scholarly journals Phenotypic characterization of Sodalis praecaptivus sp. nov., a close non-insect-associated member of the Sodalis-allied lineage of insect endosymbionts

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1400-1405 ◽  
Author(s):  
Abhishek Chari ◽  
Kelly F. Oakeson ◽  
Shinichiro Enomoto ◽  
D. Grant Jackson ◽  
Mark A. Fisher ◽  
...  
Keyword(s):  
Novel Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Sodalis Glossinidius ◽  
Large Gene ◽  
Close Relationship ◽  
Metabolic Properties ◽  
Insect Symbionts ◽  
The 16S Rrna Gene

A Gram-stain-negative bacterium, isolated from a human wound was previously found to share an unprecedentedly close relationship with Sodalis glossinidius and other members of the Sodalis-allied clade of insect symbionts. This relationship was inferred from sequence analysis of the 16S rRNA gene and genomic comparisons and suggested the strain belonged to a novel species. Biochemical and genetic analyses supported this suggestion and demonstrated that the organism has a wide repertoire of metabolic properties, which is consistent with the presence of a relatively large gene inventory. Among members of the Sodalis-allied clade, this is the first representative that has sufficient metabolic capabilities to sustain growth in minimal media. On the basis of the results of this study, we propose that this organism be classified as a representative of a novel species, Sodalis praecaptivus sp. nov. (type strain HST = DSM 27494T = ATCC BAA-2554T).

scholarly journals Halorubrum gandharaense sp. nov., an alkaliphilic haloarchaeon from commercial rock salt

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2345-2350 ◽  
Author(s):  
Yusuke Kondo ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
...  
Keyword(s):  
Rock Salt ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Temperature Ranges ◽  
Derivatives Of ◽  
The 16S Rrna Gene

A Gram-stain-negative, non-motile, pleomorphic rod-shaped, orange–red-pigmented, facultatively aerobic and haloalkaliphilic archaeon, strain MK13-1T, was isolated from commercial rock salt imported from Pakistan. The NaCl, pH and temperature ranges for growth of strain MK13-1T were 3.0–5.2 M NaCl, pH 8.0–11.0 and 15–50 °C, respectively. Optimal growth occurred at 3.2–3.4 M NaCl, pH 9.0–9.5 and 45 °C. Addition of Mg2+ was not required for growth. The major polar lipids of the isolate were C20C20 and C20C25 archaeol derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Glycolipids were not detected. The DNA G+C content was 64.1 mol%. The 16S rRNA gene sequence of strain MK13-1T was most closely related to those of the species of the genus Halorubrum, Halorubrum luteum CECT 7303T (95.9 % similarity), Halorubrum alkaliphilum JCM 12358T (95.3 %), Halorubrum kocurii JCM 14978T (95.3 %) and Halorubrum lipolyticum JCM 13559T (95.3 %). The rpoB′ gene sequence of strain MK13-1T had < 90 % sequence similarity to those of other members of the genus Halorubrum. Based on the phylogenetic analysis and phenotypic characterization, strain MK13-1T may represent a novel species of the genus Halorubrum, for which the name Halorubrum gandharaense sp. nov. is proposed, with the type strain MK13-1T ( = JCM 17823T = CECT 7963T).

Mycobacterium iranicum sp. nov., a rapidly growing scotochromogenic species isolated from clinical specimens on three different continents

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1383-1389 ◽  
Author(s):  
Hasan Shojaei ◽  
Charles Daley ◽  
Zoe Gitti ◽  
Abodolrazagh Hashemi ◽  
Parvin Heidarieh ◽  
...  
Keyword(s):  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Clinical Specimens ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
The Usa ◽  
The 16S Rrna Gene

The isolation and characterization of a novel, rapidly growing, scotochromogenic mycobacterial species is reported. Eight independent strains were isolated from clinical specimens from six different countries of the world, two in Iran, two in Italy and one in each of following countries: Greece, the Netherlands, Sweden and the USA. Interestingly, two of the strains were isolated from cerebrospinal fluid. The strains were characterized by rapid growth and presented orange-pigmented scotochromogenic colonies. DNA-based analysis revealed unique sequences in the four regions investigated: the 16S rRNA gene, the rRNA gene internal transcribed spacer 1 and the genes encoding the 65 kDa heat-shock protein and the beta-subunit of RNA polymerase. The phylogenetic analysis placed the strains among the rapidly growing mycobacteria, being most closely related to Mycobacterium gilvum . The genotypic and phenotypic data both strongly supported the inclusion of the strains investigated here as members of a novel species within the genus Mycobacterium; the name Mycobacterium iranicum sp. nov. is proposed to indicate the isolation in Iran of the first recognized strains. The type strain is M05T ( = DSM 45541T = CCUG 62053T = JCM 17461T).

Lactobacillus gigeriorum sp. nov., isolated from chicken crop

2012 ◽  
Vol 62 (2) ◽  
pp. 330-334 ◽  
Author(s):  
Sylvie Cousin ◽  
Marie-Laure Gulat-Okalla ◽  
Laurence Motreff ◽  
Catherine Gouyette ◽  
Christiane Bouchier ◽  
...  
Keyword(s):  
Lactobacillus Acidophilus ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Metabolic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

In the early 1980s, a facultatively anaerobic, non-motile, short rod, designated 202T, was isolated from a chicken crop and identified as a homofermentative lactic acid bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain was affiliated with the genus Lactobacillus, clustering within the Lactobacillus acidophilus–delbrueckii group. In this analysis, strain 202T appeared to be most closely related to the type strains of Lactobacillus intestinalis and Lactobacillus amylolyticus, with gene sequence similarities of 96.1 and 96.2 %, respectively. Strain 202T was found to differ from these two species, however, when investigated by multilocus sequence analysis, and it also differed in terms of some of its metabolic properties. On the basis of these observations, strain 202T is considered to represent a novel species in the genus Lactobacillus, for which the name Lactobacillus gigeriorum sp. nov. is proposed; the type strain is 202T ( = CRBIP 24.85T = DSM 23908T).

scholarly journals Comamonas humi sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3976-3982 ◽  
Author(s):  
Kouta Hatayama
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Polyphasic Characterization ◽  
Reciprocal Value ◽  
The 16S Rrna Gene

A bacterial strain, designated GAU11T, was isolated from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic, non-motile rods. The 16S rRNA gene sequence of strain GAU11T showed high similarity to those of Comamonas zonglianii BF-3T (98.8 %), Pseudacidovorax intermedius CC21T (96.4 %), Acidovorax caeni R-24608T (96.2 %), Alicycliphilus denitrificans K601T (96.2 %), Pseudorhodoferax soli TBEA3T (95.9 %) and Comamonas terrigena LMG 1253T (95.9 %). Strain GAU11T contained ubiquinone 8 as the sole ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Its major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain GAU11T was 68.2 mol%. The DNA–DNA relatedness between strain GAU11T and C. zonglianii DSM 22523T was 52 or 68 % (reciprocal value). Phenotypic characterization indicated that strain GAU11T represents a member of the genus Comamonas , but at the same time distinguished it from C. zonglianii DSM 22523T. From polyphasic characterization, this strain should be classified as representing a novel species of the genus Comamonas , for which the name Comamonas humi sp. nov. (type strain GAU11T = JCM 19903T = DSM 28451T) is proposed.

scholarly journals Isolation and characterization of Reyranella massiliensis gen. nov., sp. nov. from freshwater samples by using an amoeba co-culture procedure

2011 ◽  
Vol 61 (9) ◽  
pp. 2151-2154 ◽  
Author(s):  
Isabelle Pagnier ◽  
Didier Raoult ◽  
Bernard La Scola
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Isolation And Characterization ◽  
Novel Bacterium ◽  
Gene Sequence Analysis ◽  
Culture Procedure

The analysis of three water samples from two cooling towers and one river allowed us to isolate three strains of a novel species of the class Alphaproteobacteria which is phylogenetically related to uncultured alphaproteobacteria. Based upon 16S rRNA gene sequence analysis and phenotypic characterization, we propose to name this novel species Reyranella massiliensis gen. nov., sp. nov., type strain 521T ( = CSUR P115T  = DSM 23428T). The most closely related cultivable micro-organism to this novel bacterium is a member of the genus Magnetospirillum.

scholarly journals Isoptericola hypogeus sp. nov., isolated from the Roman catacomb of Domitilla

2005 ◽  
Vol 55 (4) ◽  
pp. 1715-1719 ◽  
Author(s):  
Ingrid Groth ◽  
Peter Schumann ◽  
Barbara Schütze ◽  
Juan M. Gonzalez ◽  
Leonila Laiz ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Taxonomic Study ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
The 16S Rrna Gene

In order to clarify the taxonomic position of an actinobacterium from the Roman catacomb of Domitilla, a combination of phenotypic characterization, phylogenetic analysis based on the 16S rRNA gene sequence and DNA–DNA relatedness studies was used. The results from the polyphasic taxonomic study of this organism showed that strain HKI 0342T (=DSM 16849T=NCIMB 14033T) should be considered as the type strain of a novel species of the genus Isoptericola, for which the name Isoptericola hypogeus sp. nov. is proposed.

scholarly journals Phenotypic and genomic characterization of pneumococcus-like streptococci isolated from HIV-seropositive patients

Microbiology ◽  
2010 ◽  
Vol 156 (3) ◽  
pp. 838-848 ◽  
Author(s):  
Truls M. Leegaard ◽  
Hester J. Bootsma ◽  
Dominique A. Caugant ◽  
Marc J. Eleveld ◽  
Turid Mannsåker ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Viridans Streptococci ◽  
Close Relationship ◽  
Phenotypic Tests ◽  
Hiv Seropositive

Accurate differentiation between pneumococci and other viridans streptococci is essential given their differences in clinical significance. However, classical phenotypic tests are often inconclusive, and many examples of atypical reactions have been reported. In this study, we applied various phenotypic and genotypic methods to discriminate between a collection of 12 streptococci isolated from the upper respiratory tract of HIV-seropositive individuals in 1998 and 1999. Conventional phenotypic characterization initially classified these streptococci as Streptococcus pneumoniae, as they were all sensitive to optochin and were all bile soluble. However, they did not agglutinate with anti-pneumococcal capsular antibodies and were also far more resistant to antimicrobial agents than typeable pneumococci isolated in the same period. Genotypic characterization of these isolates and control isolates by both multilocus sequence analysis (MLSA) and comparative genomic hybridization (CGH) showed that only a single isolate was genetically considered to be a true S. pneumoniae isolate, and that the remaining 11 non-typable isolates were indeed distinct from true pneumococci. Of these, 10 most closely resembled a subgroup of Streptococcus mitis isolates genetically, while one strain was identified as a Streptococcus pseudopneumoniae isolate. CGH also showed that a considerable part of the proposed pneumococcal core genome, including many of the known pneumococcal virulence factors, was conserved in the non-typable isolates. Sequencing of part of the 16S rRNA gene and investigation for the presence of ply by PCR corroborated these results. In conclusion, our findings confirm the close relationship between streptococci of the Mitis group, and show that both MLSA and CGH enable pneumococci to be distinguished from other Mitis group streptococci.

scholarly journals Escherichia ruysiae sp. nov., isolated from an international traveller

2019 ◽  
Author(s):  
Boas C.L. van der Putten ◽  
S. Matamoros ◽  
D.R. Mende ◽  
C. Schultsz ◽  
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Novel Species ◽  
Multi Drug Resistance ◽  
Rrna Gene ◽  
Accession Number ◽  
Close Relationship ◽  
The 16S Rrna Gene ◽  
Rrna Sequences ◽  
Core Genes

ABSTRACTThe Escherichia genus comprises four species and at least five lineages currently not assigned to any species, termed ‘Escherichia cryptic clades’. We isolated an Escherichia strain from an international traveller and resolved the complete DNA sequence of the chromosome and an IncI multi-drug resistance plasmid using Illumina and Nanopore whole-genome sequencing (WGS). Strain OPT1704T can be differentiated from existing Escherichia spp. using biochemical (VITEK2) and genomic tests (average nucleotide identity [ANI] and digital DNA:DNA hybridisation [dDDH]). Phylogenetic analysis based on alignment of 16S rRNA sequences and 682 concatenated core genes showed similar results. Our analysis further revealed that strain OPT1704T falls within Escherichia cryptic clade IV, and is closely related to cryptic clade III. Combining our analyses with publicly available WGS data of cryptic clades III and IV from Enterobase confirmed the close relationship between clades III and IV (>96% interclade ANI), warranting assignment of both clades to the same novel species. We propose E. ruysiae sp. nov. as a novel species, encompassing Escherichia cryptic clades III and IV (type strain OPT1704T = NCCB 100732T = NCTC 14359T).Author notesThe Genbank accession number for the 16S rRNA gene sequence of strain OPT1704T is LR745848. The Genbank accession number for the complete genome sequence of strain OPT1704T is CABVLQ000000000.

scholarly journals Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora

2004 ◽  
Vol 54 (6) ◽  
pp. 2053-2056 ◽  
Author(s):  
Tomohiko Tamura ◽  
Takeshi Sakane
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Subtropical Forest ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Monophyletic Cluster ◽  
Aerial Hyphae ◽  
Emended Description ◽  
The 16S Rrna Gene

An actinomycete that developed sporangia containing four spores in a single row at the ends of short sporangiophores on branched aerial hyphae was isolated from subtropical forest soil. The isolate contained menaquinone MK-9(H4), glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and madurose in the whole-cell hydrolysate. The 16S rRNA gene sequence indicated that the isolate formed a monophyletic cluster with Planotetraspora mira. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species of the genus Planotetraspora is proposed, Planotetraspora silvatica sp. nov. (type strain, TT 00-51T=NBRC 100141T=DSM 44746T).

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

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