scholarly journals Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus Plantarum - A Novel Lineage of Lactobacillus Phages Comprising Five New Members

2018 ◽  
Author(s):  
Ifigeneia Kyrkou ◽  
Alexander Byth Carstens ◽  
Lea Ellegaard-Jensen ◽  
Witold Kot ◽  
Athanasios Zervas ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
New Genus ◽  
Phage Genome ◽  
Probiotic Properties ◽  
New Members ◽  
Transmission Electron ◽  
The Family ◽  
High Degree ◽  
Degree Of Similarity ◽  
Insight Into

Lactobacillus plantarum is a bacterium with promising applications to the food industry and agriculture and probiotic properties. So far, bacteriophages of this bacterium have been moderately addressed. We examined the morphology and diversity of five new L. plantarum phages via transmission electron microscopy, whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. The five phages share a high degree of similarity among them and belong to the family Myoviridae. They have a long genome of 137.973-141.344 bp, a G/C content of 36,3-36,6% that is quite distinct from their host’s, and, surprisingly, seven to 15 tRNAs. Only an average 35/174 of their predicted genes were assigned a function. Overall, the comparative analyses unraveled considerable genetic diversity for our five L. plantarum phages. Hence, the new genus “Semelevirus” was proposed, which comprises exclusively the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp. Our results on Lactobacillus phages have a potential value for the development of anti-phage strategies as well as for the manipulation of L. plantarum fermentations.

scholarly journals Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus Plantarum - A Novel Lineage of Lactobacillus Phages Comprising Five New Members

2019 ◽  
Author(s):  
Ifigeneia Kyrkou ◽  
Alexander Byth Carstens ◽  
Lea Ellegaard-Jensen ◽  
Witold Kot ◽  
Athanasios Zervas ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Protein Sequencing ◽  
Probiotic Properties ◽  
Structural Protein ◽  
New Members ◽  
Transmission Electron ◽  
The Family ◽  
Associated Proteins ◽  
High Degree ◽  
Selection Of

Lactobacillus plantarum is a bacterium with promising applications to the food industry and agriculture and probiotic properties. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137.973-141.344 bp, a G/C content of 36,3-36,6% that is quite distinct from their host’s, and, surprisingly, seven to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages of this study. Hence, the new genus “Semelevirus” was proposed, which comprises exclusively the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp.. The five new Lactobacillus phages have a potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.

scholarly journals Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum—A Novel Lineage of Lactobacillus Phages Comprising Five New Members

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 611 ◽  
Author(s):  
Ifigeneia Kyrkou ◽  
Alexander Byth Carstens ◽  
Lea Ellegaard-Jensen ◽  
Witold Kot ◽  
Athanasios Zervas ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Protein Sequencing ◽  
Probiotic Properties ◽  
Structural Protein ◽  
New Members ◽  
Transmission Electron ◽  
The Family ◽  
Associated Proteins ◽  
High Degree ◽  
Selection Of

Lactobacillus plantarum is a bacterium with probiotic properties and promising applications in the food industry and agriculture. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137,973–141,344 bp, a G/C content of 36.3–36.6% that is quite distinct from their host’s, and surprisingly, 7 to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages in this study. Hence, the new genus “Semelevirus” was proposed, comprising exclusively of the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp. The five new Lactobacillus phages have potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.

scholarly journals Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, “Silenusvirus”

2019 ◽  
Author(s):  
Ifigeneia Kyrkou ◽  
Alexander Byth Carstens ◽  
Lea Ellegaard-Jensen ◽  
Witold Kot ◽  
Athanasios Zervas ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Organic Waste ◽  
New Genus ◽  
Control Strategies ◽  
Protein Sequencing ◽  
Genomic Diversity ◽  
Structural Protein ◽  
Transmission Electron ◽  
The Family ◽  
Genomic Similarity

ABSTRACTBacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus “Silenusvirus”.

scholarly journals The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1179
Author(s):  
Ueric José Borges de Souza ◽  
Luciana Cristina Vitorino ◽  
Layara Alexandre Bessa ◽  
Fabiano Guimarães Silva
Keyword(s):  
Plastid Genome ◽  
Structural Characteristics ◽  
Gc Content ◽  
Single Copy ◽  
Chloroplast Genes ◽  
Artocarpus Heterophyllus ◽  
Plastid Genomes ◽  
The Family ◽  
High Degree ◽  
Degree Of Similarity

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.

Kootenaia burkei, a new genus and species of slug from northern Idaho, United States (Gastropoda: Pulmonata: Arionidae)

Zootaxa ◽  
2003 ◽  
Vol 355 (1) ◽  
pp. 1 ◽  
Author(s):  
WILLIAM P. LEONARD ◽  
LYLE CHICHESTER ◽  
JIM BAUGH ◽  
THOMAS WILKE
Keyword(s):  
United States ◽  
New Genus ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
New Genus And Species ◽  
Molecular Analyses ◽  
The Family ◽  
Taxonomic Decision ◽  
Northern Idaho ◽  
High Degree

A new genus and species of arionid slug, Kootenaia burkei n. gen. et n. sp., are formally described from northern Idaho, United States. This taxonomic decision is based on comparative anatomical and molecular data involving representatives of a total of ten species and three additional genera (Hemphillia, Prophysaon, and Zacoleus) of the family Arionidae. The anatomical analyses show that the new genus is characterized by a major autapomorphy, the complete absence of an epiphallus, which is found in all other arionids. The molecular analyses using two mitochondrial genes and the anatomical data produce congruent topologies. Overall, there is a high degree of concordance between the anatomical and molecular datasets.

Biochemical systematics of the marine fish family Centrolophidae (Teleostei:Stromateoidei) from Australian waters

1994 ◽  
Vol 45 (7) ◽  
pp. 1157 ◽  
Author(s):  
CJS Bolch ◽  
RD Ward ◽  
PR Last
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Cladistic Analysis ◽  
Allozyme Electrophoresis ◽  
Stable Group ◽  
Fish Family ◽  
Upgma Tree ◽  
The Family ◽  
High Degree ◽  
Degree Of Similarity

The phylogenetic relationships of 11 stromateoid species (nine from the Family Centrolophidae and one each from the Nomeidae and Tetragonuridae) were examined by allozyme electrophoresis. Data from 30 loci were used for three phylogenetic analyses. Two phenetic trees were derived: a UPGMA tree derived from Nei's unbiased genetic distance, and a distance-Wagner tree based on modified Rogers' distances. A cladistic analysis, using maximum parsimony, was also carried out with loci as characters and alleles as unordered states. The tree topology of all three analyses showed a high degree of similarity, which increased confidence in the phylogenetic interpretation and generally supported the classical taxonomic theory of centrolophid relationships. The 'hard-spined' centrolophid taxa, including Seriolella, Psenopsis, Schedophilus labyrinthicus and Hyperoglyphe, formed a stable group In all trees. Psenopsis was closely allied to Seriolella in all three analyses, which supports the view that this genus is derived from Seriolella. Centrolophus and Tubbia consistently diverged from the ancestral line of taxa near the base of the tree, so may have diverged from ancestral stock earlier than previously thought. The most striking departure from current taxonomic theory was the wide separation of Schedophilus labyrinthicus and Schedophilus huttoni, indicating that the genus Schedophilus is polyphyletic. A revision of the genus is needed and should include morphological and electrophoretic analyses of all Schedophilus species, with particular reference to the type species S. medusophagus.

scholarly journals Ordovician radiolarian biodiversity : insights based on new and revised data from Kazakhstan

2003 ◽  
Vol 174 (4) ◽  
pp. 325-335 ◽  
Author(s):  
Taniel Danelian ◽  
Leonid Popov
Keyword(s):  
Carbonate Rocks ◽  
New Genus ◽  
New Members ◽  
Radiolarian Assemblage ◽  
Good State ◽  
Lower Ordovician ◽  
The Family ◽  
The World ◽  
Lower Palaeozoic ◽  
Age Range

Abstract Since the 1970s Ordovician carbonate rocks from Kazakhstan have provided well-preserved radiolarian faunas and this country remains one of the most important areas in the world to learn about Lower Palaeozoic radiolarian taxonomy and biostratigraphy. Here we describe a new lower Arenigian radiolarian assemblage and discuss all currently available Ordovician radiolarian data from Kazakhstan. The newly discovered assemblage is curiously oligospecific, despite its good state of preservation. Four morphospecies are recognised, including a new genus and two new species : Inanihella bakanasensis (Nazarov) and I.(?) akzhala n.sp, which characterise the assemblage, together with Triplococcus acanthicus n.gen n.sp. and Proventocitum sp.cf. P. procerulum. This is the oldest radiolarian assemblage from limestone lithologies of Kazakhstan and one of the very few Lower Ordovician assemblages discovered worldwide. We specify in this study the age range of the succeeding Haplentactinia armillata-Proventocitum procerulum assemblage, defined earlier by Nazarov and Popov [1980], which now covers the middle Arenigian – lower Llanvirnian (lower Abereiddian) interval. The succeeding upper Llanvirnian (Llandeilian) Haplentactinia juncta – Inanigutta unica assemblage reported by Nazarov and Popov [1980] reflects a substantial increase in radiolarian diversity, due largely to the introduction of new members of the family Inaniguttidae.

scholarly journals Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae

2020 ◽  
Vol 70 (3) ◽  
pp. 2147-2154 ◽  
Author(s):  
Guang-Da Feng ◽  
Xian-Jiao Zhang ◽  
Song-Zhen Yang ◽  
An-Zhang Li ◽  
Qing Yao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
New Genus ◽  
The Novel ◽  
New Combinations ◽  
Novel Genus ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Insight Into

During a phylogenetic analysis of Sphingorhabdus and its closely related genera in the family Sphingomonadaceae , we found that the genus Sphingorhabdus and the species Sphingopyxis baekryungensis might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus Sphingorhabdus should be reclassified into two genera (Clade I and Clade II), for which the original genus name, Sphingorhabdus , is proposed to be retained only for Clade I, and a new genus named as Parasphingorhabdus gen. nov. is proposed for Clade II with four new combinations: Parasphingorhabdus marina comb. nov., Parasphingorhabdus litoris comb. nov., Parasphingorhabdus flavimaris comb. nov. and Parasphingorhabdus pacifica comb. nov. Moreover, Sphingopyxis baekryungensis should represent a novel genus in the family Sphingomonadaceae , for which the name Novosphingopyxis gen. nov. is proposed, with a combination of Novosphingopyxis baekryungensis comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family Sphingomonadaceae .

scholarly journals A new species of Atrimitra Dall, 1918 (Gastropoda: Mitridae) from seamounts of the recently created Nazca-Desventuradas Marine Park, Chile

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8279
Author(s):  
Javier Sellanes ◽  
Richard A. Salisbury ◽  
Jan M. Tapia ◽  
Cynthia M. Asorey
Keyword(s):  
New Species ◽  
Benthic Fauna ◽  
Remotely Operated Vehicle ◽  
Present Contribution ◽  
North Central ◽  
Marine Park ◽  
The Family ◽  
Western Side ◽  
High Degree ◽  
Insight Into

We describe Atrimitra isolata sp. n. (Gastropoda: Mitridae), collected on the summit of seamounts (~200 m water depth) in the vicinity of Desventuradas Islands, Chile insular territory. Additionally, we provide some insight into the habitat of this new species based on underwater imagery taken with a remotely operated vehicle. A. isolata sp. n. is characterized by its small size (up to 26 mm), elongate-ovate shape, solid shell and smooth appearance. It has a base brown color, with some specimens being tan or yellow. It is morphologically related to counterparts from shallow depths on the west coast of North, Central and South America (i.e., Atrimitra idae, Atrimitra orientalis and Atrimitra semigranosa), but has no affinities with species of the family reported from around Easter Island, on the far western side of the Salas y Gómez ridge (e.g., Strigatella flavocingulata, Imbricariopsis punctata and Neocancilla takiisaoi), or with other Indo-Pacific species. The present contribution adds to the knowledge of the poorly studied fauna of the seamounts in the southern portion of the Nazca ridge and easternmost section of the Sala y Gómez ridge, an area characterized by the high degree of endemism of its benthic fauna, and now protected within the large and newly created Nazca-Desventuradas Marine Park.

scholarly journals Life Cycle, Ultrastructure, and Phylogeny of New Diplonemids and Their Endosymbiotic Bacteria

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
Author(s):  
Daria Tashyreva ◽  
Galina Prokopchuk ◽  
Jan Votýpka ◽  
Akinori Yabuki ◽  
Aleš Horák ◽  
...  
Keyword(s):  
Life Cycle ◽  
New Genus ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
New Members ◽  
Endosymbiotic Bacteria ◽  
Marine Protists ◽  
Two Stages ◽  
Oceanic Ecosystem ◽  
Insight Into

ABSTRACT Diplonemids represent a hyperdiverse and abundant yet poorly studied group of marine protists. Here we describe two new members of the genus Diplonema (Diplonemea, Euglenozoa), Diplonema japonicum sp. nov. and Diplonema aggregatum sp. nov., based on life cycle, morphology, and 18S rRNA gene sequences. Along with euglenozoan apomorphies, they contain several unique features. Their life cycle is complex, consisting of a trophic stage that is, following the depletion of nutrients, transformed into a sessile stage and subsequently into a swimming stage. The latter two stages are characterized by the presence of tubular extrusomes and the emergence of a paraflagellar rod, the supportive structure of the flagellum, which is prominently lacking in the trophic stage. These two stages also differ dramatically in motility and flagellar size. Both diplonemid species host endosymbiotic bacteria that are closely related to each other and constitute a novel branch within Holosporales , for which a new genus, “ Candidatus Cytomitobacter” gen. nov., has been established. Remarkably, the number of endosymbionts in the cytoplasm varies significantly, as does their localization within the cell, where they seem to penetrate the mitochondrion, a rare occurrence. IMPORTANCE We describe the morphology, behavior, and life cycle of two new Diplonema species that established a relationship with two Holospora -like bacteria in the first report of an endosymbiosis in diplonemids. Both endosymbionts reside in the cytoplasm and the mitochondrion, which establishes an extremely rare case. Within their life cycle, the diplonemids undergo transformation from a trophic to a sessile and eventually a highly motile swimming stage. These stages differ in several features, such as the presence or absence of tubular extrusomes and a paraflagellar rod, along with the length of the flagella. These morphological and behavioral interstage differences possibly reflect distinct functions in dispersion and invasion of the host and/or prey and may provide novel insight into the virtually unknown function of diplonemids in the oceanic ecosystem.

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