21,989 results match your criteria nucleotide identity


First report of infecting white clover () in Finland.

Plant Dis 2021 Jun 15. Epub 2021 Jun 15.

Finnish Food Authority, Laboratory and Research, Mustialankatu 3, Helsinki, Finland, 00790;

Soybean dwarf virus (SbDV, genus ) is a single-stranded positive-sense RNA virus able to infect several legume species. SbDV was first reported in Japan where it was associated with significant yield losses in soybean (Tamada, 1969). Since then the virus has been detected worldwide. Read More

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First Report of Bacterial Rot Caused by Pantoea endophytica on Tobacco in Liuyang, China.

Plant Dis 2021 Jun 15. Epub 2021 Jun 15.

Chinese Academy of Agricultural Sciences Institute of Tobacco Research, 243822, Qingdao, Shandong, China;

Tobacco, Nicotiana tabacum L., is produced largely in China (~1/3 of the global market). In the monsoon summer of 2020, tobacco plant petioles, where axillary buds were removed, became black-rotten, and thick ooze appeared, when squeezed. Read More

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Phocaeicola faecalis sp. nov., a strictly anaerobic bacterial strain adapted to the human gut ecosystem.

Antonie Van Leeuwenhoek 2021 Jun 15. Epub 2021 Jun 15.

State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China.

A novel strictly anaerobic, Gram-negative bacterium, designated as strain FXJYN30E22, was isolated from the feces of a healthy woman in Yining county, Xinjiang province, China. This strain was non-spore-forming, bile-resistant, non-motile and rod-shaped. It was found to belong to a single separate group in the Phocaeicola genus based on its 16 S ribosomal RNA (rRNA) gene sequence. Read More

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sp. nov. a novel actinobacterium isolated from the coral .

Int J Syst Evol Microbiol 2021 Jun;71(6)

Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, Hainan University, Haikou 570228, PR China.

Strain HNM0947, representing a novel actinobacterium, was isolated from the coral collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Read More

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Description of sp. nov., based on phylogenomic analysis.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar - 751023, India.

A novel strain of a member of the genus strain PS-1, was isolated from the skin of fresh water pufferfish () collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. Read More

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UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction.

Front Genet 2021 28;12:660366. Epub 2021 May 28.

Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.

A recent refinement in high-throughput sequencing involves the incorporation of unique molecular identifiers (UMIs), which are random oligonucleotide barcodes, on the library preparation steps. A UMI adds a unique identity to different DNA/RNA input molecules through polymerase chain reaction (PCR) amplification, thus reducing bias of this step. Here, we propose an alignment free framework serving as a preprocessing step of fastq files, called UMIc, for deduplication and correction of reads building consensus sequences from each UMI. Read More

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A case of peritoneal dialysis-associated peritonitis caused by Rhodococcus kroppenstedtii.

BMC Infect Dis 2021 Jun 13;21(1):565. Epub 2021 Jun 13.

Department of Infectious Diseases, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, 321# Zhongshan Road, Gulou District, Nanjing City, Jiangsu Province, 210008, P. R. China.

Background: Rhodococcus kroppenstedtii is an aerobic, gram-positive bacterium firstly identified in the environment, which has not been reported in human-related infection. Herein, we reported the first case of peritoneal dialysis (PD)-associated peritonitis caused by R. kroppenstedtii which was identified by whole genome sequencing. Read More

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De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance.

BMC Plant Biol 2021 Jun 12;21(1):271. Epub 2021 Jun 12.

Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China.

Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity.

Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. Read More

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Citrobacter arsenatis sp. nov., an arsenate-reducing bacterium isolated from freshwater sediment.

Antonie Van Leeuwenhoek 2021 Jun 11. Epub 2021 Jun 11.

School of Environmental Science and Engineering, Hubei Key Laboratory of Mine Environmental Pollution Control and Remediation, Hubei Polytechnic University, Huangshi, China.

A novel arsenate-reducing bacterium, LY-1, was isolated from freshwater sediment in Huangshi, China. Morphological analysis indicated that the cells were shaped like rods and were gram-negative. The major fatty acids (> 10%) were C, summed feature 3 (C ω7c, C ω6c) and summed feature 8 (C ω7c, C ω6c). Read More

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Complete genome sequence of hollyhock vein yellowing virus, a novel monopartite begomovirus infecting hollyhock in Pakistan.

Arch Virol 2021 Jun 11. Epub 2021 Jun 11.

Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.

Hollyhock (Alcea rosea, family Malvaceae) is an ornamental plant grown widely in gardens across South Asia. In a bed of ornamental plants near the village of Chakri (Punjab Province, Pakistan) in 2014, hollyhock plants showing two distinct symptom types were identified: yellow vein mosaic and leaf crumple. PCR amplification with universal primers amplified a begomovirus from separate nucleic acid extracts of single plants of each type but amplified a betasatellite only from the plant with the yellow vein mosaic symptoms. Read More

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Major genetic discontinuity and novel toxigenic species in taxonomy.

Elife 2021 Jun 11;10. Epub 2021 Jun 11.

School of Biomedical Sciences, University of Western Australia, Nedlands, Australia.

infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 genomes spanning the eight currently defined phylogenetic clades. Read More

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Characterization of a Novel Bacteriophage swi2 Harboring Two Lysins Can Naturally Lyse .

Front Microbiol 2021 25;12:670799. Epub 2021 May 25.

College of Veterinary Medicine, Qingdao Agricultural University, Shandong, China.

The novel virulent bacteriophage swi2 was isolated from a pig farm, and its biological characteristics, genome architecture, and infection-related properties were characterized. Phage swi2 has a high titer of 1.01 × 10 PFU/mL with good tolerance to UV rays and remains stable in the pH range of 6-10 and at temperatures less than 50°C. Read More

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sp. nov., an endophytic actinomycete isolated from the root of (L.).

Int J Syst Evol Microbiol 2021 Jun;71(6)

Actinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.

An endophytic actinobacterium, designated strain CA1R205, was isolated from the surface-sterilized root of L. collected from Ratchaburi province, Thailand. The taxonomic position of this strain was evaluated using a polyphasic approach. Read More

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sp. nov. (sv. septentrionale) and sp. nov. (sv. septentrionale) associated with legumes native to Canada possess rearranged symbiosis genes and numerous insertion sequences.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada.

Six bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of legumes native to Canada were previously characterized and 1) placed in two novel lineages within the genus and 2) assigned to symbiovar septentrionale. Here we verified the taxonomic status of these strains using genomic and phenotypic analyses. Phylogenetic analyses of five protein encoding partial gene sequences as well as 52 full length ribosome protein subunit gene sequences confirmed placement of the novel strains in two highly supported lineages distinct from named species. Read More

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First report of pearl millet bacterial leaf blight caused by Pantoea stewartii subspecies indologenes in India.

Plant Dis 2021 Jun 9. Epub 2021 Jun 9.

University of Mysore, 29243, Applied Botany and Biotechnology, Mysore, Karnataka, India;

Pearl millet (Cenchrus americanus L.) field-grown plants of cv. 7042S shown unusual water-soaked lesions on leaf tips spreading towards the leaf base from Manasagangothri region (12. Read More

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Complete mitochondrial genome and phylogenetic analysis of the copper shark (Günther, 1870).

Mitochondrial DNA B Resour 2021 May 18;6(6):1659-1661. Epub 2021 May 18.

Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.

Copper shark ( Günther, 1870) is one of the most widely distributed but least known species in the family Carcharhinidae. Herein, we report the first complete mitogenome of . The overall structure of the 16,704 bp mitogenome was similar to that of other species and showed the highest average nucleotide identity (97. Read More

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Streptomyces venezuelae NRRL B-65442: genome sequence of a model strain used to study morphological differentiation in filamentous actinobacteria.

J Ind Microbiol Biotechnol 2021 Jun 8. Epub 2021 Jun 8.

Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

For over a decade, Streptomyces venezuelae has been used to study the molecular mechanisms that control morphological development in streptomycetes and it is now a well-established model strain. Its rapid growth and ability to sporulate in a near-synchronised manner in liquid culture, unusual among streptomycetes, greatly facilitates the application of modern molecular techniques such as ChIP-seq and RNA-seq, as well as fluorescence time-lapse imaging of the complete Streptomyces life cycle. Here we describe a high-quality genome sequence of our isolate of the strain (NRRL B-65442) consisting of an 8. Read More

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sp. nov., isolated from rhizosphere soil of .

Int J Syst Evol Microbiol 2021 Jun;71(6)

Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China.

A novel Gram-stain positive, facultatively anaerobic, motile, irregularly rod-shaped bacterium, designated GY 10621, was isolated from rhizosphere soil of in Beihai City, Guangxi Province, PR China, and characterized using a polyphasic taxonomic approach. GY 10621 was positive for catalase and oxidase. Growth occurred at 4-42 °C (optimum 30-37 °C), at pH 5. Read More

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First Report of Aloe vera Rust Caused by Uromyces aloes in an Ornamental Nursery in the United States.

Plant Dis 2021 Jun 8. Epub 2021 Jun 8.

Penn State University, Plant Pathology, University Park, Pennsylvania, United States;

Aloe vera (L.) Burm. f. Read More

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sp. nov. isolated from refrigerated dry-aged beef.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany.

A polyphasic approach was applied to investigate the diversity of microbiota that evolved during cold storage beef ripening. Isolate V4/DAB/S4/2a with a unique BOX-rep-PCR fingerprint profile revealed more than 99 % nucleotide identities upon pairwise comparisons of 16S rDNA sequences from the type strains DSM 101070, DSM 108989, DSM 26521 and DSM 29166, placing it within the / branch of the genus . Additional based comparison revealed DSM 101070 as the nearest relative, with 98. Read More

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Complete genome sequence of viola mottle virus, revealing its synonymous relationship to tulip virus X.

Arch Virol 2021 Jun 7. Epub 2021 Jun 7.

Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Viola mottle virus (VMoV) was discovered in Viola odorata showing symptoms of reduced growth, leaf mottling, and whitish stripes on flowers in northern Italy in 1977. This virus has been provisionally classified as a member of the genus Potexvirus based on its morphological, serological, and biological characteristics. However, since genetic information of VMoV has never been reported, the taxonomic status of this virus is unclear. Read More

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First Report of Brown Rot Caused by on Apple in Italy.

Plant Dis 2021 Jun 7. Epub 2021 Jun 7.

University of Torino, DISAFA - Dept. Agricultural, Forestry and Food Sciences, Largo Braccini 2, Grugliasco, TO, Italy, 10095.

Brown rot is a common apple disease in Italy, caused by Monilinia fructicola, M. laxa and M. fructigena (Martini et al. Read More

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First report of Grapevine yellow speckle viroid 1 infecting grapevine (Vitis vinifera L.) in Canada.

Plant Dis 2021 Jun 7. Epub 2021 Jun 7.

Agriculture and AgriFood Canada , Research and development center , 430 Gouin, Saint-Jean-sur-Richelieu, Quebec, Canada, J3B3E6;

Quebec is the third largest wine grape producer in Canada in acreage, tonnage, and wine grape sales (Carisse et al. 2017; Ben Moussa et al. 2019). Read More

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Virology features of a family cluster of SARS-CoV-2 infections in Shanghai, China.

Biosaf Health 2021 Jun 1. Epub 2021 Jun 1.

Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China.

The global spread of SARS-CoV-2 is currently continuing, and the World Health Organization has announced the risk assessment of the viruses as high. In this study, we analyzed virology features of SARS-CoV-2 causing a family cluster outbreak. Among the six family members, five have been laboratory-confirmed infection of SARS-CoV-2 viruses. Read More

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Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by , and Description of Three Putative Novel Species, sp. nov., sp. nov. and sp. nov.

Front Microbiol 2021 19;12:666689. Epub 2021 May 19.

Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada.

is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including from necrotic wheat leaf tissues. Read More

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Harmless or Threatening? Interpreting the Results of Molecular Diagnosis in the Context of Virus-Host Relationships.

Front Microbiol 2021 21;12:647730. Epub 2021 May 21.

National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.

Molecular methods, established in the 1980s, expanded and delivered tools for the detection of vestigial quantities of nucleic acids in biological samples. Nucleotide sequencing of these molecules reveals the identity of the organism it belongs to. However, the implications of such detection are often misinterpreted as pathogenic, even in the absence of corroborating clinical evidence. Read More

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sp. nov., a Nitrogen-Fixing Bacterium Isolated From Forest Soil by Using Optimized Culture Method.

Front Microbiol 2021 21;12:647132. Epub 2021 May 21.

Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea.

A bacterial strain, designated strain G-1-1-14, was isolated from Kyonggi University forest soil during a study of previously uncultured bacterium. The cells of strain G-1-1-14 were motile by means of peritrichous flagella, Gram-stain-negative, rod-shaped, and able to grow autotrophically with hydrogen and fix nitrogen. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain G-1-1-14 belonged to the genus . Read More

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Genome analysis and optimization of γ-aminobutyric acid (GABA) production by lactic acid bacteria from plant materials.

J Gen Appl Microbiol 2021 Jun 5. Epub 2021 Jun 5.

Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University.

Gamma-aminobutyric acid (GABA) plays a key role as an inhibitory neurotransmitter in the mammalian sympathetic nervous system and has other health benefits. Molecular characterization, genome analysis, and optimization were investigated to improve GABA production of a selected strain of lactic acid bacteria. Eleven isolates from plant materials were screened for GABA productivity and were identified based on phenotypic and genotypic characteristics. Read More

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Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation.

Antonie Van Leeuwenhoek 2021 Jun 6. Epub 2021 Jun 6.

Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea.

A straw coloured, motile and Gram-stain-negative bacterium, designated RP-1-19 was isolated from soil of Arctic station, Svalbard, Norway. Based on the phylogenetic analysis of its 16S rRNA gene sequence, strain RP-1-19 formed a lineage within the family Oxalobacteraceae and clustered together within the genus Massilia. The closest members were M. Read More

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Complete genome sequences of anemone mosaic virus and ranunculus mild mosaic virus isolated from anemone imported from the Netherlands into Japan.

Arch Virol 2021 Jun 6. Epub 2021 Jun 6.

Narita Branch, Yokohama Plant Protection Station, Aza-Tennamino, Komaino, Narita, Chiba, 282-0021, Japan.

Anemone mosaic virus (AnMV) and ranunculus mild mosaic virus (RanMMV) infect anemone plants, which exhibit characteristic mosaic patterns on their leaves. Employing next-generation sequencing of plant material imported from the Netherlands, the complete genome sequences of these two viruses were determined for the first time. AnMV and RanMMV have 9698 and 9537 nucleotides (nt), respectively, excluding the poly(A) tail. Read More

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