Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained ...from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as 'Candidatus Peribacter riflensis', Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.
Cronobacter sakazakii is a foodborne pathogen that causes septicemia, meningitis, and necrotizing enterocolitis in neonates and infants. The current research details the full genome sequences of two ...extremely persistent C. sakazakii strains (H322 and GK1025B) isolated from powdered infant formula (PIF) manufacturing settings. In addition, the genetic attributes associated with five plasmids, pH322_1, pH322_2, pGK1025B_1, pGK1025B_2, and pGK1025B_3 are described.
Using PacBio single-molecule real-time (SMRT
) sequencing technology, whole genome sequence (WGS) assemblies of C. sakazakii H322 Sequence type (ST)83, clonal complex CC 83) and GK1025B (ST64, CC64) were generated. Plasmids, also sequenced, were aligned with phylogenetically related episomes to determine, and identify conserved and missing genomic regions.
A truncated ~ 13 Kbp type 6 secretion system (T6SS) gene cluster harbored on virulence plasmids pH322_2 and pGK1025B_2, and a second large deletion (~ 6 Kbp) on pH322_2, which included genes for a tyrosine-type recombinase/integrase, a hypothetical protein, and a phospholipase D was identified. Within the T6SS of pH322_2 and pGK1025B_2, an arsenic resistance operon was identified which is in common with that of plasmids pSP291_1 and pESA3. In addition, PHASTER analysis identified an intact 96.9 Kbp Salmonella SSU5 prophage gene cluster in pH322_1 and pGK1025B_1 and showed that these two plasmids were phylogenetically related to C. sakazakii plasmids: pCS1, pCsa767a, pCsaC757b, pCsaC105731a. Plasmid pGK1025B_3 was identified as a novel conjugative Cronobacter plasmid. Furthermore, WGS analysis identified a ~ 16.4 Kbp type 4 secretion system gene cluster harbored on pGK1025B_3, which contained a phospholipase D gene, a key virulence factor in several host-pathogen diseases.
These data provide high resolution information on C. sakazakii genomes and emphasizes the need for furthering surveillance studies to link genotype to phenotype of strains from previous investigations. These results provide baseline data necessary for future in-depth investigations of C. sakazakii that colonize PIF manufacturing facility settings and genomic analyses of these two C. sakazakii strains and five associated plasmids will contribute to a better understanding of this pathogen's survival and persistence within various "built environments" like PIF manufacturing facilities.
Sponges (phylum Porifera) are ancient, marine and inland water, filter feeding metazoans. In recent years, diseased sponges have been increasingly occurring in marine and freshwater environments. ...Endemic freshwater sponges of the Lubomirskiidae family are widely distributed in the coastal zone of Lake Baikal. The strain
sp. SLB01 was isolated previously from the diseased sponge
(Pallas, 1776), although its pathogenicity is still unknown. The aim of this study was to confirm whether the
sp. strain SLB01 is the pathogen found in Baikal sponge. To address this aim, we infected the cell culture of primmorphs of the sponge
with strain SLB01 and subsequently reisolated and sequenced the strain
sp. PLB02. The results showed that the isolated strain has more than 99% homology with strain SLB01. The genomes of both strains contain genes vioABCDE of violacein biosynthesis and floc formation, for strong biofilm, in addition to the type VI secretion system (T6SS) as the main virulence factor. Based on a comparison of complete genomes, we showed the similarity of the studied bacterial strains of
spp. with the described strain of
MTR. This study will help expand our understanding of microbial interactions and determine one of the causes in the development of diseases and death in Baikal sponges.
Analysis of the completely determined genomes of the plant-derived Acholeplasma brassicae strain O502 and A. palmae strain J233 revealed that the circular chromosomes are 1,877,792 and 1,554,229 bp ...in size, have a G + C content of 36 and 29%, and encode 1,690 and 1,439 proteins, respectively. Comparative analysis of these sequences and previously published genomes of A. laidlawii strain PG-8, 'Candidatus Phytoplasma asteris' strains, 'Ca. P. australiense' and 'Ca. P. mali' show a limited shared basic genetic repertoire. The acholeplasma genomes are characterized by a low number of rearrangements, duplication and integration events. Exceptions are the unusual duplication of rRNA operons in A. brassicae and an independently introduced second gene for a single-stranded binding protein in both genera. In contrast to phytoplasmas, the acholeplasma genomes differ by encoding the cell division protein FtsZ, a wide variety of ABC transporters, the F0F1 ATP synthase, the Rnf-complex, SecG of the Sec-dependent secretion system, a richly equipped repertoire for carbohydrate metabolism, fatty acid, isoprenoid and partial amino acid metabolism. Conserved metabolic proteins encoded in phytoplasma genomes such as the malate dehydrogenase SfcA, several transporters and proteins involved in host-interaction, and virulence-associated effectors were not predicted for the acholeplasmas.
Genomoviridae is a virus family belonging to circular replication associated protein encoding ssDNA (CRESS-DNA) viruses, which have diverse genomic architecture and are widely distributed among ...different ecosystems. In this study, we characterized 39 novel genomovirus genomes including 3 from wild egrets, 9 from wild cranes, as well as 27 from wild finches in three different types of cloacal swabs of wild bird sampled in the station of Xinqing bird ringing, Maoershan Nature Reserve in Heilongjiang Province, Changbai Mountain in Jilin Province, and Hangzhou Wetland Park in Zhejiang Province, China. Here, using a Rep sequence phylogeny-based analysis, we divided the 39 genomoviruses into 8 genera within the family Genomoviridae, including Gemycircularvirus (n=20), Gemykibivirus (n=3), Gemygorvirus (n=2), Gemyvongvirus (n=2), Gemykolovirus (n=3), Gemykrogvirus (n=6), Gemytondvirus (n=1), Gemyduguivirus (n=1) and one unclassified genomovirus. The 39 genomovirus genomes belong to 36 species (27 of which are new) based on the currently accepted genomovirus pairwise nucleotide sequence identity species demarcation threshold of 78%. Overall, the research enriches our knowledge of CRESS-DNA viral diversity in China and emphasizes the prevalence of genomoviruses in nature.
•This study investigated wild birds associated genomovirus using viral metagenomics.•We uncovered the structure of these genomoviruses and phylogenetic trees based on Rep proteins. The 39 novel genomoviruses belonging to 36 species, 27 of which are novel.•Our study expands the known diversity of CRESS-DNA virus associated with wild birds and adds to the rapidly increasing genomovirus database.
One of the most important aspects of mitochondrial (mt) genome evolution in Metazoa is constancy of size and gene content of mtDNA, whose plasticity is maintained through a great variety of gene ...rearrangements probably mediated by tRNA genes. The trend of mtDNA to maintain the same genetic structure within a phylum (e.g., Chordata) is generally accepted, although more recent reports show that a considerable number of transpositions are observed also between closely related organisms. Base composition of mtDNA is extremely variable. Genome GC content is often low and, when it increases, the two complementary bases distribute asymmetrically, creating, particularly in vertebrates, a negative GC-skew. In mammals, we have found coding strand base composition and average degree of gene conservation to be related to the asymmetric replication mechanism of mtDNA. A quantitative measurement of mtDNA evolutionary rate has revealed that each of the various components has a different evolutionary rate. Non-synonymous rates are gene specific and fall in a range comparable to that of nuclear genes, whereas synonymous rates are about 22-fold higher in mt than in nuclear genes. tRNA genes are among the most conserved but, when compared to their nuclear counterparts, they evolve 100 times faster. Finally, we describe some molecular phylogenetic reconstructions which have produced unexpected outcomes, and might change our vision of the classification of living organisms.
Sweet potatoes (Ipomea batatas L.) are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle ...virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), and Sweet potato latent virus (SPLV), have been detected in sweet potato fields at a high (~95%) incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88%) nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.
Viruses of the Parvoviridae family constitute a most diverse and intriguing field of research. Parvoviruses can differ widely in their structure, genome organization and expression, virus–cell ...interactions, and impact on hosts. The translational implication of research on parvoviruses is relevant, since many viruses are important human and veterinary pathogens, while other viruses can be engineered as tools for oncolytic therapy or as sophisticated gene delivery vectors. Exploring the diversity and inherent complexity in the biology of these apparently simple viruses is a still challenging topic for the scientific community. The Special Issue of Viruses is a collection of recent contributions in the field of parvovirus research, encompassing many aspects of basic and translational research on viruses of the family Parvoviridae, including on their structure, replication, and gene expression in addition to virus–host interactions and the development of vaccines and viral vectors.
Hepatitis B virus (HBV) is a worldwide public health concern. The circulation of strains carrying mutations in the viral proteins implies both clinical and therapeutics challenges. HBV complete ...genomes (HBV-CGs) were reported from injecting drug users and HBV chronically infected patients from Argentina—including Amerindians—although no studies were conducted in blood donors. Here, we described HBV-CG sequences from the latter population. Some of the HBV sequences classified as B2 and C2 subgenotypes clustering together with Asian isolates, while others, such as D3, F1b, and F4, were homologous to European and Latin America sequences. New substitutions for all analyzed open reading frames and changes in the HBsAg hydrophobicity profiles were detected. Several HBV-CG subgenotypes are described for the first time in this population. Mutations observed in X, PreS, and P proteins have been associated with advanced liver disease, hepatocellular carcinoma, and/or natural resistance to nucleos(t)ide antiviral treatment. It deserves to be highlighted that these substitutions were detected in a population without epidemiological risk factors for viral infection, and most importantly, without any previous antiviral treatment (natural resistance). Regarding the remaining mutations, further research is warranted in order to determine their clinical and therapeutics relevance.
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