scholarly journals A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria,Paenibacillus larvaeandBrevibacillus laterosporus

2018 ◽  
Vol 84 (22) ◽  
Author(s):  
Jordan A. Berg ◽  
Bryan D. Merrill ◽  
Donald P. Breakwell ◽  
Sandra Hope ◽  
Julianne H. Grose
Keyword(s):  
Molecular Markers ◽  
16S Rrna ◽  
Related Species ◽  
Ecological Niche ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Closely Related Species ◽  
Content Type

ABSTRACTPaenibacillus larvaeandBrevibacillus laterosporusare two bacteria that are members of thePaenibacillaceaefamily. Both are commonly found in beehives and have historically been difficult to distinguish from each other due to related genetic and phenotypic characteristics and a shared ecological niche. Here, we discuss the likely mischaracterization of three 16S rRNA sequences previously published asP. larvaeand provide the phylogenetic evidence that supported the GenBank reassignment of the sequences asB. laterosporus. We explore the issues that arise by using only 16S rRNA or other single-gene analyses to distinguish between these bacteria. We also present three sets of molecular markers, two sets that distinguishP. larvaefromB. laterosporusand other closely related species within thePaenibacillusgenus and a third set that distinguishesB. laterosporusfromP. larvaeand other closely related species within theBrevibacillusgenus. These molecular markers provide a tool for proper identification of these oft-mistaken species.IMPORTANCE16S rRNA gene sequencing in bacteria has long been held as the gold standard for typing bacteria and, for the most part, is an excellent method of taxonomically identifying different bacterial species. However, the high level of 16S rRNA sequence similarity of some published strains ofP. larvaeandB. laterosporus, as well as possible horizontal gene transfer events within their shared ecological niche, complicates the use of 16S rRNA sequence as an effective molecular marker for differentiating these two species. Additionally, shared characteristics of these bacteria limit the effectiveness of using traditional phenotypic identification assays, such as the catalase test. The results from this study provide PCR methods to quickly differentiate between these two genera and will be useful when studyingBrevibacillus,Paenibacillus, and other disease-relevant bacteria commonly found in beehives.

scholarly journals Roseomonas algicola sp. nov., isolated from a green alga, Pediastrum duplex

2020 ◽  
Vol 70 (11) ◽  
pp. 5634-5639 ◽  
Author(s):  
Hyung Min Kim ◽  
Shehzad Abid Khan ◽  
Dong Min Han ◽  
Byung Hee Chun ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
Green Alga ◽  
Type Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, strictly aerobic bacterium, designated strain PeD5T, was isolated from a green alga Pediastrum duplex from the Nakdong river of the Republic of Korea. Cells were non-motile cocci, catalase-negative and oxidase-positive. Growth of PeD5T was observed at 25–40 °C (optimum, 35 °C) and pH 5.0–10.0 (optimum, pH 7–8), and in the presence of 0–0.25% (w/v) NaCl (optimum, 0%). PeD5T contained C16:0, C18:1ω7c 11-methyl, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c) as major cellular fatty acids (>5%) and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified aminolipid were detected as major polar lipids. The genomic DNA G+C content of PeD5T was 71.0 mol%. PeD5T was most closely related to Roseomonas stagni HS-69T with a 97.6% 16S rRNA sequence similarity and shared less than 96.3% 16S rRNA sequence similarities with type strains of other species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that PeD5T formed a phyletic lineage with Roseomonas stagni HS-69T within the genus Roseomonas . On the basis of results of phenotypic, chemotaxonomic and molecular analysis, strain PeD5T clearly represents a novel species of the genus Roseomonas , for which the name Roseomonas algicola sp. nov. is proposed. The type strain is PeD5T (=KACC 19925T=JCM 33309T).

scholarly journals Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 424-431 ◽  
Author(s):  
Víctor Gonzalo Arnau ◽  
Leandro Arturo Sánchez ◽  
Osvaldo Daniel Delgado
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Psychrotolerant Bacterium ◽  
Type Strains

A psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus Pseudomonas and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).

Genome-based reclassification of Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii as later heterotypic synonyms of Caldicellulosiruptor acetigenus

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Neeli Habib ◽  
Manik Prabhu Narsing Rao ◽  
Min Xiao ◽  
Sohail Ahmad Jan ◽  
Wen-Jun Li
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Relationship Of

The present study was carried out to re-clarify the taxonomic relationship of Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii . The 16S rRNA sequence similarities between these species of the genus Caldicellulosiruptor were above the threshold values (98.65%) for bacterial species delineation. Similarly, the digital DNA–DNA hybridization and average nucleotide and amino acid identity values were greater than the thresholds for bacterial species delineation. In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii clade together. The results of our analysis indicated that these three taxa are conspecific. Therefore, Caldicellulosiruptor lactoaceticus Mladenovska et al. 1997 and Caldicellulosiruptor kristjanssonii Bredholt et al. 1999 should be reclassified as later heterotypic synonyms of Caldicellulosiruptor acetigenus (Nielsen et al. 1994) Onyenwoke et al. 2006.

scholarly journals Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1913-1919 ◽  
Author(s):  
Luis Collado ◽  
Ronald Jara ◽  
Susana González
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Wild Bird ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Faecal Samples ◽  
Study Results

Two Gram-stain-negative, gently curved rod-shaped isolates (WBE14T and WBE19), recovered from wild bird faecal samples in the city of Valdivia (Southern Chile) were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that these isolates belonged to the genus Helicobacter . This was further confirmed by a phylogenetic analyses based on the 16S rRNA, 60 kDa heat-shock protein (cpn60) and gyrase subunit B (gyrB) genes, where both strains formed a novel phylogenetic line within this genus. The 16S rRNA gene sequence similarity of strain WBE14T to the type strains of all other species of the genus Helicobacter examined ranged from 89.4 to 97.0 %; Helicobacter brantae and Helicobacter pametensis were the most closely related species. However, on the basis of the protein-coding genes Helicobacter pullorum and Helicobacter canadensis are the most closely related species. These data, together with their different morphological and biochemical characteristics, revealed that these strains represent a novel species, for which the name Helicobacter valdiviensis sp. nov. is proposed, with the type strain WBE14T ( = CECT 8410T = LMG 27920T).

Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2572-2578 ◽  
Author(s):  
Mie Johanne Hansen ◽  
Mads Frost Bertelsen ◽  
Henrik Christensen ◽  
Anders Miki Bojesen ◽  
Magne Bisgaard
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
Related Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Quinone Profile ◽  
The Family

A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae . Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges–Proskauer and indole; no X- or V-factor dependency; and acid production from l-arabinose (slow), l-fucose, maltose and trehalose, but not from dulcitol, d-mannitol, d-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994T) are C14 : 0, C16 : 0, C16 : 1ω7c and the summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is characteristic of members of the Pasteurellaceae . The quinone profile of Bisgaard taxon 57 (DSM 23800T) was similar to that of other genera in the Pasteurellaceae . The DNA G+C content of strain Baika1T is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae . On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1T ( = CCUG 59994T = DSM 23800T), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.

Ramlibacter algicola sp. nov., isolated from a freshwater alga Cryptomonas obovoidea

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Hyung Min Kim ◽  
Dong Min Han ◽  
Byung Hee Chun ◽  
Hye Su Jung ◽  
Kyung Hyun Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
Freshwater Alga ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Strictly Aerobic ◽  
Whole Genome ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, strictly aerobic, catalase-negative, oxidase-positive and non-motile rod-shaped bacterium, designated strain CrO1T, was isolated from a freshwater alga Cryptomonas obovoidea in the Nakdong river of South Korea. Colonies of CrO1T were white, convex and circular and growth was observed at 25–40 °C (optimum, 37 °C) and pH 6.0–9.0 (optimum, pH 7) and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). CrO1T contained C16 : 0, summed feature 5 (comprising C18 : 0ante and/or C18 : 2ω6,9c), C18 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) as the major cellular fatty acids (>5 %) and ubiquinone-8 as the sole respiratory quinone. Phosphatidylethanolamine was detected as the major polar lipid. The DNA G+C content of CrO1T, calculated from the whole genome sequence was 69.6 mol%. CrO1T was most closely related to Ramlibacter humi 18x22-1T with a 97.6 % 16S rRNA sequence similarity and shared less than 97.4 % 16S rRNA sequence similarities with other type strains. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences revealed that CrO1T formed a distinct phyletic lineage within the genus Ramlibacter . On the basis of the results of phenotypic, chemotaxonomic and molecular analysis, CrO1T clearly represents a novel species of the genus Ramlibacter , for which the name Ramlibacter algicola sp. nov. is proposed. The type strain is CrO1T (=KACC 19926T=JCM 33302T).

scholarly journals The Genus Caedibacter Comprises Endosymbionts of Paramecium spp. Related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria)

2002 ◽  
Vol 68 (12) ◽  
pp. 6043-6050 ◽  
Author(s):  
Cora L. Beier ◽  
Matthias Horn ◽  
Rolf Michel ◽  
Michael Schweikert ◽  
Hans-Dieter Görtz ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Sister Group ◽  
Rrna Gene ◽  
Paramecium Tetraurelia ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Bacterial Endosymbionts

ABSTRACT Obligate bacterial endosymbionts of paramecia able to form refractile inclusion bodies (R bodies), thereby conferring a killer trait upon their ciliate hosts, have traditionally been grouped into the genus Caedibacter. Of the six species described to date, only the Paramecium caudatum symbiont Caedibacter caryophilus has been phylogenetically characterized by its 16S rRNA gene sequence, and it was found to be a member of the Alphaproteobacteria related to the Rickettsiales. In this study, the Caedibacter taeniospiralis type strain, an R-body-producing cytoplasmatic symbiont of Paramecium tetraurelia strain 51k, was investigated by comparative 16S rRNA sequence analysis and fluorescence in situ hybridization with specific oligonucleotide probes. C. taeniospiralis is not closely related to C. caryophilus (80% 16S rRNA sequence similarity) but forms a novel evolutionary lineage within the Gammaproteobacteria with the family Francisellaceae as a sister group (87% 16S rRNA sequence similarity). These findings demonstrate that the genus Caedibacter is polyphyletic and comprises at least two phylogenetically different bacterial species belonging to two different classes of the Proteobacteria. Comparative phylogenetic analysis of C. caryophilus, five closely related Acanthamoeba endosymbionts (including one previously uncharacterized amoebal symbiont identified in this study), and their hosts suggests that the progenitor of the alphaproteobacterial C. caryophilus lived within acanthamoebae prior to the infection of paramecia.

Nonomuraea montanisoli sp. nov., isolated from mountain forest soil

2021 ◽  
Author(s):  
Suchart Chanama ◽  
Chanwit Suriyachadkun ◽  
Manee Chanama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Related Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Mountain Forest ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
A Genome

A novel actinomycete, strain SMC 257T, was isolated from a soil sample collected from mountain forest, Nan Province, Thailand. Strain SMC 257T formed tightly closed spiral spore chains on aerial mycelia. A polyphasic approach was used for the taxonomic study of this strain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 257T belonged to the genus Nonomuraea , and the closest phylogenetically related species were Nonomuraea roseoviolacea subsp. carminata JCM 9946T (98.9 % 16S rRNA gene sequence similarity), Nonomuraea rhodomycinica TBRC 6557T (98.4 %), and Nonomuraea roseoviolacea subsp. roseoviolacea JCM 3145T (98.3 %). Genome sequencing revealed a genome size of 9.76 Mbp and a G+C content of 72.3 mol%. The genome average nucleotide identity (ANI) and the digital DNA–DNA hybridization (dDDH) values that distinguished this novel strain from its closest related species were species boundary of 95–96 % and 70 %, respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars were glucose, ribose, madurose and mannose. The major menaquinone was MK-9(H4). The polar lipid profile consisted of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lysophosphatidylethanolamine, diphosphatidylglycerol, N-phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were C17 : 0 10-methyl and iso-C16 : 0. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, strain SMC 257T is considered to represent a novel species of the genus Nonomuraea , for which the name Nonomuraea montanisoli is proposed. The type strain is SMC 257T (=TBRC 13065T=NBRC 114772T).

Sulfitobacter maritimus sp. nov., isolated from coastal sediment

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Feng-Bai Lian ◽  
Yong-Qin Li ◽  
Jing Zhang ◽  
Shan Jiang ◽  
Zong-Jun Du
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
Content Type ◽  
A Genome ◽  
Bacterium Strain

A facultatively anaerobic bacterium, strain S0837T, was isolated from the marine sediment of Jingzi Wharf, Weihai, China. Cells of the novel strain were Gram-stain-negative, non-flagellated, non-gliding, non-pigmented and rod-shaped. Cells were around 0.3–0.5×1.0–1.4 µm in size and often appeared singly. Optimum growth occurred at 33 °C, with 2 % (w/v) NaCl and at pH 7.0–7.5. On the basis of the results of 16S rRNA gene sequences, stain S0837T had the closest relative with Sulfitobacter delicatus KCTC 32183T (98.0 %). Genome sequencing revealed a genome size of 3 785 026 bp, a G+C content of 59.8 mol% and several genes related with sulphur oxidation. The strain shared 98.0 % 16S rRNA sequence similarities with closely related type species and shared ANI value below 95–96 %, dDDH value of showed relatedness of 27.4, 25.2 and 25.2 % respectively with the closely related type species. Strain S0837T had ubiquinone-10 as the sole respiratory quinone, and possessed summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c) as the major fatty acid. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain S0837T should represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter maritimus sp. nov. is proposed. The type strain is S0837T (=MCCC 1K04635T=KCTC 72860T).

Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1089-1095 ◽  
Author(s):  
Markus Haber ◽  
Sigal Shefer ◽  
Assunta Giordano ◽  
Pierangelo Orlando ◽  
Agata Gambacorta ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Sea Salts ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The Mediterranean

Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family Flavobacteriaceae within the phylum Bacteroidetes , with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family Flavobacteriaceae , for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.

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