scholarly journals Rouxiella chamberiensis gen. nov., sp. nov., a member of the family Enterobacteriaceae isolated from parenteral nutrition bags

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1812-1818 ◽  
Author(s):  
Anne Le Flèche-Matéos ◽  
Marion Levast ◽  
Fabienne Lomprez ◽  
Yolande Arnoux ◽  
Clément Andonian ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parenteral Nutrition ◽  
Gas Production ◽  
New Taxon ◽  
16S Rrna Sequence ◽  
Gene Encoding ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
16S Rrna Sequence Analysis

Parenteral nutrition bags for newborns were found contaminated by a previously undescribed member of the family Enterobacteriaceae . The six isolates studied by rrs gene (encoding 16S rRNA) sequence analysis and multi-locus sequence analysis (MLSA) formed a discrete branch close to the genera Ewingella , Rahnella , Yersinia , Hafnia and Serratia . Phenotypically, the new taxon was distinct from these five genera. The new taxon gave positive results in Voges–Proskauer, Simmons citrate and o-nitrophenyl-β-galactoside hydrolysis tests; fermented d-glucose, d-mannitol, l-rhamnose, melibiose, l-arabinose and d-xylose; hydrolysed aesculin; and did not ferment maltose, trehalose, raffinose, d-sorbitol, sucrose or cellobiose. Tests for motility, gas production, urease, gelatinase and nitrate reduction were also negative. All isolates failed to grow at 37 °C. The DNA G+C content of strain 130333T was 53 mol%. On the basis of data obtained in this study, the six isolates represent a novel species of a new genus in the family Enterobacteriaceae , named Rouxiella chamberiensis gen. nov., sp. nov. The type strain of the type species is 130333T ( = CIP 110714T = DSM 28324T).

scholarly journals Campylobacter iguaniorum sp. nov., isolated from reptiles

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 975-982 ◽  
Author(s):  
Maarten J. Gilbert ◽  
Marja Kik ◽  
William G. Miller ◽  
Birgitta Duim ◽  
Jaap A. Wagenaar
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Fragment Length Polymorphism ◽  
16S Rrna Sequence ◽  
Ionization Time ◽  
Content Type ◽  
Ambient Temperatures ◽  
Link Type ◽  
16S Rrna Sequence Analysis

During sampling of reptiles for members of the class Epsilonproteobacteria , strains representing a member of the genus Campylobacter not belonging to any of the established taxa were isolated from lizards and chelonians. Initial amplified fragment length polymorphism, PCR and 16S rRNA sequence analysis showed that these strains were most closely related to Campylobacter fetus and Campylobacter hyointestinalis . A polyphasic study was undertaken to determine the taxonomic position of five strains. The strains were characterized by 16S rRNA and atpA sequence analysis, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and conventional phenotypic testing. Whole-genome sequences were determined for strains 1485ET and 2463D, and the average nucleotide and amino acid identities were determined for these strains. The strains formed a robust phylogenetic clade, divergent from all other species of the genus Campylobacter . In contrast to most currently known members of the genus Campylobacter , the strains showed growth at ambient temperatures, which might be an adaptation to their reptilian hosts. The results of this study clearly show that these strains isolated from reptiles represent a novel species within the genus Campylobacter , for which the name Campylobacter iguaniorum sp. nov. is proposed. The type strain is 1485ET ( = LMG 28143T = CCUG 66346T).

scholarly journals Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 129-134 ◽  
Author(s):  
Roshan Kumar ◽  
Vatsala Dwivedi ◽  
Namita Nayyar ◽  
Helianthous Verma ◽  
Amit Kumar Singh ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
16S Rrna Sequence Analysis

Strain RK1T, a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium was isolated from a hexachlorocyclohexane (HCH) dumpsite, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RK1T belongs to the family Sphingobacteriaceae and showed highest sequence similarity to Parapedobacter koreensis Jip14T (95.63 %). The major cellular fatty acids of strain RK1T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c), iso-C15 : 0 3-OH and C16 : 0. The major respiratory pigment and polyamine of RK1T were menaquinone (MK-7) and homospermidine, respectively. The main polar lipids were phosphatidylethanolamine and sphingolipid. The G+C content of the DNA was 44.5 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly demonstrated that strain RK1T represents a novel species of the genus Parapedobacter , for which the name Parapedobacter indicus sp. nov. is proposed. The type strain is RK1T ( = DSM 28470T = MCC 2546T).

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.

scholarly journals Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1186-1193 ◽  
Author(s):  
René Kaden ◽  
Cathrin Spröer ◽  
Daniel Beyer ◽  
Peter Krolla-Sidenstein
Keyword(s):  
Water Reservoir ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
New Taxon ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Drinking Water Reservoir ◽  
The Family ◽  
Emended Description

A Gram-stain-negative, oxidase and phosphatase-positive and catalase-negative, short rod-shaped bacterium was isolated from sediment of a drinking water reservoir in Germany. Based on 16S rRNA gene sequence and phenotypic properties, the bacterium belongs to the genus Rhodoferax within the family Comamonadaceae . The new taxon differed from related species mainly with respect to its fatty acid composition, low growth temperature, lack of pigments in young cultures and ability to utilize glycerol and d-mannose but not urea. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0, and C18 : 1ω7c. The only ubiquinone detected was ubiquinone Q-8. The DNA G+C content was 60.3–61 mol%. Because of the phenotypic and genotypic differences from the most closely related taxa, the new strain represents a novel species for which the name Rhodoferax saidenbachensis sp. nov. is proposed. The type strain is ED16T ( = CCUG 57711T = ATCC BAA-1852T = DSM 22694T). An emended description of the genus Rhodoferax is proposed. Based on the results of this study, strain T118T (Albidiferax ferrireducens) is properly placed in the genus Rhodoferax as Rhodoferax ferrireducens.

Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4289-4293 ◽  
Author(s):  
Yeon-Ju Kim ◽  
Sang-Rae Kim ◽  
Ngoc-Lan Nguyen ◽  
Deok-Chun Yang
Keyword(s):  
Novel Species ◽  
Strictly Aerobic ◽  
Biochemical Tests ◽  
16S Rrna Sequence ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
16S Rrna Sequence Analysis ◽  
Physiological And Biochemical ◽  
Motile By Gliding

A novel bacterial strain, designated DCY54T, was isolated from a field cultivated with ginseng in Yongin, Republic of Korea. Cells were Gram-reaction-negative, yellow-pigmented, rod-shaped, non-spore-forming, and strictly aerobic. They were motile by gliding and produced flexirubin-type pigments. Growth occurred optimally at 25–30 °C, at pH 5.0–7.0 and in the presence of 0–1 % NaCl. The 16S rRNA sequence analysis demonstrated that strain DCY54T was most closely related to Flavobacterium defluvii EMB117T (96.9 %). The only isoprenoid quinone of strain DCY 54T was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major cellular fatty acids (>15 %) were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 33.3 mol%. Phylogenetic inference and phenotypic data supported affiliation of strain DCY54T to the genus Flavobacterium . Several physiological and biochemical tests differentiated strain DCY54T from the species of the genus Flavobacterium with validly published names. On the basis of data from a polyphasic study, strain DCY54T represents a novel species of the genus Flavobacterium for which the name Flavobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY54T ( = KCTC 23318T = JCM 17336T).

Parasulfuritortus cantonensis gen. nov., sp. nov., a microaerophilic sulfur-oxidizing bacterium isolated from freshwater sediment

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Zhangzhang Xie ◽  
Surong Li ◽  
Weitie Lin ◽  
Jianfei Luo
Keyword(s):  
Sulfide Oxidation ◽  
Draft Genome ◽  
Anaerobic Growth ◽  
Freshwater Sediment ◽  
Rrna Gene ◽  
Gene Encoding ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Sulfur Oxidizing

A novel sulfur-oxidizing bacterium, designated strain LSR1T, was enriched and isolated from a freshwater sediment sample collected from the Pearl River in Guangzhou, PR China. The strain was an obligate chemolithoautotroph, using thiosulfate or sulfide as an electron donor and energy source. Growth of strain LSR1T was observed at 15–40 °C, pH 6.0–7.5 and NaCl concentrations of 0–1.5 %. Strain LSR1T was microaerophilic, with growth only at oxygen content less than 10 %. Anaerobic growth was also observed when using nitrate as the sole electron acceptor. The major cellular fatty acids were C16 : 0 and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). The DNA G+C content of the draft genome sequence was 67.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LSR1T formed a lineage within the family Thiobacillaceae , showing sequence identities of 92.87, 92.33 and 90.80 % with its closest relative genera Sulfuritortus , Annwoodia and Thiobacillus , respectively. The genome of strain LSR1T contained multiple genes encoding sulfur-oxidizing enzymes that catalyse thiosulfate and sulfide oxidation, and the gene encoding cbb 3-type cytochrome c oxidase and bd-type quinol oxidase, which enables strain LSR1T to perform sulphur oxidation under microaerophilic conditions. On the basis of phenotypic, genotypic and phylogenetic results, strain LSR1T is considered to represent a novel species of a new genus Parasulfuritortus within the family Thiobacillaceae , for which the name Parasulfuritortus cantonensis gen. nov., sp. nov. is proposed. The type strain is LSR1T (=GDMCC 1.1549=JCM 33645).

scholarly journals Chitinimonas arctica sp. nov., isolated from Arctic tundra soil

2020 ◽  
Vol 70 (5) ◽  
pp. 3455-3461 ◽  
Author(s):  
Qiang Xu ◽  
Fan Jiang ◽  
Xuyang Da ◽  
Yumin Zhang ◽  
Yingchao Geng ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Arctic Tundra ◽  
Tundra Soil ◽  
16S Rrna Sequence ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Bacterium Strain ◽  
Arctic Tundra Soil

A Gram-stain-negative, rod-shaped, green-pigmented, aerobic and motile bacterium, strain R3-44T, was isolated from Arctic tundra soil. Stain R3-44T clustered closely with members of the genus Chitinimonas , which belongs to the family Burkholderiaceae , and showed the highest 16S rRNA sequence similarity to Chitinimonas naiadis AR2T (96.10%). Strain R3-44T grew optimally at pH 7.0, 28 °C and in the presence of 0–0.5 % (w/v) NaCl. The predominant respiratory isoprenoid quinone of strain R3-44T was identified as ubiquinone Q-8. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipid and unidentified phospholipid. The main fatty acids were summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c, 40.6 %) and C16 : 0 (29.3 %). The DNA G+C content of strain R3-44T was 60.8 mol%. On the basis of the evidence presented in this study, strain R3-44T represents a novel species of the genus Chitinimonas , for which the name Chitinimonas arctica sp. nov. is proposed, with the type strain R3-44T (=CCTCC AB 2010422T=KCTC 72602T).

scholarly journals Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 267-273 ◽  
Author(s):  
Leilei Li ◽  
Jessy Praet ◽  
Wim Borremans ◽  
Olga C. Nunes ◽  
Célia M. Manaia ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Acid Production ◽  
Type Species ◽  
23S Rrna ◽  
Bumble Bee ◽  
Rrna Gene ◽  
New Taxon ◽  
Content Type ◽  
Link Type ◽  
The Family

In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as ‘Commensalibacter intestini’, except for two isolates (R-52486 and LMG 28161T) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161T was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877T (96.5 %), which corresponded with genus level divergence in the family Acetobacteraceae . Isolate LMG 28161T was subjected to whole-genome shotgun sequencing; a 16S–23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae . The DNA G+C content of strain LMG 28161T was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161T were similar to those of established AAB species [with C18 : 1ω7c (43.1 %) as the major component], but the amounts of fatty acids such as C19 : 0 cyclo ω8c, C14 : 0 and C14 : 0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161T ( = DSM 28636T = R-52487T) as the type strain of the type species.

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

Sign in / Sign up

Export Citation Format

Share Document