We report a complete genome of Pectobacterium brasiliense strain 21PCA_AGRO2 isolated from napa cabbage, in which the genome consists of a circular chromosome comprising 4,919,671 bp with 4,399 ...coding DNA sequences, 22 rRNA genes, 77 tRNA genes, and 9 noncoding RNA genes.
Members of the family
are metabolically versatile and ubiquitous in natural environments, with extraordinary genome feature of two chromosomes. Here we reported the complete genome of
NSCS20N07D
, a ...recently described novel genus-level species in the family
. It contained two circular chromosomes with a size of 2,593,992 bp with G+C content of 31.2 mol%, and a plasmid with a size of 5,539 bp. The larger chromosome (Chr. I) had a genome size of 1,426,504 bp with G+C content of 31.6 mol%, and the smaller one (Chr. II) had a genome size of 1,161,949 bp with G+C content of 30.8 mol%. The two chromosomes have strikingly similar G+C contents with difference of <1% and similar percentages of coding regions. Interestingly, by comparison to 134 species affiliated with seven genera within the family
,
NSCS20N07D
possessed the smallest genome size and lowest G+C content. Clusters of orthologous groups of proteins functional categories revealed that the two chromosomes had different distributions of functional classes, indicating they take different cellular functions. Surprisingly, Chr. II had a large proportion of unknown genes than Chr. I. Metabolic characteristics predicted that Chr. I performed the essential metabolism, which can be complemented by the Chr. II, such as amino acids biosynthesis. Microbial community analysis of
surface seawater revealed that
accounted for one to four sequences among more than 20,000 of 16S ribosomal RNA gene V4 contigs, representing it apparently appeared as a rare species. What's more,
was anticipated to be specific to the pelagic ocean. This study will provide new insight into more understanding the genomic and metabolic features of multiple chromosomes in prokaryote and emphasize the ecological distribution of the members in the family
as a rare species.
Bats are of significant interest as reservoirs for various zoonotic viruses with high diversity. During the past two decades, many herpesviruses have been identified in various bats worldwide by ...genetic approaches, whereas there have been few reports on the isolation of infectious herpesviruses. Herein, we report the prevalence of herpesvirus infection of bats captured in Zambia and genetic characterization of novel gammaherpesviruses isolated from striped leaf-nosed bats
). By our PCR screening, herpesvirus DNA polymerase (DPOL) genes were detected in 29.2% (7/24) of Egyptian fruit bats (
), 78.1% (82/105) of
, and one Sundevall's roundleaf bat (
) in Zambia. Phylogenetic analyses of the detected partial DPOL genes revealed that the Zambian bat herpesviruses were divided into seven betaherpesvirus groups and five gammaherpesvirus groups. Two infectious strains of a novel gammaherpesvirus, tentatively named Macronycteris gammaherpesvirus 1 (MaGHV1), were successfully isolated from
bats, and their complete genomes were sequenced. The genome of MaGHV1 encoded 79 open reading frames, and phylogenic analyses of the DNA polymerase and glycoprotein B demonstrated that MaGHV1 formed an independent lineage sharing a common origin with other bat-derived gammaherpesviruses. Our findings provide new information regarding the genetic diversity of herpesviruses maintained in African bats.
A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the ...Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents. This study demonstrated a successful procedure to sequence the SARS-CoV-2 whole genome with average ∼2351 depth and 98.1% of total the reads aligned against the reference sequence (SARS-CoV-2, isolate Wuhan-Hu-1, complete genome). Although genome coverage varied, complete genomes were retrieved for both reagent sets with a reduced cost. This study proposed an alternative approach of high throughput sequencing using Ion torrent technology for the sequencing of SARS-CoV-2 in developing countries where sequencing facilities are low. This blended sequencing technique also offers a low cost protocol in developing countries like Bangladesh.
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ABSTRACT
Shigella flexneri
was associated with gingivitis, a periodontal disease, in the rhesus monkey. We report the circularized 4.8-Mbp complete genome of
Shigella flexneri
strain P099 isolated ...from the gum of an adult rhesus monkey,
Macaca mulatta
, with clinical symptoms of gingivitis.
To date, a small number of temperate phages are known to infect members of the genus Erwinia. In this study, the genomes of temperate phages vB_EhrS_49 and vB_EhrS_59 infecting Erwinia horticola, the ...causative agent of beech black bacteriosis in Ukraine, were sequenced and annotated. Their genomes reveal no significant similarity to that of any previously reported viruses of Enterobacteriaceae. At the same time, phages 49 and 59 share extensive nucleotide sequence identity across the regions encoding head assembly, DNA packaging, and lysis. Despite significant homology between structural modules, the organization of distal tail morphogenesis genes is different. Furthermore, a number of putative morons and DNA methylases have been found in both phage genomes. Due to the revealed synteny as well as the structure of lysogeny module, phages 49 and 59 are suggested to be novel members of the lambdoid phage group. Conservative structural genes together with varying homology across the nonstructural region of the genomes make phages 49 and 59 highly promising objects for studying the genetic recombination and evolution of microbial viruses. The obtained data may as well be helpful for better understanding of relationships among Erwinia species.
Vibrios are a group of very important bacterial pathogens in marine aquaculture industry and cause serious aquatic animal diseases, such as shrimp acute hepatopancreatic necrosis disease (AHPND). A ...new AHPND pathogen, the
Vibrio owensii
strain SH-14, was isolated from diseased shrimp in Shanghai, China. In this study, to better understand the pathogenesis of AHPND at the genomic level, the genome of the strain SH-14 was completely sequenced and analyzed. The SH-14 consists of two circular chromosomes of 3,689,702 bp and 2,430,445 bp, and of two plasmids named as pVHvo (69,148 bp) and pVHvo-R (78,918 bp), respectively. The pVHvo encodes the bi-toxic genes of
pirAB
, responsible for shrimp AHPND. The whole genomes contain a total of 5703 predicted open reading frames (ORFs), 129 tRNA genes and 37 rRNA genes. The average nucleotide identities (ANIs) between the SH-14 and the other
V. owensii
strains are all greater than 95%, confirming a new
V
.
owensii
strain of the SH-14. The taxonomic affiliation of the SH-14 is also supported by whole-genome alignment and nucleotide identity dotplot analyses. These results pave the way for further study of spread and epidemic of shrimp AHPND.
•L. plantarum LZ206 has strong antimicrobial activity against food-borne pathogens.•We present the complete genome sequence of L. plantarum LZ206.•The genome contains a 3,212,951-bp chromosome and ...three plasmids.•A plantaricin gene cluster involving in bacteriocins biosynthesis was identified.•LZ206 could protect food products from pathogens contamination in food industry.
Lactobacilli strains have been considered as important candidates for manufacturing “natural food”, due to their antimicrobial properties and generally regarded as safe (GRAS) status. Lactobacillus plantarum LZ206 is a potential probiotic strain isolated from raw cow milk, with antimicrobial activity against various pathogens, including Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes), Gram-negtive bacteria (Escherichia coli and Salmonella enterica), and fungus Candida albicans. To better understand molecular base for its antimicrobial activity, entire genome of LZ206 was sequenced. It was revealed that genome of LZ206 contained a circular 3,212,951-bp chromosome, two circular plasmids and one predicted linear plasmid. A plantaricin gene cluster, which is responsible for bacteriocins biosynthesis and could be associated with its broad-spectrum antimicrobial activity, was identified based on comparative genomic analysis. Whole genome sequencing of L. plantarum LZ206 might facilitate its applications to protect food products from pathogens’ contamination in the dairy industry.
Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has ...rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications.
A macroalgal polysaccharide-degrading bacterial strain, Polaribacter sejongensis NJDZ03, was isolated from the surface of a species of Desmarestia, a seaweed genus endemic to Antarctica. To explore ...the mechanism underlying the multiple polysaccharide-degrading abilities of this strain, we sequenced and analyzed its complete genome. We found that the genome comprises a 4,078,668 bp circular chromosome containing 3484 coding genes, including 18 rRNA operons whose genes are arranged in the order of 16S–23S-5S rRNA. Gene annotation revealed the existence of three putative polysaccharide utilization loci (PULs) consisting of several agarase, carrangeenase, and alginate lyase genes, repectively. These PULs are likely responsible for the strong agar-, alginate-, and carrageenan-degrading capabilities of P. sejongensis NJDZ03, especially its ability to degrade diverse carrageenans, including κ-carrageenan, τ-carrageenan, and λ-carrageenan. Our findings should provide new insights into the carbon cycle of the Antarctic oceanic ecosystem.
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