scholarly journals Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae

2010 ◽  
Vol 60 (3) ◽  
pp. 659-663 ◽  
Author(s):  
Shu-Kun Tang ◽  
Jin-Yuan Wu ◽  
Yun Wang ◽  
Peter Schumann ◽  
Wen-Jun Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Agar Plate ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
The Family ◽  
Novel Genus And Species ◽  
Unknown Phospholipid

A Gram-stain-positive, coccoid, non-motile, halotolerant actinobacterium, designated YIM 45900T, was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The peptidoglycan type was A4α with an l-Lys–l-Ser–d-Asp interpeptide bridge. The cell-wall sugars contained galactose and fucose. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylinositol, a glucosamine-containing phospholipid and an unknown phospholipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism falls within the radius of the suborder Micrococcineae and its closest phylogenetic neighbours are the genera of the family Dermacoccaceae. Strain YIM 45900T showed 16S rRNA gene sequences similarity values of 93.1–95.9 % with members of the genera Dermacoccus, Demetria and Kytococcus. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel genus and species, Yimella lutea gen. nov., sp. nov., are proposed. The type strain of Yimella lutea is YIM 45900T (=DSM 19828T =KCTC 19231T =CCTCC AB 207007T).

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2289-2295 ◽  
Author(s):  
Madalin Enache ◽  
Takashi Itoh ◽  
Tadamasa Fukushima ◽  
Ron Usami ◽  
Lucia Dumitru ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Marker ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Rpob Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The Family

In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.

scholarly journals Poritiphilus flavus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coral Porites lutea

2020 ◽  
Vol 70 (11) ◽  
pp. 5620-5626 ◽  
Author(s):  
Guanghua Wang ◽  
Shuailiang Xu ◽  
Ge Dang ◽  
Jianfeng Liu ◽  
Hongfei Su ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Porites Lutea ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, non-endospore-forming, non-motile, aerobic bacterium (strain R33T) was isolated from coral Porites lutea and subjected to a polyphasic taxonomic study. The G+C content was 44.5 mol%. The only detected respiratory quinone was menaquinone 6 (MK-6). The major cellular fatty acids were iso-C15 : 0 and iso-C15 : 1 ω6c. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Global alignment based on 16S rRNA gene sequences indicated that strain R33T shares the highest sequence identity of 93.2 % with Muriicola marianensis A6B8T in the family Flavobacteriaceae . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R33T forms a distinct branch in a stable clade comprising strain R33T and members of the genera Muriicola , Robiginitalea , Eudoraea and Zeaxanthinibacter . The phylogenomic analysis also supported this 16S rRNA gene-based phylogenetic result. Comparative genomic analysis indicated that strain R33T is rich in AraC-type DNA-binding domain-containing protein-coding genes, which means the regulation of carbon utilization is very complex. Low 16S rRNA gene identity, different polar lipids and/or cellular fatty acid profiles could readily distinguish strain R33T from any validly published type strains. Therefore, strain R33T is suggested to represent a new species in a new genus, for which the name Poritiphilus flavus gen. nov., sp. nov. is proposed. The type strain is R33T (=MCCC 1K03853T=KCTC 72443T).

Description of a novel coccoid cyanobacterial genus and species Sinocapsa zengkensis gen. nov. sp. nov. (Sinocapsaceae, incertae sedis), with taxonomic notes on genera in Chroococcidiopsidales

Phytotaxa ◽  
2019 ◽  
Vol 409 (3) ◽  
pp. 146-160 ◽  
Author(s):  
YILANG WANG ◽  
FANGFANG CAI ◽  
NANNAN JIA ◽  
RENHUI LI
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Concrete Surface ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Incertae Sedis ◽  
Molecular Features ◽  
The Family

A new terrestrial coccoid cyanobacterial strain was isolated in depression of a rough concrete surface in village Zengkeng, Fujian Province, China. This strain, named CHAB 6571, was characterized by a polyphasic approach. The strain exhibited morphological similarity to the Aliterlella species but differed in its larger cell sizes and irregular arranged thylakoids. 16S rRNA gene sequences of the strain had the maximum homology as 94.13 % to the genus Aliterella. The phylogeny based on 16S rRNA gene sequences revealed that there were four separated coccoid cyanobacterial clusters formed in the position representing Chroococcidiopsidales, at the vicinity of Nostocales and away from other coccoid cyanobacterial orders such as Chroococcales, Pleurocapsales and Synechococcales. These four main clusters as the CHAB 6571 in cluster A, genus Aliterella of the family Aliterellaceae in cluster B, Chroococcidiopsis sensu stricto of Chroococcidiopsidaceae in cluster C, and genera Chroogloeocystis and Gloeocapsopsis in cluster D, were likely to represent four different families with their 16S rRNA gene sequences similarities as 90–94%. However, the 16S rRNA phylogenetic results also revealed that the Chroococcidiopsidales were not monophyletic since the organisms belonging to Oscillatoriales such as Cephalothrix, Aerosakkonema and Microseira were phylogenetically mixed into the Chroococcidiopsidales. Combining the morphological, ecological and molecular features, CHAB 6571 as a new genus and species, as well as a novel family were therefore established, named Sinocapsa zengkensis (Sinocapsaceae, incertae sedis).

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Halovarius luteus gen. nov., sp. nov., an extremely halophilic archaeon from a salt lake

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2420-2425 ◽  
Author(s):  
Maliheh Mehrshad ◽  
Mohammad Ali Amoozegar ◽  
Ali Makhdoumi ◽  
Mehrnoosh Rasooli ◽  
Basaer Asadi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hypersaline Environment ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Brine Sample ◽  
The Family ◽  
Extremely Halophilic Archaeon

An extremely halophilic archaeon, strain DA50T, was isolated from a brine sample of Urmia lake, a hypersaline environment in north-west Iran. Strain DA50T was orange-pigmented, motile, pleomorphic and required at least 2.5 M NaCl but not MgCl2 for growth. Optimal growth was achieved at 4.0 M NaCl and 0.3 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 45 °C, while it was able to grow over a pH range of 6.5–8.0 and a temperature range of 25–50 °C. Analysis of 16S rRNA gene sequences revealed that strain DA50T is a member of the family Halobacteriaceae, showing a low level of similarity with other members of this family. Highest similarities, 94.4, 94.0 and 93.9 %, were obtained with the 16S rRNA gene sequences of the type strains of Natrialba aegyptia, Halobiforma lacisalsi and Halovivax asiaticus, respectively. Polar lipid analyses revealed that strain DA50T contains phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Four unidentified glycolipids and two minor phospholipids were also observed. The only quinone present was MK-8(II-H2). The G+C content of its DNA was 62.3 mol%. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain DA50T is thus considered to represent a novel species of a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halovarius luteus gen. nov., sp. nov. is proposed. The type strain of Halovarius luteus is DA50T ( = IBRC-M 10912T = CECT 8510T).

scholarly journals Zhouia amylolytica gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from sediment of the South China Sea

2006 ◽  
Vol 56 (12) ◽  
pp. 2825-2829 ◽  
Author(s):  
Zhi-Pei Liu ◽  
Bao-Jun Wang ◽  
Xin Dai ◽  
Xing-Yu Liu ◽  
Shuang-Jiang Liu
Keyword(s):  
South China Sea ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
South China ◽  
The South China Sea ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
China Sea ◽  
The Family

Three Gram-negative, non-spore-forming strains were isolated from sediment from the South China Sea, China, and their taxonomic positions were investigated using a polyphasic approach. Strains HN-171T, HN-172 and HN-181 grew optimally at 30 °C, in the presence of 4.5–5.0 NaCl % (w/v) and at pH 7.2–7.4. They contained MK-6 as the predominant respiratory quinone and contained iso-C15 : 1 G, iso-C15 : 0, summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c/t) and C15 : 0 as the major fatty acids. The DNA G+C content of strain HN-171T was 34.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain HN-171T, together with strains HN-172 and HN-181, formed a distinct evolutionary lineage within the family Flavobacteriaceae. The 16S rRNA gene sequences of strains HN-171T, HN-172 and HN-181 shared 99.8–100 % similarity with each other, and the sequence of strain HN-171T exhibited similarity values below 90.2 % with those of other members of the family Flavobacteriaceae. The closest relative of HN-171T was Coenonia anatina LMG 14382T (90.2 %). On the basis of their phenotypic and phylogenetic properties, the three isolates represent a novel genus and a novel species, for which the name Zhouia amylolytica gen. nov., sp. nov. is proposed. The type strain is HN-171T (=CGMCC 1.6114T=JCM 14016T).

Taonella mepensis gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from activated sludge

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2472-2476 ◽  
Author(s):  
Xue-dong Xi ◽  
Wei-liang Dong ◽  
Jun Zhang ◽  
Yan Huang ◽  
Zhong-li Cui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Close Relatives

A novel Gram-negative, non-spore-forming, rod-shaped strain, H1T, was isolated from activated sludge by micromanipulation. No close relatives among cultured bacterial isolates were found; phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H1T forms a deep single branch in the family Rhodospirillaceae . Cells of strain H1T were slightly curved to straight rods (1.2–1.4×1.5–1.7 µm) and motile by a single polar flagellum. Strain H1T was able to grow in the presence of 0–4 % NaCl and grew optimally at 37 °C and pH 6.0–7.0. Chemotaxonomic analysis revealed that strain H1T possessed Q-10 as the predominant ubiquinone and C18 : 1ω7c, C16 : 0 and C19 : 0 cyclo ω8c as the major fatty acids. The DNA G+C content of strain H1T was 65.1 mol%. Comparative analysis of 16S rRNA gene sequences, and phenotypic and chemotaxonomic data, indicate that strain H1T should represent a novel genus and species of the family Rhodospirillaceae . The name Taonella mepensis gen. nov., sp. nov. is proposed. The type strain of Taonella mepensis is H1T ( = CICC 10529T  = CCTCC AB 2012861T  = KACC 16940T).

scholarly journals Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

2010 ◽  
Vol 60 (6) ◽  
pp. 1271-1279 ◽  
Author(s):  
Hélène Marchandin ◽  
Corinne Teyssier ◽  
Josiane Campos ◽  
Hélène Jean-Pierre ◽  
Frédéric Roger ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
The Family ◽  
The 16S Rrna Gene

Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388T (=AIP 149.07T=CIP 109806T=DSM 21255T=CCUG 56017T) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes ‘Bacilli’, ‘Clostridia’, Thermolithobacteria and ‘Erysipelotrichi’ in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.

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