scholarly journals Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts

2007 ◽  
Vol 57 (12) ◽  
pp. 2908-2911 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Seon-Young Lee ◽  
Byung-Yong Kim ◽  
Hyung-Jun Noh ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Phylogenetic Affiliation ◽  
Dna Reassociation ◽  
Compost Facility

Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145T and HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145T and HC148T and comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genus Ureibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existing Ureibacillus species were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains of Ureibacillus species ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type was l-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145T and HC148T were 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145T and HC148T represent members of the genus Ureibacillus, for which the names Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., respectively, are proposed. The type strain of U. composti is HC145T (=KACC 11361T =DSM 17951T) and the type strain of U. thermophilus is HC148T (=KACC 11362T =DSM 17952T).

scholarly journals Streptococcus orisuis sp. nov., isolated from the pig oral cavity

2007 ◽  
Vol 57 (6) ◽  
pp. 1272-1275 ◽  
Author(s):  
Kazuko Takada ◽  
Masatomo Hirasawa
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Mutans Streptococci ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Oral Streptococci ◽  
The Novel ◽  
Bacterial Strains

Five bacterial strains, designated as NUM 1001T, NUM 1002, NUM 1003, NUM 1004 and NUM 1005, were isolated from the oral cavities of pigs. Colonies grown on mitis salivarius agar were similar in morphology to those of mutans streptococci. The novel isolates were analysed biochemically using the Rapid ID 32 Strep microsystem, subjected to DNA–DNA hybridization with oral streptococci and had their 16S rRNA genes sequenced. On the basis of the phylogenetic and phenotypic evidence obtained, the strains represent a novel species of the genus Streptococcus, for which the name Streptococcus orisuis sp. nov. is proposed. The type strain is NUM 1001T (=JCM 14035T=DSM 18307T).

scholarly journals Reappraisal of the taxonomy of Streptococcus suis serotypes 20, 22 and 26: Streptococcus parasuis sp. nov.

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 438-443 ◽  
Author(s):  
R. Nomoto ◽  
F. Maruyama ◽  
S. Ishida ◽  
M. Tohya ◽  
T. Sekizaki ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Streptococcus Suis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Link Type ◽  
Reference Strains

In order to clarify the taxonomic position of serotypes 20, 22 and 26 of Streptococcus suis , biochemical and molecular genetic studies were performed on isolates (SUT-7, SUT-286T, SUT-319, SUT-328 and SUT-380) reacted with specific antisera of serotypes 20, 22 or 26 from the saliva of healthy pigs as well as reference strains of serotypes 20, 22 and 26. Comparative recN gene sequencing showed high genetic relatedness among our isolates, but marked differences from the type strain S. suis NCTC 10234T, i.e. 74.8–75.7 % sequence similarity. The genomic relatedness between the isolates and other strains of species of the genus Streptococcus , including S. suis, was calculated using the average nucleotide identity values of whole genome sequences, which indicated that serotypes 20, 22 and 26 should be removed taxonomically from S. suis and treated as a novel genomic species. Comparative sequence analysis revealed 99.0–100 % sequence similarities for the 16S rRNA genes between the reference strains of serotypes 20, 22 and 26, and our isolates. Isolate STU-286T had relatively high 16S rRNA gene sequence similarity with S. suis NCTC 10234T (98.8 %). SUT-286T could be distinguished from S. suis and other closely related species of the genus Streptococcus using biochemical tests. Due to its phylogenetic and phenotypic similarities to S. suis we propose naming the novel species Streptococcus parasuis sp. nov., with SUT-286T ( = JCM 30273T = DSM 29126T) as the type strain.

Ureibacillus suwonensis sp. nov., isolated from cotton waste composts

2006 ◽  
Vol 56 (3) ◽  
pp. 663-666 ◽  
Author(s):  
Byung-Yong Kim ◽  
Seon-Young Lee ◽  
Hang-Yeon Weon ◽  
Soon-Wo Kwon ◽  
Seung-Joo Go ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Aerobic ◽  
Phylogenetic Affiliation ◽  
Cotton Waste ◽  
Ureibacillus Thermosphaericus ◽  
Isoprenoid Quinones

The taxonomic position of two spore-forming strains 6T19T and 6T29, isolated from cotton composts for the cultivation of oyster mushroom (Pleurotus ostreatus), was investigated by a polyphasic approach. Cells of strains 6T19T and 6T29 were rod-shaped, Gram-negative and strictly aerobic. Sequencing and comparative analyses for the 16S rRNA genes of these strains clearly showed their phylogenetic affiliation to the genus Ureibacillus. Their closest relatives Ureibacillus thermosphaericus and Ureibacillus terrenus have sequence similarity of 96·9 and 97·5 %, respectively. The isoprenoid quinones of isolate 6T19T were MK-9, MK-8, MK-7, MK-10 and MK-6 (45 : 27 : 18 : 5 : 4 %), the peptidoglycan type was l-lys←d-Asp and the main cellular fatty acid was i-C16 : 0. DNA–DNA hybridization experiments resulted in relatedness values of 37 % between 6T19T and U. thermosphaericus DSM 10633T and 41 % between 6T19T and U. terrenus DSM 12654T. Based on the polyphasic data, strains 6T19T and 6T29 can be described as members of a novel species of the genus Ureibacillus, for which the name Ureibacillus suwonenesis sp. nov. is proposed. The type strain is 6T19T (=KACC 11287T=DSM 16752T).

scholarly journals Opening a next-generation black box: ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

2021 ◽  
Author(s):  
Martin Hahn ◽  
Andrea Huemer ◽  
Alexandra Pitt ◽  
Matthias Hoetzinger
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxon Richness ◽  
Large Set ◽  
Free Living ◽  
Environmental Distribution ◽  
Living Bacteria

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. We used a faster evolving protein-encoding marker to reveal ecological patterns hidden within a single OTU defined by >99% 16S rRNA sequence similarity. The studied taxon, subcluster PnecC of the genus Polynucleobacter, represents a ubiquitous group of planktonic freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. Besides the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. A unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca-rich and Ca-poor habitats, which strongly resembled the vicariance of plant species on silicate and limestone soils. The presented new cultivation-independent approach opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.

scholarly journals Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2320-2325 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
Cheng-Zhe Wen ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sea Urchins ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Moderate Amount ◽  
Polar Lipid Profile

A Gram-stain-negative, aerobic, rod-shaped, yellow-pigment-producing bacterium (designated strain CC-CZW007T) was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW007T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity to Vitellibacter vladivostokensis JCM 11732T (96.8 %), Vitellibacter soesokkakensis KCTC 32536T (96.4 %), Vitellibacter nionensis KCTC 32420T (95.8 %) and Vitellibacter aestuarii JCM 15496T (95.6 %) and lower sequence similarity to members of other genera. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW007T with respect to other species of the genus Vitellibacter. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, unidentified lipids and aminolipids; a moderate amount of aminophospholipid was also detected. The DNA G+C content was 34.7 mol%. The predominant quinone system was menaquinone (MK-6). On the basis of polyphasic taxonomic evidence presented here, strain CC-CZW007T is proposed to represent a novel species within the genus Vitellibacter, for which the name Vitellibacter echinoideorum sp. nov. is proposed. The type strain is CC-CZW007T ( = BCRC 80886T = JCM 30378T).

Thalassobacter stenotrophicus Macián et al. 2005 is a later synonym of Jannaschia cystaugens Adachi et al. 2004, with emended description of the genus Thalassobacter

2005 ◽  
Vol 55 (5) ◽  
pp. 1959-1963 ◽  
Author(s):  
M. J. Pujalte ◽  
M. C. Macián ◽  
D. R. Arahal ◽  
E. Garay
Keyword(s):  
16S Rrna ◽  
Genomic Dna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Sequence Comparisons ◽  
Emended Description

The type strains of Jannaschia cystaugens (LMG 22015T) and Thalassobacter stenotrophicus (CECT 5294T) were analysed by means of genomic DNA–DNA hybridization, comparison of 16S rRNA gene sequences and phenotypic properties determined under the same methodological conditions. J. cystaugens LMG 22015T showed DNA–DNA relatedness levels of 72 % when hybridized with the genomic DNA of T. stenotrophicus CECT 5294T. Sequence comparisons revealed that the 16S rRNA genes of the two strains had a similarity of 99·8 %. The cellular fatty acid and polar lipid compositions of the two strains and their DNA mol% G+C contents were almost identical. Bacteriochlorophyll a (Bchl a) and polyhydroxybutyrate were produced by both strains under the same culture conditions. Their closest phylogenetic neighbours were Jannaschia helgolandensis and Jannaschia rubra; however, the low sequence similarity values (95·7–95·9 %) and several important differences in phenotypic traits (ionic requirements, Bchl a production and polar lipids) support the distinction between the genera Thalassobacter and Jannaschia. Thus, we propose the unification of J. cystaugens (LMG 22015T) and T. stenotrophicus (CECT 5294T) as Thalassobacter stenotrophicus (type strain, CECT 5294T=DSM 16310T). An emended description of the genus Thalassobacter is also presented.

scholarly journals Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China

2007 ◽  
Vol 57 (7) ◽  
pp. 1402-1407 ◽  
Author(s):  
M. C. Gutiérrez ◽  
A. M. Castillo ◽  
M. Kamekura ◽  
Y. Xue ◽  
Y. Ma ◽  
...  
Keyword(s):  
16S Rrna ◽  
Inner Mongolia ◽  
Saline Lake ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Family ◽  
Extremely Halophilic Archaeon

Strain SH-6T was isolated from the sediment of Lake Shangmatala, a saline lake in Inner Mongolia (China). Cells were pleomorphic. The organism was neutrophilic and required at least 2.5 M (15 %) NaCl, but not MgCl2, for growth; optimal growth occurred at 4.3 M (25 %) NaCl. The G+C content of its DNA was 63.1 mol%. 16S rRNA gene sequence analysis revealed that strain SH-6T is a member of the family Halobacteriaceae, but there was a low level of similarity with other members of this family. Highest sequence similarity (94.6 %) was obtained with the 16S rRNA genes of the type strains of Natronolimnobius innermongolicus and Natronolimnobius baerhuensis. Polar lipid analyses revealed that strain SH-6T contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C20C20 and C20C25 glycerol diethers together with the glycolipid S2-DGD-1. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain SH-6T is thus considered to represent a novel species in a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halopiger xanaduensis gen. nov., sp. nov. is proposed. The type strain of Halopiger xanaduensis is SH-6T (=CECT 7173T=CGMCC 1.6379T=JCM 14033T).

scholarly journals Mucilaginibacter koreensis sp. nov., isolated from leaf mould

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2274-2279 ◽  
Author(s):  
Cheol Su Park ◽  
Kyudong Han ◽  
Tae-Young Ahn
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-staining-negative, strictly aerobic, rod-shaped, pale-pink pigmented bacterial strain, designated TF8T, was isolated from leaf mould in Cheonan, Republic of Korea. Its taxonomic position was determined through a polyphasic approach. Optimal growth occurred on R2A agar without NaCl supplementation, at 25–28 °C and at pH 6.0–7.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TF8T belongs to the genus Mucilaginibacter in the family Sphingobacteriaceae . The sequence similarity between 16S rRNA genes of strain TF8T and the type strains of other species of the genus Mucilaginibacter ranged from 92.1 to 94.7 %. The closest relatives of strain TF8T were Mucilaginibacter lutimaris BR-3T (94.7 %), M. soli R9-65T (94.5 %), M. litoreus BR-18T (94.5 %), M. rigui WPCB133T (94.0 %) and M. daejeonensis Jip 10T (93.8 %). The major isoprenoid quinone was MK-7 and the major cellular fatty acids were iso-C15 : 0 (33.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 24.8 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 13.0 %). The major polar lipids of TF8T were phosphatidylethanolamine and three unidentified aminophospholipids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of the data presented here, strain TF8T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter koreensis sp. nov. is proposed. The type strain is TF8T ( = KACC 17468T = JCM 19323T).

scholarly journals Agarivorans albus gen. nov., sp. nov., a γ-proteobacterium isolated from marine animals

2004 ◽  
Vol 54 (3) ◽  
pp. 693-697 ◽  
Author(s):  
Midori Kurahashi ◽  
Akira Yokota
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Marine Animals ◽  
16S Rdna Sequence ◽  
Gram Negative ◽  
Dna Reassociation ◽  
Agarivorans Albus

Six bacterial strains were isolated from healthy marine organisms that were collected from the coast of the Kanto area in Japan. Phylogenetic analysis based on 16S rDNA sequence similarity showed that the six isolates formed a separate cluster in the γ-Proteobacteria and were related to the genera Alteromonas and Glaciecola (<91·6 % similarity). The isolates were related closely to each other (DNA–DNA reassociation values of 74–93 %). The isolates had a polar flagellum and were Gram-negative, mesophilic, strictly aerobic rods that required salt for growth. Distinct phenotypic features of this group included the ability to hydrolyse agar and white pigmentation of colonies. The DNA G+C content of the isolates was 48–50 mol%. The major quinone was Q-8. Phenotypic characteristics of the isolates differed from those of members of the genera Alteromonas and Glaciecola. The name Agarivorans albus gen. nov., sp. nov. is proposed for the six isolates; the type strain is MKT 106T (=IAM 14998T=LMG 21761T).

Investigation of microbial communities on reverse osmosis membranes used for process water production

2007 ◽  
Vol 55 (8-9) ◽  
pp. 181-190 ◽  
Author(s):  
L.A. Bereschenko ◽  
A.J.M. Stams ◽  
G.H.J. Heilig ◽  
G.J.W. Euverink ◽  
M.M. Nederlof ◽  
...  
Keyword(s):  
16S Rrna ◽  
Reverse Osmosis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Universal Primers ◽  
Feed Water ◽  
Rrna Gene ◽  
Membrane Pore ◽  
Phylogenetic Affiliation ◽  
Ro Membrane

In the present study, the diversity and the phylogenetic affiliation of bacteria in a biofouling layer on reverse osmosis (RO) membranes were determined. Fresh surface water was used as a feed in a membrane-based water purification process. Total DNA was extracted from attached cells from feed spacer, RO membrane and product spacer. Universal primers were used to amplify the bacterial 16S rRNA genes. The biofilm community was analysed by 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) and the phylogenetic affiliation was determined by sequence analyses of individual 16S rDNA clones. Using this approach, we found that five distinct bacterial genotypes (Sphingomonas, Beta proteobacterium, Flavobacterium, Nitrosomonas and Sphingobacterium) were dominant genera on surfaces of fouled RO membranes. Moreover, the finding that all five “key players” could be recovered from the cartridge filters of this RO system, which cartridge filters are positioned before the RO membrane, together with literature information where these bacteria are normally encountered, suggests that these microorganisms originate from the feed water rather than from the RO system itself, and represent the fresh water bacteria present in the feed water, despite the fact that the feed water passes an ultrafiltration (UF) membrane (pore size approximately 40 nm), which is able to remove microorganisms to a large extent.

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