Journal: International Journal of Microbiology

Article Title: Genotypic and Phenotypic Assessment of Hyaluronidase among Type Strains of a Select Group of Staphylococcal Species

doi: 10.1155/2009/614371

Figure Lengend Snippet: Southern analysis of chromosomal DNA from Staphylococcus species hybridized with a probe specific for hysA . Panel (a) S. aureus NCH 239 (1), NCH 240 (2), NCH 241 (3), NCH 242 (4), NCH 243 (5), NCH 244 (6), NCH 245 (7), NCH 246 (8), S. auricularis ATCC 33753 T (9), S. capitis subsp. capitis ATCC 27840 T (10), S. caprae ATCC 35538 T (11), S. carnosus subsp. carnosus ATCC 51365 T (12), S. chromogenes ATCC 43764 T (13), S. cohnii subsp. cohnii ATCC 29974 T (14), S. delphini ATCC 49171 T (15), S. hominis subsp. hominis ATCC 27844 T (16), S. aureus NCH 78 (17), and NCH 88 (18). Panel (b) S. aureus NTH 74 (1), NTH 75 (2), NTH 76 (3), NTH 77 (4), NTH 78 (5), NTH 79 (6), NTH 80 (7), NTH 81 (8), S. intermedius ATCC 29663 T (9), S. lugdunensis ATCC 43809 T (10), S. saprophyticus ATCC 19701 T (11), S. schleiferi subsp. schleiferi ATCC 43808 T (12), S. epidermidis ATCC 12228 (13), S. aureus NTH 125 (14), NCH 265 (15), S. intermedius ATCC 29633 T (16), NCH 78 (17), and NCH 88 (18). Panel (c) S. aureus NCH 47 (1), NCH 48 (2), NCH 49 (3), NCH 51 (4), S. sciuri subsp. sciuri ATCC 29062 T (5), S. simulans ATCC 27848 T (6), S. warneri ATCC 27836 T (7), S. xylosus ATCC 29971 T (8), S. aureus NTH 13 (9), NCH 78 (10), NCH 79 (11), NTH 82 (12), NCH 88 (13), S. haemolyticus ATCC 29970 T (14), NCH 328 (15), NCH 331 (16), NCH 78 (17), and NCH 88 (18). M: marker (kilobases).

Article Snippet: Other species examined were S. auricularis ATCC 33753 T , S. capitis subsp. capitis ATCC 27840 T , S. caprae ATCC 35538 T , S. carnosus subsp. carnosus ATCC 51365 T , S. chromogenes ATCC 43764 T , S. cohnii subsp. cohnii ATCC 29974 T , S. delphini ATCC 49171 T , S. epidermidis ATCC 14990 T , S. epidermidis ATCC 12228, S. haemolyticus ATCC 29970 T , S. hominis subsp. hominis ATCC 27844 T , S. hyicus subsp. hyicus ATCC 11249 T , S. intermedius ATCC 29663 T , S. lugdunensis ATCC 43809 T , S. saprophyticus ATCC 19701 T , S. schleiferi subsp. coagulans ATCC 49549 T , S. schleiferi subsp. schleiferi ATCC 43808 T , S. sciuri subsp. sciuri ATCC 29062 T , S. simulans ATCC 27848 T , S. warneri ATCC 27836 T , and S. xylosus ATCC 29971 T . Strains were maintained as frozen (−80°C) stocks in brain heart infusion broth (BHI; Difco Laboratories, Detroit, Mich.) containing 25% (w/v) glycerol and routinely streaked for isolation on tryptic soy broth (TSB; Difco) containing agar (1.5%).

Techniques: Marker

Journal: Pathogens

Article Title: Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

doi: 10.3390/pathogens13040343

Figure Lengend Snippet: Sequence similarity of the Staphylococcus hsinchuensis sp. nov. H164 T and its closely related type strains.

Article Snippet: Comparative analysis of the 16S rRNA gene sequences revealed that the type strains S . urealyticus ATCC 49330 T (98.4% similarity), Staphylococcus canis H16/1A T (98.4%), Staphylococcus lloydii 23_2_7_LY T (98.2%), Staphylococcus kloosii ATCC 43959 T (98.2%), S. cohnii ATCC 29974 T (98.2%), Staphylococcus petrasii CCM 84118 T (98.2%), Staphylococcus durrellii 27_4_6_LY T (98.1%), Staphylococcus arlettae ATCC 43956 T (98.1%), and S. gallinarum ATCC 35539 T (98.0%) were the closest neighbors to the novel strain H164 T . These values were lower than the suggested cutoff value for species delineation (98.7%) [ ].

Techniques: Sequencing

Journal: Pathogens

Article Title: Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

doi: 10.3390/pathogens13040343

Figure Lengend Snippet: Average nucleotide identity (ANI) and dDDH prediction values (%) between the strain H164 T and its closely related species.

Article Snippet: Comparative analysis of the 16S rRNA gene sequences revealed that the type strains S . urealyticus ATCC 49330 T (98.4% similarity), Staphylococcus canis H16/1A T (98.4%), Staphylococcus lloydii 23_2_7_LY T (98.2%), Staphylococcus kloosii ATCC 43959 T (98.2%), S. cohnii ATCC 29974 T (98.2%), Staphylococcus petrasii CCM 84118 T (98.2%), Staphylococcus durrellii 27_4_6_LY T (98.1%), Staphylococcus arlettae ATCC 43956 T (98.1%), and S. gallinarum ATCC 35539 T (98.0%) were the closest neighbors to the novel strain H164 T . These values were lower than the suggested cutoff value for species delineation (98.7%) [ ].

Techniques:

Journal: Pathogens

Article Title: Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

doi: 10.3390/pathogens13040343

Figure Lengend Snippet: Differential biochemical characteristics of Staphylococcus hsinchuensis sp. nov. H164 T and the closest related species of the genus Staphylococcus strains: 1. Staphylococcus hsinchuensis H164 T ; 2. Staphylococcus cohnii NCTC 11041 T ; 3. Staphylococcus urealyticus DSM 6178 T ; 4. Staphylococcus gallinarum DSM 20610 T ; and 5. Staphylococcus nepalensis CCM 7045 T . +, positive; −, negative.

Article Snippet: Comparative analysis of the 16S rRNA gene sequences revealed that the type strains S . urealyticus ATCC 49330 T (98.4% similarity), Staphylococcus canis H16/1A T (98.4%), Staphylococcus lloydii 23_2_7_LY T (98.2%), Staphylococcus kloosii ATCC 43959 T (98.2%), S. cohnii ATCC 29974 T (98.2%), Staphylococcus petrasii CCM 84118 T (98.2%), Staphylococcus durrellii 27_4_6_LY T (98.1%), Staphylococcus arlettae ATCC 43956 T (98.1%), and S. gallinarum ATCC 35539 T (98.0%) were the closest neighbors to the novel strain H164 T . These values were lower than the suggested cutoff value for species delineation (98.7%) [ ].

Techniques:

Journal: Pathogens

Article Title: Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

doi: 10.3390/pathogens13040343

Figure Lengend Snippet: Cellular fatty acid compositions (%) of Staphylococcus hsinchuensis sp. nov. and its phylogenetically closely related species. Strains: 1, Staphylococcus hsinchuensis sp. nov. H164 T ; 2, Staphylococcus ureilyticus ATCC49330 T ; 3, Staphylococcus cohnii ATCC 29974 T ; 4, Staphylococcus nepalensis CCUG 48991 T ; and 5, Staphylococcus gallinarum BCRC 13913 T . Values are percentages of total fatty acids. Fatty acids present at >10% are indicated in bold. TR, trace amount.

Article Snippet: Comparative analysis of the 16S rRNA gene sequences revealed that the type strains S . urealyticus ATCC 49330 T (98.4% similarity), Staphylococcus canis H16/1A T (98.4%), Staphylococcus lloydii 23_2_7_LY T (98.2%), Staphylococcus kloosii ATCC 43959 T (98.2%), S. cohnii ATCC 29974 T (98.2%), Staphylococcus petrasii CCM 84118 T (98.2%), Staphylococcus durrellii 27_4_6_LY T (98.1%), Staphylococcus arlettae ATCC 43956 T (98.1%), and S. gallinarum ATCC 35539 T (98.0%) were the closest neighbors to the novel strain H164 T . These values were lower than the suggested cutoff value for species delineation (98.7%) [ ].

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Main Genome Assembly Features of SC5, SCC ATCC 29974 and SCU ATCC 49330 Strains

Article Snippet: Notably, comparisons between the draft genome assembly of SC5 with the SCC ATCC 29974 and SCU ATCC 49330 type strains resulted in ANIb values of 95.4% and 91.0%, respectively ( ).

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Heatmap of ANIb between genomes of Staphylococcus cohnii isolates. ANIb values are represented using a gray scale color map, with darker colors indicating higher levels of identity, according to the scale represented on the top. Strain identifiers are indicated on the rows. The panel on the left indicates cluster memberships, according to the following color codes: green = B, dark purple = A1, and light purple = A2. Columns and row dendrograms are used to group SC strains based on patterns of genome identity profiles. The novel SC5 isolate and the two type strains SCC ATCC 29974 and SCU ATCC 49330 are highlighted in red and underlined. The SE4.1, SE 4.2, and SE3.10 strains that are also discussed in the text are highlighted in red.

Article Snippet: Notably, comparisons between the draft genome assembly of SC5 with the SCC ATCC 29974 and SCU ATCC 49330 type strains resulted in ANIb values of 95.4% and 91.0%, respectively ( ).

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Heatmap of gene presence/absence profiles of Staphylococcus cohnii isolates. Similarity of gene presence/absence profiles were estimated by computing pairwise Pearson correlation values between all the 66 genomes considered in the study. Pearson correlation coefficients are represented using a gray scale color map. Darker colors indicated higher correlation (similarity) of gene presence/absence profiles. Strain identifiers are indicated on the rows. The panel on the left is used to indicate cluster memberships, with the color codes defined in . Similar to , dendrograms are applied to the columns and rows to delineate groups of isolates with similar gene absence prevalence profiles. SC5 and the two type strains SCC ATCC 29974 and SCU ATCC 49330 are highlighted in red and underlined. The SE4.1, SE 4.2, and SE3.10 strains are highlighted in red.

Article Snippet: Notably, comparisons between the draft genome assembly of SC5 with the SCC ATCC 29974 and SCU ATCC 49330 type strains resulted in ANIb values of 95.4% and 91.0%, respectively ( ).

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Phylogenetic tree of Staphylococcus cohnii isolates based on concatenated alignment of 1,468 core genes. Branch colors indicate the different groups identified in this study, according to the color code defined in . Bootstrap values below 95 are reported on the corresponding branches. The SE4.1, SE 4.2, and SE3.10 strains are marked in red. SC5 isolate and the two type strains SCC ATCC 29974 and SCU ATCC 49330 are highlighted in red and underlined.

Article Snippet: Notably, comparisons between the draft genome assembly of SC5 with the SCC ATCC 29974 and SCU ATCC 49330 type strains resulted in ANIb values of 95.4% and 91.0%, respectively ( ).

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Staphylococcus cohnii Genome Metadata ^a , ^b

Article Snippet: Notably, comparisons between the draft genome assembly of SC5 with the SCC ATCC 29974 and SCU ATCC 49330 type strains resulted in ANIb values of 95.4% and 91.0%, respectively ( ).

Techniques: Isolation

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Main Genome Assembly Features of SC5, SCC ATCC 29974 and SCU ATCC 49330 Strains

Article Snippet: The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively.

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Heatmap of ANIb between genomes of Staphylococcus cohnii isolates. ANIb values are represented using a gray scale color map, with darker colors indicating higher levels of identity, according to the scale represented on the top. Strain identifiers are indicated on the rows. The panel on the left indicates cluster memberships, according to the following color codes: green = B, dark purple = A1, and light purple = A2. Columns and row dendrograms are used to group SC strains based on patterns of genome identity profiles. The novel SC5 isolate and the two type strains SCC ATCC 29974 and SCU ATCC 49330 are highlighted in red and underlined. The SE4.1, SE 4.2, and SE3.10 strains that are also discussed in the text are highlighted in red.

Article Snippet: The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively.

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Heatmap of gene presence/absence profiles of Staphylococcus cohnii isolates. Similarity of gene presence/absence profiles were estimated by computing pairwise Pearson correlation values between all the 66 genomes considered in the study. Pearson correlation coefficients are represented using a gray scale color map. Darker colors indicated higher correlation (similarity) of gene presence/absence profiles. Strain identifiers are indicated on the rows. The panel on the left is used to indicate cluster memberships, with the color codes defined in . Similar to , dendrograms are applied to the columns and rows to delineate groups of isolates with similar gene absence prevalence profiles. SC5 and the two type strains SCC ATCC 29974 and SCU ATCC 49330 are highlighted in red and underlined. The SE4.1, SE 4.2, and SE3.10 strains are highlighted in red.

Article Snippet: The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively.

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Phylogenetic tree of Staphylococcus cohnii isolates based on concatenated alignment of 1,468 core genes. Branch colors indicate the different groups identified in this study, according to the color code defined in . Bootstrap values below 95 are reported on the corresponding branches. The SE4.1, SE 4.2, and SE3.10 strains are marked in red. SC5 isolate and the two type strains SCC ATCC 29974 and SCU ATCC 49330 are highlighted in red and underlined.

Article Snippet: The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively.

Techniques:

Journal: Genome Biology and Evolution

Article Title: Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

doi: 10.1093/gbe/evab020

Figure Lengend Snippet: Staphylococcus cohnii Genome Metadata ^a , ^b

Article Snippet: The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively.

Techniques: Isolation