scholarly journals Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov.

2020 ◽  
Vol 11 ◽  
Author(s):  
Lina Liu ◽  
Yu Feng ◽  
Li Wei ◽  
Fu Qiao ◽  
Zhiyong Zong
Keyword(s):  
Species Identification ◽  
Genome Sequencing ◽  
Dna Hybridization ◽  
Novel Species ◽  
Bacterial Species ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Carbapenem Resistant ◽  
The Family ◽  
Human Infections

Kluyvera is a genus within the family Enterobacteriaceae and can cause various human infections but remains poorly studied. A carbapenem-resistant blaNDM–1-carrying Kluyvera strain 090646T was isolated from a hospital sink in Chengdu, Sichuan province, China. Whole genome sequencing of the strain revealed that it had 28.2 to 42.3% in silico DNA-DNA hybridization (isDDH) scores and 84.15 to 90.10% average nucleotide identity (ANI) values with other Kluyvera species. Both values are well below the ≥ 70.0% isDDH and ≥ 95–96% ANI cutoffs to define bacterial species, suggesting that the strain represents a novel species of the genus Kluyvera, for which the name Kluyvera sichuanensis. nov. is proposed. Type strain of K. sichuanensis is 090646T (=GDMCC 1.1872T =KCTC 82166T). Strain 090646T can be differentiated from other Kluyvera species by its ability to utilize D-sorbitol but not β-galactosidase (ONPG), D-mannose, glycerin, raffinose, nor sucrose. There were 47 genome sequences labeled as Kluyvera in GenBank, which were curated for precise species identification. Only 33 of the 47 genomes were indeed of Kluyvera and four novel Kluyvera genomospecies were identified, highlighting that the species assignation of bacterial genomes in GenBank need to be curated. Genome sequencing for more strains is required to understand the genus Kluyvera.

scholarly journals Amycolatopsis Camponoti Sp. Nov., New Tetracenomycin-Producing Actinomycete Isolated from Carpenter Ant Camponotus Vagus

2021 ◽  
Author(s):  
Yuliya V Zakalyukina ◽  
Ilya A Osterman ◽  
Jacqueline Wolf ◽  
Meina Neumann-Schaal ◽  
Imen Nouioui ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Morphological Characteristics ◽  
Rrna Gene ◽  
Species Demarcation ◽  
Genome Sequences ◽  
Cellular Fatty Acids ◽  
Carpenter Ant

Abstract An actinobacterial strain A23T, isolated from adult ant Camponotus vagus collected in Ryazan region (Russia) and established as tetracenomycin X producer, was subjected to a polyphasic taxonomic study. Morphological characteristics of this strain included well-branched substrate mycelium and aerial hyphae fragmented into rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain A23T was most closely related to Amycolatopsis pretoriensis DSM 44654T (99.9%). Average nucleotide identity and digital DNA–DNA hybridization values between the genome sequences of isolate A23T and its closest relative, Amycolatopsis pretoriensis DSM 44654T, were 39.5% and 88.6%, which were below the 70% and 95-96% cut-off point recommended for bacterial species demarcation, respectively. The genome size of the isolate A23T is 10,560,374 bp with a DNA G+C content of 71.2 mol%. The whole-organism hydrolysates contain arabinose and galactose as main diagnostic sugars as well as ribose and rhamnose. It contained MK-9(H4) as the predominant menaquinone and iso-C16:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major cellular fatty acids. Based on the phenotypic, genomic and phylogenetic data, isolate A23T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis camponoti sp. nov. is proposed, and the type strain is A23T (=DSM 111725T =VKM 2882T).

scholarly journals Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina: TABLE 1 

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Claudia Carolina Carbonari ◽  
Nahuel Fittipaldi ◽  
Sarah Teatero ◽  
Taryn B. T. Athey ◽  
Luis Pianciola ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Epidemiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Shiga Toxin ◽  
Whole Genome ◽  
Escherichia Coli O157 ◽  
Genome Sequences ◽  
High Quality ◽  
Human Infections

Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.

scholarly journals Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm

2020 ◽  
Vol 8 (6) ◽  
pp. 855 ◽  
Author(s):  
Alexandra Irrgang ◽  
Natalie Pauly ◽  
Bernd-Alois Tenhagen ◽  
Mirjam Grobbel ◽  
Annemarie Kaesbohrer ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Multidrug Resistant ◽  
Meat Production ◽  
Whole Genome ◽  
Phenotypic Resistance ◽  
Long Read ◽  
Pig Farm ◽  
Human Infections

Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans to non-human reservoirs (i.e., environment, animals, food). In Germany, the occurrence of CPE in livestock and food has been systematically monitored since 2016. In the 2019 monitoring, an OXA-48-producing E. coli (19-AB01443) was recovered from a fecal sample of a fattening pig. Phenotypic resistance was confirmed by broth microdilution and further characterized by PFGE, conjugation, and combined short-/long-read whole genome sequencing. This is the first detection of this resistance determinant in samples from German meat production. Molecular characterization and whole-genome sequencing revealed that the blaOXA-48 gene was located on a common pOXA-48 plasmid-prototype. This plasmid-type seems to be globally distributed among various bacterial species, but it was frequently associated with clinical Klebsiella spp. isolates. Currently, the route of introduction of this plasmid/isolate combination into the German pig production is unknown. We speculate that due to its strong correlation with human isolates a transmission from humans to livestock has occurred.

scholarly journals Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology

2013 ◽  
Vol 6 ◽  
pp. GEI.S12732 ◽  
Author(s):  
Archana Sharma ◽  
T. Satyanarayana
Keyword(s):  
Comparative Genomics ◽  
Molecular Biology ◽  
Genome Sequencing ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Bacillus Species ◽  
Genome Sequences ◽  
Wide Range ◽  
Sequencing Platforms ◽  
Analytical Tools

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

scholarly journals Draft Genome Sequences of Itaconate-Producing Ustilaginaceae

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Elena Geiser ◽  
Florian Ludwig ◽  
Thiemo Zambanini ◽  
Nick Wierckx ◽  
Lars M. Blank
Keyword(s):  
Metabolic Engineering ◽  
Genome Sequencing ◽  
De Novo ◽  
Draft Genome ◽  
Essential Genes ◽  
Smut Fungi ◽  
Genome Sequences ◽  
The Family

Some smut fungi of the family Ustilaginaceae produce itaconate from glucose. De novo genome sequencing of nine itaconate-producing Ustilaginaceae revealed genome sizes between 19 and 25 Mbp. Comparison to the itaconate cluster of U. maydis MB215 revealed all essential genes for itaconate production contributing to metabolic engineering for improving itaconate production.

scholarly journals Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 625-632 ◽  
Author(s):  
Javier Pascual ◽  
Marina García-López ◽  
Gerald F. Bills ◽  
Olga Genilloud
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Bacterial Species ◽  
Phenotypic Traits ◽  
Terminal Electron Acceptor ◽  
Content Type ◽  
Link Type ◽  
Natural Park ◽  
Fatty Acid Compositions

During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770T was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770T belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis , P. koreensis , P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770T in the genus Pseudomonas . DNA–DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas , for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770T ( = DSM 28040T = LMG 27940T).

scholarly journals Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 632-637 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Hae-Ran Lee ◽  
Ki-Kwang Kim ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Bacterial Species ◽  
Angelica Sinensis ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three exopolysaccharide-producing bacteria, designated strains DRP28T, DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8–97.4 %. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28T, DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9–42.7 mol% and DNA hybridization values of 82.6–86.8 %; the strains exhibited DNA–DNA hybridization values of only 20.4–41.3 % with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28T, DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28T ( = KACC 15075T  = NBRC 107757T).

scholarly journals Actinopolymorpha pittospori sp. nov., an endophyte isolated from surface-sterilized leaves of an apricot tree (Pittosporum phylliraeoides)

2011 ◽  
Vol 61 (11) ◽  
pp. 2616-2620 ◽  
Author(s):  
Onuma Kaewkla ◽  
Christopher M. M. Franco
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Biochemical Studies ◽  
Apricot Tree ◽  
Physiological And Biochemical ◽  
Wall Components

A member of the genus Actinopolymorpha, designated PIP 143T, was isolated from the leaves of an Australian native apricot tree (Pittosporum phylliraeoides). The isolate was a Gram-reaction-positive, aerobic actinobacterium, with a well-developed substrate mycelium that fragmented into small rods. Phylogenetic evaluation based on 16S rRNA gene sequences placed the isolate in the family Nocardioidaceae. Strain PIP 143T was most closely related to Actinopolymorpha cephalotaxi I06-2230T (98.7 %) and Actinopolymorpha rutila YIM 45725T (98.1 %). Chemotaxonomic data, including cell-wall components, menaquinones and fatty acids, confirmed the affiliation of strain PIP 143T to the genus Actinopolymorpha. Phylogenetic analysis and physiological and biochemical studies, in combination with DNA–DNA hybridization studies, allowed the differentiation of strain PIP 143T from its closest phylogenetic neighbours with validly published names. Therefore, a novel species is proposed, with the name Actinopolymorpha pittospori sp. nov. The type strain is PIP 143T ( = DSM 45354T  = ACM 5288T  = NRRL B-24810T).

scholarly journals Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Nay C. Dia ◽  
Johan Van Vaerenbergh ◽  
Cinzia Van Malderghem ◽  
Jochen Blom ◽  
Theo H. M. Smits ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Close Relation ◽  
Genome Sequences ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Link Type ◽  
Amplification Assay

This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum . A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum . Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum . The genome sequences of the strains had average nucleotide identity values ranging from 94.35–95.19 % and in silico DNA–DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.

scholarly journals Ketobacter nezhaii sp. nov., a marine bacterium isolated from coastal sediment

2020 ◽  
Vol 70 (9) ◽  
pp. 4960-4965 ◽  
Author(s):  
Jianyang Li ◽  
Mingming Qi ◽  
Qiliang Lai ◽  
Xianhua Liu ◽  
Zongze Shao
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Heterotrophic Bacterium ◽  
Coastal Sediment ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Optimum Ph

A Gram-stain-negative, motile, aerobic and heterotrophic bacterium, designated as GYS_M3HT, was isolated from marine coastal sediment sampled at Xiamen Island. Cells were rod-shaped with one polar flagellum and weakly positive for oxidase and catalase. Growth of the strain occurred at pH 6–9 (optimum, pH 7–8), at 15–37 °C (optimum, 28 °C) and with NaCl concentrations of 1.0–6.0 % (optimum, 2.0 %). It had highest 16S rRNA similarity (97.7 %) to Ketobacter alkanivorans GI5T, followed by the members of the genus Alcanivorax (lower than 91.2 %). The results of phylogenetic analysis indicated that it belonged to the genus Ketobacter within the family Alcanivoracaceae . In addition, the average nucleotide identity and digital DNA–DNA hybridization values between strain GYS_M3HT and K. alkanivorans GI5T were 71.4 and 19.7 %, respectively, indicating that strain GYS_M3HT belonged to a novel species. Its genome consisted of 5 318 758 bp, with a genomic DNA G+C content of 50.0 mol%. The respiratory quinone was Q-8 and the dominant fatty acids were identified as iso-C15 : 0 (25.4 %), C16 : 1  ω6c/C16 : 1  ω7c (14.4 %) and iso-C13 : 0 (7.2 %). The main polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Therefore, based on phenotypic, chemotaxonomic and phylogenetic results, strain GYS_M3HT represents a novel species within the genus Ketobacter , for which the name Ketobacter nezhaii sp. nov. is proposed, with the type strain GYS_M3HT (=MCCC 1A13808T=KCTC 72247T).

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