Lactobacillus delbrueckii subsp. jakobsenii subsp. nov., isolated from dolo wort, an alcoholic fermented beverage in Burkina Faso

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3720-3726 ◽  
Author(s):  
David B. Adimpong ◽  
Dennis S. Nielsen ◽  
Kim I. Sørensen ◽  
Finn K. Vogensen ◽  
Hagrétou Sawadogo-Lingani ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Genome Sequence ◽  
Type Species ◽  
Alcoholic Beverage ◽  
Lactobacillus Delbrueckii ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Split Decomposition ◽  
Content Type ◽  
Link Type

Lactobacillus delbrueckii is divided into five subspecies based on phenotypic and genotypic differences. A novel isolate, designated ZN7a-9T, was isolated from malted sorghum wort used for making an alcoholic beverage (dolo) in Burkina Faso. The results of 16S rRNA gene sequencing, DNA–DNA hybridization and peptidoglycan cell-wall structure type analyses indicated that it belongs to the species L. delbrueckii . The genome sequence of isolate ZN7a-9T was determined by Illumina-based sequencing. Multilocus sequence typing (MLST) and split-decomposition analyses were performed on seven concatenated housekeeping genes obtained from the genome sequence of strain ZN7a-9T together with 41 additional L. delbrueckii strains. The results of the MLST and split-decomposition analyses could not establish the exact subspecies of L. delbrueckii represented by strain ZN7a-9T as it clustered with L. delbrueckii strains unassigned to any of the recognized subspecies of L. delbrueckii . Strain ZN7a-9T additionally differed from the recognized type strains of the subspecies of L. delbrueckii with respect to its carbohydrate fermentation profile. In conclusion, the cumulative results indicate that strain ZN7a-9T represents a novel subspecies of L. delbrueckii closely related to Lactobacillus delbrueckii subsp. lactis and Lactobacillus delbrueckii subsp. delbrueckii for which the name Lactobacillus delbrueckii subsp. jakobsenii subsp. nov. is proposed. The type strain is ZN7a-9T = DSM 26046T = LMG 27067T.

scholarly journals Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3478-3484 ◽  
Author(s):  
Lars Ganzert ◽  
Janosch Schirmack ◽  
Mashal Alawi ◽  
Kai Mangelsdorf ◽  
Wolfgang Sand ◽  
...  
Keyword(s):  
Type Species ◽  
Dimethyl Sulfide ◽  
Membrane Lipids ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Methanosarcina Barkeri ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Content Type ◽  
Link Type

A novel methanogenic archaeon, strain MC-15T, was isolated from a floating biofilm on a sulphurous subsurface lake in Movile Cave (Mangalia, Romania). Cells were non-motile sarcina-like cocci with a diameter of 2–4 µm, occurring in aggregates. The strain was able to grow autotrophically on H2/CO2. Additionally, acetate, methanol, monomethylamine, dimethylamine and trimethylamine were utilized, but not formate or dimethyl sulfide. Trypticase peptone and yeast extract were not required for growth. Optimal growth was observed at 33 °C, pH 6.5 and a salt concentration of 0.05 M NaCl. The predominant membrane lipids of MC-15T were archaeol and hydroxyarchaeol phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol as well as hydroxyarchaeol phosphatidylserine and archaeol glycosaminyl phosphatidylinositol. The closely related species, Methanosarcina vacuolata and Methanosarcina horonobensis, had a similar composition of major membrane lipids to strain MC-15T. The 16S rRNA gene sequence of strain MC-15T was similar to those of Methanosarcina vacuolata DSM 1232T (sequence similarity 99.3 %), Methanosarcina horonobensis HB-1T (98.8 %), Methanosarcina barkeri DSM 800T (98.7 %) and Methanosarcina siciliae T4/MT (98.4 %). DNA–DNA hybridization revealed 43.3 % relatedness between strain MC-15T and Methanosarcina vacuolata DSM 1232T. The G+C content of the genomic DNA was 39.0 mol%. Based on physiological, phenotypic and genotypic differences, strain MC-15T represents a novel species of the genus Methanosarcina , for which the name Methanosarcina spelaei sp. nov. is proposed. The type strain is MC-15T ( = DSM 26047T = JCM 18469T).

scholarly journals Genome sequence analyses show that Neisseria oralis is the same species as ‘ Neisseria mucosa var. heidelbergensis’

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3920-3926 ◽  
Author(s):  
Julia S. Bennett ◽  
Keith A. Jolley ◽  
Martin C. J. Maiden
Keyword(s):  
Genome Sequence ◽  
Type Species ◽  
Whole Genome Sequence ◽  
23S Rrna ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Neisseria Mucosa

Phylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing ‘ Neisseria mucosa var. heidelbergensis’ and that this group was of equivalent taxonomic status to other well-described species of the genus Neisseria . Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava . Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. We suggest that strains previously identified as representing ‘ N. mucosa var. heidelbergensis’ and deposited in culture collections should be renamed N. oralis . Finally, one of the strains of N. oralis was able to ferment lactose, due to the presence of β-galactosidase and lactose permease genes, a characteristic previously thought to be unique to Neisseria lactamica , which therefore cannot be thought of as diagnostic for this species; however, the rMLST and cgMLST analyses confirm that N. oralis is most closely related to N. mucosa .

Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2986-2991 ◽  
Author(s):  
Dirk Wagner ◽  
Janosch Schirmack ◽  
Lars Ganzert ◽  
Daria Morozova ◽  
Kai Mangelsdorf
Keyword(s):  
Type Species ◽  
Dimethyl Sulfide ◽  
Membrane Lipids ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Content Type ◽  
Methanosarcina Mazei ◽  
Link Type ◽  
Siberian Permafrost

A methanogenic archaeon, strain SMA-21T, was isolated from a permafrost-affected soil by serial dilution in liquid medium. The cells were non-motile, stained Gram-negative and grew as irregular cocci with a diameter of 1.3–2.5 µm. Optimal growth was observed at 28 °C, pH 7.8 and 0.02 M NaCl. The strain grew on H2/CO2, methanol and acetate, but not on formate, ethanol, 2-butanol, 2-propanol, monomethylamine, dimethylamine, trimethylamine or dimethyl sulfide. Major membrane lipids of strain SMA-21T were archaeol phosphatidylglycerol, archaeol phosphatidylethanolamine and the corresponding hydroxyarchaeol compounds. The G+C content of the genomic DNA was 40.9 mol%. The 16S rRNA gene sequence was closely related to those of Methanosarcina mazei DSM 2053T (similarity 99.9 %) and Methanosarcina horonobensis HB-1T (similarity 98.7 %). On basis of the level of DNA–DNA hybridization (22.1 %) between strain SMA-21T and Methanosarcina mazei DSM 2053T as well as of phenotypic and genotypic differences, strain SMA-21T was assigned to a novel species of the genus Methanosarcina , for which the name Methanosarcina soligelidi sp. nov. is proposed. The type strain is SMA-21T ( = DSM 20065T = JCM 18468).

scholarly journals Bacillus luteus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1580-1586 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Bacterial Strains ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5 %) were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0 with minor (<5 but >1 %) amounts of iso-C17 : 0, anteiso-C17 : 0 B/iso-C17 : 0 I and C16 : 1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes . Both strains had a sequence similarity of 97.6 % with Bacillus saliphilus 6AGT and <96.8 % with other members of the genus Bacillus . Sequence similarity between strain JC167T and 168 was 100 %. Strain JC167T showed 25.8±1 % reassociation (based on DNA–DNA hybridization) with B. saliphilus DSM 15402T ( = 6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus , for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T ( = KCTC 33100T = LMG 27257T).

scholarly journals Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil

2020 ◽  
Vol 70 (4) ◽  
pp. 2449-2456 ◽  
Author(s):  
Jiyoun Kim ◽  
Geeta Chhetri ◽  
Inhyup Kim ◽  
Byungjo Lee ◽  
Wonhee Jang ◽  
...  
Keyword(s):  
Gamma Radiation ◽  
Type Species ◽  
Gamma Ray ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Radiation Resistant ◽  
The Republic

A gamma radiation-resistant and pink-pigmented bacterial strain, designated as 17Sr1-39T, was isolated from a gamma ray-irradiated soil sample collected in the Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, flagellated, asporogenous, rod-shaped and methylotrophic. Results of 16S rRNA gene sequence analysis showed that strain 17Sr1-39T was phylogenetically related to Methylobacterium currus PR1016AT (97.3 %), Methylobacterium aquaticum DSM 16371T (97.2 %), Methylobacterium platani PMB02T (97.0 %), Methylobacterium frigidaeris IER25-16T (96.6 %), Methylobacterium terrae 17Sr1-28T (96.6 %) and Methylobacterium organophilum JCM 2833T (93.4 %). The G+C content calculated based on the genome sequence was 70.4 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 17Sr1-39T and M. currus , M. aquaticum , M. platani , M. frigidaeris , M. terrae and M. organophilum were 77.3–89.9 and 22–38.2 %, respectively. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the data from phenotypic tests and genotypic differences between strain 17Sr1-39T and its close phylogenetic relatives, strain 17Sr1-39T represented a new species belonging to the genus Methylobacterium , for which the name Methylobacterium terricola sp. nov. (=KACC 52905T=NBRC 112874T) is proposed.

Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov., isolated from the desert

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 1006-1011 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Major Polar Lipid ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Hydrolysed Casein

Two strains of bacteria, JC213T and JC215T, were isolated from desert soil. Colonies were red to pink and cells Gram-stain-negative. Both strains were oxidase- and catalase-positive and hydrolysed casein. In both strains, phosphatidylethanolamine was the major polar lipid, iso-C15 : 0 was the major fatty acid and the bacteriohopane derivative, BHD1, was the major hopanoid. The genomic DNA G+C contents of strains JC213T and JC215T were 52.7 and 46.3 mol%, respectively. 16S rRNA gene sequence comparisons indicated that both strains belong to the genus Pontibacter within the family Cytophagaceae and the phylum Bacteroidetes . Strain JC213T showed the highest sequence similarity to Pontibacter populi HLY7-15T (96.6 %) and with other species of the genus Pontibacter sequence similarity was less than 96 %. Strain JC215T exhibited highest sequence similarity with Pontibacter lucknowensis DM9T (95.1 %) and shared 95 % or less sequence similarity with other species of the genus Pontibacter . The sequence similarity between strains JC213T and JC215T was 95.8 %. Distinct morphological, physiological and genotypic differences from previously described taxa support JC213T and JC215T being representatives of two novel species of the genus Pontibacter , for which the names Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov. are proposed and the type strains are JC213T ( = KCTC 32442T = LMG 27669T) and JC215T ( = KCTC 32443T = LMG 27670T), respectively.

scholarly journals Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3109-3119 ◽  
Author(s):  
Tobias C. Olofsson ◽  
Magnus Alsterfjord ◽  
Bo Nilson ◽  
Èile Butler ◽  
Alejandra Vásquez
Keyword(s):  
Apis Mellifera ◽  
Type Species ◽  
Novel Species ◽  
Lactobacillus Delbrueckii ◽  
Rrna Gene ◽  
Genetic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Respective Type ◽  
Type Strains

We previously discovered a symbiotic lactic acid bacterial (LAB) microbiota in the honey stomach of the honeybee Apis mellifera. The microbiota was composed of several phylotypes of Bifidobacterium and Lactobacillus . 16S rRNA gene sequence analyses and phenotypic and genetic characteristics revealed that the phylotypes isolated represent seven novel species. One grouped with Lactobacillus kunkeei and the others belong to the Lactobacillus buchneri and Lactobacillus delbrueckii subgroups of Lactobacillus . We propose the names Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov. for these novel species, with the respective type strains being Fhon13NT ( = DSM 26257T = CCUG 63287T), Bin4NT ( = DSM 26254T = CCUG 63291T), Hon2NT ( = DSM 26255T = CCUG 63289T), Hma8NT ( = DSM 26256T = CCUG 63629T), Hma2NT ( = DSM 26263T = CCUG 63633T), Bma5NT ( = DSM 26265T = CCUG 63301T) and Biut2NT ( = DSM 26262T = CCUG 63631T).

Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lake

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 522-527 ◽  
Author(s):  
Janosch Schirmack ◽  
Kai Mangelsdorf ◽  
Lars Ganzert ◽  
Wolfgang Sand ◽  
Alexandra Hillebrand-Voiculescu ◽  
...  
Keyword(s):  
Type Species ◽  
Dimethyl Sulfide ◽  
Membrane Lipids ◽  
Secondary Alcohol ◽  
Methanogenic Archaea ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Anoxic Sediment ◽  
Content Type ◽  
Link Type

A novel strain of methanogenic archaea, designated MC-20T, was isolated from the anoxic sediment of a subsurface lake in Movile Cave, Mangalia, Romania. Cells were non-motile, Gram-stain-negative rods 3.5–4.0 µm in length and 0.6–0.7 µm in width, and occurred either singly or in short chains. Strain MC-20T was able to utilize H2/CO2, formate, 2-propanol and 2-butanol as substrate, but not acetate, methanol, ethanol, dimethyl sulfide, monomethylamine, dimethylamine or trimethylamine. Neither trypticase peptone nor yeast extract was required for growth. The major membrane lipids of strain MC-20T were archaeol phosphatidylethanolamine and diglycosyl archaeol, while archaeol phosphatidylinositol and glycosyl archaeol were present only in minor amounts. Optimal growth was observed at 33 °C, pH 7.4 and 0.08 M NaCl. Based on phylogenetic analysis of 16S rRNA gene sequences, strain MC-20T was closely affiliated with Methanobacterium oryzae FPiT (similarity 97.1 %) and Methanobacterium lacus 17A1T (97.0 %). The G+C content of the genomic DNA was 33.0 mol%. Based on phenotypic and genotypic differences, strain MC-20T was assigned to a novel species of the genus Methanobacterium for which the name Methanobacterium movilense sp. nov. is proposed. The type strain is MC-20T ( = DSM 26032T = JCM 18470T).

Salinimicrobium sediminis sp. nov., isolated from a deep-sea sediment

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 984-988 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Major Polar Lipid ◽  
Sequence Comparisons ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

Strain JC207T was isolated from a deep (265 m) sea sediment, and appeared as dark yellow colonies on agar plates with cells staining Gram-negative. Catalase, oxidase and caseinase were positive, while chitinase, gelatinase and amylase were negative. Major (>5 %) fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, iso-C14 : 0 and iso-C15 : 1G. Strain JC207T contained phosphatidylethanolamine as the major polar lipid, with minor amounts of five unidentified lipids. A bacterial hopane derivative, diplopterol and adenosylhopane were the major hopanoids. Genomic DNA G+C content was 47.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC207T represented a member of the genus Salinimicrobium within the family Flavobacteriaceae of the phylum Bacteroidetes . Strain JC207T had sequence similarity with Salinimicrobium terrae YIM-C338T (98 %), Salinimicrobium xinjiangense BH206T (97.6 %) and other members of the genus Salinimicrobium (<96.8 %). However, strain JC207T showed an average of 23.6±4 and 37±4 relatedness (based on DNA–DNA hybridization) with Salinimicrobium terrae CGMCC 1.6308T ( = YIM-C338T) and Salinimicrobium xinjiangense KCTC 12883T ( = BH206T), respectively. Morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC207T as a representative of a novel species in the genus Salinimicrobium , for which the name Salinimicrobium sediminis sp. nov. is proposed. The type strain is JC207T ( = KCTC 32444T = CGMCC 1.12641T).

scholarly journals Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2643-2649 ◽  
Author(s):  
Yuko Kudo ◽  
Kaihei Oki ◽  
Koichi Watanabe
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Lactobacillus Delbrueckii ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as Lactobacillus delbrueckii , the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of L. delbrueckii . Together, the results of phenotypic characterization, DNA–DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of L. delbrueckii were all >88.7 %) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221T ( = JCM 17838T  = DSM 24966T).

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