scholarly journals Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 2998-3004 ◽  
Author(s):  
En-Min Zhou ◽  
Tian-Tian Yu ◽  
Lan Liu ◽  
Hong Ming ◽  
Yi-Rui Yin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Strains YIM 77562T and YIM 77580, two novel Gram-staining-positive, filamentous bacterial isolates, were recovered from the Rehai geothermal field, Tengchong, Yunnan province, south-west China. Good growth was observed at 50–55 °C and pH 7.0. Aerial mycelium was absent on all media tested. Substrate mycelium was well-developed, long and moderately flexuous, and formed abundant, single, warty, ornamented endospores. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains indicated that they belong to the family Thermoactinomycetaceae . Similarity levels between the 16S rRNA gene sequences of the two strains and those of type strains of members of the Thermoactinomycetaceae were 88.33–93.24 %; the highest sequence similarity was with Hazenella coriacea DSM 45707T. In both strains, the predominant menaquinone was MK-7, the diagnostic diamino acid was meso-diaminopimelic acid and the major cellular fatty acids were iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids and unidentified phospholipids. The genomic DNA G+C contents of strains YIM 77562T and YIM 77580 were 45.5 and 44.2 mol%, respectively. DNA–DNA relatedness data suggest that the two isolates represent a single species. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that the two strains represent a single novel species in a new genus, Geothermomicrobium terrae gen. nov., sp. nov. The type strain of Geothermomicrobium terrae is YIM 77562T ( = CCTCC AA 2011022T = JCM 18057T).

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).

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 Haemophilus seminalis sp. nov., isolated from human semen

2020 ◽  
Vol 70 (4) ◽  
pp. 2588-2595 ◽  
Author(s):  
Min-ling Zheng ◽  
Liang-hui Li ◽  
Bin Liu ◽  
Yu-bo Lin ◽  
Xiao-tuan Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Human Semen ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Two Haemophilus -like isolates with similar biochemical characteristics, designated strains SZY H1T and SZY H2, were isolated from human semen specimens. Cells were Gram-negative, non-motile, non-acid-fast, pleomorphic rods or coccobacilli. The major fatty acids (>10 %) were C16 : 0, C14 : 0, iso-C16 : 0 and/or C14 : 0 3-OH and C16 : 1 ω6c and/or C16 : 1 ω7c. The polar lipids were determined to be phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminophospholipid, two unidentified polar lipids and four unidentified aminolipids. The major polyamine was found to be cadaverine. The near-full-length (1462 nt) 16S rRNA gene sequences analysis showed the two isolates were nearly identical (>99.8 %), and closely matched Haemophilus haemolyticus ATCC 33390T with 98.9–99.1 % sequence similarities. Phylogenetic analysis based on 16S rRNA gene sequences and concatenation of 30 protein markers also revealed that the isolates clustered together with H. haemolyticus ATCC 33390T, and formed a distinct lineage well separated from the other members of the genus Haemophilus . Further, the average nucleotide identity values between the two isolates and their related species were below the established cut-off values for species delineation (95 %). Based on these findings, the two isolates are considered to represent a new species of the genus Haemophilus , for which name Haemophilus seminalis sp. nov. is proposed. The type strain is SZY H1T (=NBRC 113782T=CGMCC 1.17137T).

scholarly journals Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2424-2430 ◽  
Author(s):  
Kristin Mühldorfer ◽  
Stephanie Speck ◽  
Gudrun Wibbelt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Five bacterial strains isolated from bats of the family Vespertilionidae were characterized by phenotypic tests and multilocus sequence analysis (MLSA) using the 16S rRNA gene and four housekeeping genes (rpoA, rpoB, infB, recN). Phylogenetic analyses of individual and combined datasets indicated that the five strains represent a monophyletic cluster within the family Pasteurellaceae . Comparison of 16S rRNA gene sequences demonstrated a high degree of similarity (98.3–99.9 %) among the group of bat-derived strains, while searches in nucleotide databases indicated less than 96 % sequence similarity to known members of the Pasteurellaceae . The housekeeping genes rpoA, rpoB, infB and recN provided higher resolution compared with the 16S rRNA gene and subdivided the group according to the bat species from which the strains were isolated. Three strains derived from noctule bats shared 98.6–100 % sequence similarity in all four genes investigated, whereas, based on rpoB, infB and recN gene sequences, 91.8–96 % similarity was observed with and between the remaining two strains isolated from a serotine bat and a pipistrelle bat, respectively. Genome relatedness as deduced from recN gene sequences correlated well with the results of MLSA and indicated that the five strains represent a new genus. Based on these results, it is proposed to classify the five strains derived from bats within Vespertiliibacter pulmonis gen. nov., sp. nov. (the type species), Vespertiliibacter genomospecies 1 and Vespertiliibacter genomospecies 2. The genus can be distinguished phenotypically from recognized genera of the Pasteurellaceae by at least three characteristics. All strains are nutritionally fastidious and require a chemically defined supplement with NAD for growth. The DNA G+C content of strain E127/08T is 38.2 mol%. The type strain of Vespertiliibacter pulmonis gen. nov., sp. nov. is E127/08T ( = CCUG 64585T = DSM 27238T). The reference strains of Vespertiliibacter genomospecies 1 and 2 are E145/08 and E157/08, respectively.

Brevibacillus fulvus sp. nov., isolated from a compost pile

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 506-512 ◽  
Author(s):  
Kouta Hatayama ◽  
Hirofumi Shoun ◽  
Yasuichi Ueda ◽  
Akira Nakamura
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two strains, designated K2814T and K282, were isolated from a compost pile in Japan. These strains were Gram-stain-variable, aerobic, motile and endospore-forming rods. The strains produced a characteristic brown non-diffusible pigment. The 16S rRNA gene sequences of the strains were 100 % identical and had high similarity to that of Brevibacillus levickii LMG 22481T (97.3 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that these strains belong to the genus Brevibacillus . Strains K2814T and K282 contained meso-diaminopimelic acid in their cell walls. Strains K2814T and K282 contained MK-7 (96.0 and 97.2 %, respectively) and MK-8 (4.0 and 2.8 %, respectively) as the major and minor menaquinones, respectively. Their major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. The DNA G+C contents of strains K2814T and K282 were 48.8 and 49.8 mol%, respectively. Polar lipids of strain K2814T were composed of phosphatidyl-N-methylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, three unidentified polar lipids, an unidentified aminophospholipid and an unidentified aminolipid. The level of DNA–DNA relatedness between strains K2814T and K282 was 99 or 100 %, and levels between strain K2814T and the type strains of seven related species of the genus Brevibacillus , including Brevibacillus levickii LMG 22481T, were below 59 %. From the chemotaxonomic and physiological data and the levels of DNA–DNA relatedness, these two strains should be classified as representing a novel species of the genus Brevibacillus , for which the name Brevibacillus fulvus sp. nov. (type strain K2814T = JCM 18162T = ATCC BAA-2417T = DSM 25523T) is proposed.

Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 60-65 ◽  
Author(s):  
Kouta Hatayama ◽  
Kouji Esaki ◽  
Teruhiko Ide
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity ◽  
The 16S Rrna Gene

Two novel bacterial strains, designated Kc1T and Kc5T, were isolated from soil in Japan. Cells of the novel strains were Gram-reaction-positive, aerobic or facultatively anaerobic, motile rods. Phylogenetic analyses based on 16S rRNA gene sequences indicated that both strains belonged to the genus Cellulomonas . The 16S rRNA gene sequences of strains Kc1T and Kc5T showed closest similarity to that of Cellulomonas terrae DB5T (98.1 % and 98.4 % similarity, respectively), and the 16S rRNA gene similarity between the two novel strains was 97.8 %. In both strains, the major menaquinone was MK-9(H4), the predominant polar lipids were diphosphatidylglycerol and phosphatidylinositol mannosides, and the peptidoglycan contained ornithine and glutamic acid. Cell-wall sugars were identified as rhamnose, galactose and mannose in strain Kc1T and rhamnose and glucose in strain Kc5T. The DNA G+C contents of strains Kc1T and Kc5T were 73.6 mol% and 75.8 mol%, respectively. Based on the chemotaxonomic and physiological data and the results of DNA–DNA hybridizations, the two strains represent two novel species within the genus Cellulomonas , for which the names Cellulomonas soli sp. nov. (type strain Kc1T  = DSM 24484T  = JCM 17535T) and Cellulomonas oligotrophica sp. nov. (type strain Kc5T = DSM 24482T = JCM 17534T) are proposed.

Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1073-1082 ◽  
Author(s):  
Hisako Hirayama ◽  
Hiroyuki Fuse ◽  
Mariko Abe ◽  
Masayuki Miyazaki ◽  
Takamichi Nakamura ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Type I ◽  
Marine Environments ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Two aerobic methane-oxidizing bacterial strains were isolated from distinct marine environments in Japan. Strains IT-4T and T2-1 were Gram-stain-negative, aerobic, motile, plump short rods or oval-shaped bacteria with a single polar flagellum and type I intracytoplasmic membranes. They were obligate methanotrophs that grew only on methane or methanol. Each strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. The strains grew best at 37 °C, and did not grow at 45 °C. NaCl was required for growth within a concentration range of 1–8 % (w/v). The major phospholipid fatty acids were C16 : 0, C16 : 1ω7c, and C16 : 1ω5t. The major isoprenoid quinone was MQ-8. The DNA G+C content was 50.9–51.7 mol%. The 16S rRNA gene sequences of the strains showed 99.4 % similarity to each other, and DNA–DNA hybridization analysis indicated that the strains were representatives of the same species. The 16S rRNA gene sequences were highly similar to some marine environmental sequences (94.0–97.7 % similarity), but did not show similarities more than 94 % with sequences of members of other related genera, such as Methylomicrobium , Methylobacter , Methylomonas and Methylosarcina . Phylogenies based on 16S rRNA gene sequences and deduced partial PmoA sequences, and the physiological and chemotaxonomic characteristics revealed that strains IT-4T and T2-1 represent a novel species of a new genus in the family Methylococcaceae , for which the name Methylomarinum vadi gen. nov., sp. nov. is proposed. The type strain is IT-4T ( = JCM 13665T = DSM 18976T).

Glacieibacterium frigidum gen. nov., sp. nov., a novel member of the family Sphingosinicellaceae isolated from a glacier

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Qing Liu ◽  
Lei-Lei Yang ◽  
Hong-Can Liu ◽  
Guo-Qing Zhang ◽  
Yu-Hua Xin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, rod-shaped, yellow bacterium, designated as LB1R16T, was isolated from the Laigu glacier on the Tibetan Plateau, PR China. Strain LB1R16T was catalase-positive, oxidase-negative and grew at 0–28 °C, pH 6.0–8.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LB1R16T belongs to the family Sphingosinicellaceae but formed an independent lineage. The highest level of 16S rRNA gene sequence similarities were found to Polymorphobacter arshaanensis DJ1R-1T (95.24 %), Sphingoaurantiacus capsulatus YLT33T (94.78 %) and Sandarakinorhabdus limnophila DSM 17366T (94.67 %). The genomic DNA G+C content was 68.8 mol%. The main cellular fatty acids were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and C12 : 0-OH. The respiratory quinone was ubiquinone-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid, one unidentified phospholipid and two unidentified polar lipids, which were different from the type strains of Polymorphobacter arshaanensis , Sphingoaurantiacus capsulatus and Sandarakinorhabdus limnophila . Based on a polyphasic approach, a novel species of a new genus, Glacieibacterium frigidum gen. nov., sp. nov., within the family Sphingosinicellaceae is proposed. The type strain is LB1R16T (=CGMCC 1.11941T=NBRC 113873T).

Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

scholarly journals Molecular Characterization of anEndozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximusL.)

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Irene Cano ◽  
Ronny van Aerle ◽  
Stuart Ross ◽  
David W. Verner-Jeffreys ◽  
Richard K. Paley ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Mass Mortality ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

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