The Experts below are selected from a list of 1332 Experts worldwide ranked by ideXlab platform
Hans-w. Ackermann - One of the best experts on this subject based on the ideXlab platform.
-
Comparative Analysis of 37 Acinetobacter Bacteriophages.
Viruses, 2017Co-Authors: Dann Turner, Hans-w. Ackermann, Rob Lavigne, Andrew M. Kropinski, J. Sutton, Darren M. ReynoldsAbstract:Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.
-
Streptococcus thermophilus bacteriophages.
International Dairy Journal, 2010Co-Authors: Andrea Del Lujan Quiberoni, Sylvain Moineau, Geneviève M. Rousseau, Jorge Reinheimer, Hans-w. AckermannAbstract:At least 345 bacteriophages infecting Streptococcus thermophilus starter cultures have been isolated; general characteristics include high thermal resistance, short latent periods and large burst size. Phages with such characteristics are primed to thrive in the cheese making environment, lysing bacterial cultures and generating low-quality fermented products. All S. thermophilus phages isolated to date are members of the Siphoviridae family and the Caudovirales order and appear to constitute a polythetic phage species comprising two large groups, cos- and pac-types, based on the mode of DNA packaging. Comparative analyses have shown that S. thermophilus phage genomes are similarly organized into distinct modular regions and allow the detection of a core genome region. Several PCR-based techniques have been designed to detect them in cheese whey and milk samples. Similar S. thermophilus phages are globally distributed and endemic in specific dairy environments. The biogeography of S. thermophilus phages reinforces their current classification.
-
Bacteriophage observations and evolution.
Research in Microbiology, 2003Co-Authors: Hans-w. AckermannAbstract:Bacteriophages are classified into one order and 13 families. Over 5100 phages have been examined in the electron microscope since 1959. At least 4950 phages (96%) are tailed. They constitute the order Caudovirales and three families. Siphoviridae or phages with long, noncontractile tails predominate (61% of tailed phages). Polyhedral, filamentous, and pleomorphic phages comprise less than 4% of bacterial viruses. Bacteriophages occur in over 140 bacterial or archaeal genera. Their distribution reflects their origin and bacterial phylogeny. Bacteriophages are polyphyletic, arose repeatedly in different hosts, and constitute 11 lines of descent. Tailed phages appear as monophyletic and as the oldest known virus group.
-
Bacteriophage observations and evolution
Research in Microbiology, 2003Co-Authors: Hans-w. AckermannAbstract:Bacteriophages are classified into one order and 13 families. Over 5100 phages have been examined in the electron microscope since 1959. At least 4950 phages (96%) are tailed. They constitute the order Caudovirales and three families. Siphoviridae or phages with long, noncontractile tails predominate (61% of tailed phages). Polyhedral, filamentous, and pleomorphic phages comprise less than 4% of bacterial viruses. Bacteriophages occur in over 140 bacterial or archaeal genera. Their distribution reflects their origin and bacterial phylogeny. Bacteriophages are polyphyletic, arose repeatedly in different hosts, and constitute 11 lines of descent. Tailed phages appear as monophyletic and as the oldest known virus group. © 2003 Éditions scientifiques et médicales Elsevier SAS. All rights reserved.
-
tailed bacteriophages the order Caudovirales
Advances in Virus Research, 1998Co-Authors: Hans-w. AckermannAbstract:Publisher Summary This chapter discusses the common properties of tailed phages and potential criteria for their classification as an order and situating tailed phages with respect to other viruses. Tailed bacteriophages have a common origin and constitute an order with three families, named Caudovirales. Their structured tail is unique. Tailed phages share a series of high-level taxonomic properties and show many facultative features that are unique or rare in viruses—for example, tail appendages and unusual bases. They share with other viruses, especially herpesviruses, elements of morphogenesis and lifestyle that are attributed to convergent evolution. Tailed phages present three types of lysogeny, exemplified by phages λ, Mu, and P1. Lysogeny appears as a secondary property acquired by horizontal gene transfer. Amino acid sequence alignments (notably of DNA polymerases, integrases, and peptidoglycan hydrolases) indicate frequent events of horizontal gene transfer in tailed phages. Common capsid and tail proteins have not been detected. Present-day tailed phages appear as chimeras, but their monophyletic origin is still inscribed in their morphology, genome structure, and replication strategy. It may also be evident in the three-dimensional structure of capsid and tail proteins. It is unlikely to be found in amino acid sequences because constitutive proteins must be so old that relationships were obliterated and most or all replication-, lysogeny-, and lysis-related proteins appear to have been borrowed.
Don Cowan - One of the best experts on this subject based on the ideXlab platform.
-
Exploring Viral Diversity in a Unique South African Soil Habitat
Scientific Reports, 2018Co-Authors: Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don CowanAbstract:© 2017 The Author(s). The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high fre quency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.
Jane Segobola - One of the best experts on this subject based on the ideXlab platform.
-
Exploring Viral Diversity in a Unique South African Soil Habitat.
Scientific Reports, 2018Co-Authors: Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don A. CowanAbstract:The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.
-
Exploring Viral Diversity in a Unique South African Soil Habitat
Scientific Reports, 2018Co-Authors: Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don CowanAbstract:© 2017 The Author(s). The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high fre quency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.
Evelien Adriaenssens - One of the best experts on this subject based on the ideXlab platform.
-
Exploring Viral Diversity in a Unique South African Soil Habitat.
Scientific Reports, 2018Co-Authors: Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don A. CowanAbstract:The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.
-
Exploring Viral Diversity in a Unique South African Soil Habitat
Scientific Reports, 2018Co-Authors: Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don CowanAbstract:© 2017 The Author(s). The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high fre quency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.
-
Metagenomic analysis of the viral community in Namib Desert hypoliths
Environmental Microbiology, 2014Co-Authors: Evelien Adriaenssens, Pieter De Maayer, Enrico Rubagotti, Edward P. Rybicki, Marla I. Tuffin, Don A. CowanAbstract:Summary Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert. The taxonomic composition of the hypolithic viral communities was investigated and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales, in particular the family Siphoviridae, were most prevalent. Functional analysis and comparison with other metaviromes revealed a relatively high frequency of cell wall-degrading enzymes, ribonucleotide reductases (RNRs) and phage-associated genes. Phylogenetic analyses of terL and phoH marker genes indicated that many of the sequences were novel and distinct from known isolates, and the class distribution of the RNRs suggests that this is a novel environment. The composition of the viral hypolith fraction containing many Bacillus-infecting phages was not completely consistent with Namib hypolith phylotypic surveys of the bacterial hosts, in which the cyanobacterial genus Chroococcidiopsis was found to be dominant. This could be attributed to the lack of sequence information about hypolith viruses/bacteria in public databases or the possibility that hypolithic communities incorporate viruses from the surrounding soil.
Philip Hugenholtz - One of the best experts on this subject based on the ideXlab platform.
-
evaluation of a concatenated protein phylogeny for classification of tailed double stranded dna viruses belonging to the order Caudovirales
Nature microbiology, 2019Co-Authors: Maria Džunkova, Pierrealain Chaumeil, Donovan H Parks, Philip HugenholtzAbstract:Viruses of bacteria and archaea are important players in global carbon cycling as well as drivers of host evolution, yet the taxonomic classification of viruses remains a challenge due to their genetic diversity and absence of universally conserved genes. Traditional classification approaches employ a combination of phenotypic and genetic information which is no longer scalable in the era of bulk viral genome recovery through metagenomics. Here, we evaluate a phylogenetic approach for the classification of tailed double-stranded DNA viruses from the order Caudovirales by inferring a phylogeny from the concatenation of 77 single-copy protein markers using a maximum-likelihood method. Our approach is largely consistent with the International Committee on Taxonomy of Viruses, with 72 and 89% congruence at the subfamily and genus levels, respectively. Discrepancies could be attributed to misclassifications and a small number of highly mosaic genera confounding the phylogenetic signal. We also show that confidently resolved nodes in the concatenated protein tree are highly reproducible across different software and models, and conclude that the approach can serve as a framework for a rank-normalized taxonomy of most tailed double-stranded DNA viruses. Phylogenetic analysis based on a concatenated set of 77 single-copy marker genes enabled the classification of tailed double-stranded DNA viruses from large datasets, and was reproducible across software and models, providing a framework that could be applied to other viruses.