule, designated Z. (ojcius.net)
In particular, tracts of identical DNA provide evidence for recent genetic exchange, which in turn helps define BSC-like clusters of genomes (Arevalo et al. (peercommunityin.org)

To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. (mdpi.com)
The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. (microbial-ecology.net)

Tailed dsDNA phages encapsidate their genome as a linear molecule, but depending on the terminal genomic arrangement, many complete phage genomes assemble into a "circular" contig (i.e., a contig with direct terminal repeats) [ 12 ]. (biomedcentral.com)

The researchers compared the gut metagenomes taken from stool samples of 31 early PD patients to 28 healthy age-matched controls. (alzforum.org)
Thus, further investigation is crucial for correlating the detection of viral metagenomes in samples with the risk of infection. (edu.pe)
Phylonium: Fast Estimation of Evolutionary Distances from Large Samples of Similar Genomes. (cdc.gov)

Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. (biomedcentral.com)
This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. (biomedcentral.com)

If supernatant addition was answerable for inducing manufacturing of our hypothetical phage receptor, it will clarify the curious delay of 12 h, throughout which we observed no phage an infection. (rorek.org)
However, the detection of a viral genome alone does not necessarily indicate there is a risk of infection or disease development. (edu.pe)
Dissecting host-plasmid and host-phage associations is critical to understanding the ecology of antibiotic resistance and the pathways of resistance gene transmission in the clinic, and is a prerequisite for designing and implementing interventions to reduce the threat of bacterial infection. (cd-genomics.com)

The Silveira Lab at the University of Miami, Florida is hiring a Postdoctoral Associate to study the tripartite relationships between phage-bacteria interactions in coral reef. (phagedirectory.com)
Notably, the majority of these MTases share close homology with those encoded by gut bacteria, suggesting their exchange during phage-bacterium interactions. (embl.de)

Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. (biomedcentral.com)
To understand these processes through comprehensive analyses of microbial ecology, evolution and metabolism, sequenced reference genomes of representative native prokaryotes are crucial. (biomedcentral.com)

Addition of these phylogenetically classified, diverse, and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes. (biomedcentral.com)

We sequenced isolates from Colombia, Guatemala, Costa Rica, and the Netherlands and complemented them with publicly available genomes from Europe, Africa, and the Middle East. (cdc.gov)

Both strains possessed WO-like phage regions and type I and type IV secretion systems. (uibk.ac.at)

Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. (biomedcentral.com)

Increased MTase copies are associated with higher genome methylation densities, specific methylation motifs, and elevated prevalence of certain phage groups. (embl.de)

2018). This discontinuity has been criticized as being an artefact of various biases in genome databases (Murray, Gao, and Wu 2020), but appears to be a general feature of relatively unbiased metagenome-assembled genomes as well (Olm et al. (peercommunityin.org)

Genome Biol. (wikipedia.org)

This transformative conference will bring together experts in phage genomes and metagenomes to discuss the latest advances in genome annotations and annotations. (edu.au)
Each edge is annotated with the genomes to which it belongs, in addition to the gene annotations given by Prokka, and whether or not it is a paralog. (rorek.org)

The presence of c4 antisense RNAs in bacteria is to be expected, since the P1 and P7 phages are temperate and can stably integrate into the host genome. (wikipedia.org)
Pawel Markwitz (University of Wroclaw, Poland) and colleagues published a new paper in ISME on genome-driven elucidation of phage-host interplay and the impact of phage resistance evolution on bacterial fitness . (phagedirectory.com)
Furthermore, these MTases can be employed to accurately predict phage-host relationships. (embl.de)
Overall, the findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems, with a substantial contribution from phage-encoded MTases. (embl.de)
The "Gratiaviridae" phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. (biomedcentral.com)
When time's up, an infecting phage lyses its host cell, thus releasing the assembled virions. (asmblog.org)
The phage Lactobacillus phiadh modulates the level of its host bacterium, #Lactobacillus gasseri , which affects the host's immune system. (metabiom.org)

Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. (biomedcentral.com)

P, Verhelst B, ..., Reusch TBH, Van de Peer Y (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. (mardata.de)

Genome Science, 2017]. (alzforum.org)

But with two projects, communities are forming to generate high quality genomes to benefit researchers. (doe.gov)

However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown. (biomedcentral.com)
Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections. (cdc.gov)

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