scholarly journals Vibrio Gaelis sp. nov. Isolated From the Skin of Southern Atlantic Sharpnose-puffer (Canthigaster Figueiredoi)

2021 ◽  
Author(s):  
Gustavo Pitta Reis de Azevedo ◽  
Hannah K. Mattsson ◽  
Luciane Tonon ◽  
Tatiane Arruda ◽  
Vinicius Salazar ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Reconstruction ◽  
Gene Clusters ◽  
The Novel ◽  
Optimum Growth ◽  
Gram Negative ◽  
Different Types ◽  
Genomic Taxonomy ◽  
A New Species ◽  
Genome Distance

Abstract Description of a Gram-negative, motile, circular-shaped bacterial strain, designated A621T obtained from the skin of the pufferfish Canthigaster figuereidoi (Tetraodontidae Family), collected in Arraial do Cabo, Brazil. Optimum growth occurs at 20 - 28 °C in the presence of 3% NaCl. The Genome sequence of the novel isolate consisted of 4.224 Mb, 4,431 coding genes and G+C content of 44.5%. Genomic taxonomy analysis based on Average Amino Acid (AAI), Genome-to-Genome-Distance (GGDH) and phylogenetic reconstruction placed A621T (= CBAS 741T) into a new species of the genus Vibrio (Vibrio gaelis sp. nov.). The genome of the novel species contains 4 gene clusters (~56.17 Kbp in total) coding for different types of bioactive compounds that hint to several possible ecological roles in the pufferfish host.

scholarly journals Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Neža Čadež ◽  
Nicolas Bellora ◽  
Ricardo Ulloa ◽  
Miha Tome ◽  
Hrvoje Petković ◽  
...  
Keyword(s):  
Yeast Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Single Copy ◽  
The Novel ◽  
Orthologous Genes ◽  
Parasitic Fungi ◽  
Ethanol Yields ◽  
A New Species

During a survey of Nothofagus trees and their parasitic fungi in Andean Patagonia (Argentina), genetically distinct strains of Hanseniaspora were obtained from the sugar-containing stromata of parasitic Cyttaria spp. Phylogenetic analyses based on the single-gene sequences (encoding rRNA and actin) or on conserved, single-copy, orthologous genes from genome sequence assemblies revealed that these strains represent a new species closely related to Hanseniaspora valbyensis. Additionally, delimitation of this novel species was supported by genetic distance calculations using overall genome relatedness indices (OGRI) between the novel taxon and its closest relatives. To better understand the mode of speciation in Hanseniaspora, we examined genes that were retained or lost in the novel species in comparison to its closest relatives. These analyses show that, during diversification, this novel species and its closest relatives, H. valbyensis and Hanseniaspora jakobsenii, lost mitochondrial and other genes involved in the generation of precursor metabolites and energy, which could explain their slower growth and higher ethanol yields under aerobic conditions. Similarly, Hanseniaspora mollemarum lost the ability to sporulate, along with genes that are involved in meiosis and mating. Based on these findings, a formal description of the novel yeast species Hanseniaspora smithiae sp. nov. is proposed, with CRUB 1602H as the holotype.

scholarly journals Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood

2007 ◽  
Vol 57 (3) ◽  
pp. 566-571 ◽  
Author(s):  
Zubair Aslam ◽  
Chang Soo Lee ◽  
Kyoung-Ho Kim ◽  
Wan-Taek Im ◽  
Leonid N. Ten ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Novel Species ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Optimum Growth ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
Positive Strain

A novel facultatively methylotrophic, Gram-negative, rod-shaped bacterium, designated strain S2R03-9T, was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, motile by means of a single polar flagellum, non-sporulating and catalase- and oxidase-positive. Strain S2R03-9T grew in the presence of 0–1 % (w/v) NaCl and at pH 6.0–10.0, with optimum growth in the absence of NaCl and at pH 7.0. It grew at temperatures in the range 20.0–30.0 °C, with optimum growth at 30 °C. Colonies grown on R2A medium were non-pigmented, opaque and creamy white. Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was most closely related to Methylobacterium organophilum JCM 2833T (96.6 % similarity) and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 95.0 %. The DNA G+C content was 64.9 mol%. The phylogenetic analysis, the phenotypic assessment and the chemotaxonomic data (major ubiquinone, Q-10; major fatty acids, C18 : 1 and C18 : 0) showed that S2R03-9T represents a novel species within the genus Methylobacterium in the class Alphaproteobacteria, for which the name Methylobacterium jeotgali sp. nov. is proposed. The type strain is S2R03-9T (=KCTC 12671T=LMG 23639T).

scholarly journals Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska

2005 ◽  
Vol 55 (1) ◽  
pp. 473-478 ◽  
Author(s):  
Elena V. Pikuta ◽  
Damien Marsic ◽  
Asim Bej ◽  
Jane Tang ◽  
Paul Krader ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Optimum Growth ◽  
Facultative Anaerobe ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Ph Range

A novel, psychrotolerant, facultative anaerobe, strain FTR1T, was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells were observed with sizes 0·6–0·7×0·9–1·5 μm. Growth occurred within the pH range 6·5–9·5 with optimum growth at pH 7·3–7·5. The temperature range for growth of the novel isolate was 0–28 °C and optimum growth occurred at 24 °C. The novel isolate does not require NaCl; growth was observed between 0 and 5 % NaCl with optimum growth at 0·5 % (w/v). The novel isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were acetate, ethanol and CO2. Strain FTR1T was sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. 16S rRNA gene sequence analysis showed 99·8 % similarity between strain FTR1T and Carnobacterium alterfunditum, but DNA–DNA hybridization between them demonstrated 39±1·5 % relatedness. On the basis of genotypic and phenotypic characteristics, it is proposed that strain FTR1T (=ATCC BAA-754T=JCM 12174T=CIP 108033T) be assigned to the novel species Carnobacterium pleistocenium sp. nov.

Shewanella indica sp. nov., isolated from sediment of the Arabian Sea

2011 ◽  
Vol 61 (9) ◽  
pp. 2058-2064 ◽  
Author(s):  
Pankaj Verma ◽  
Prashant Kumar Pandey ◽  
Arvind Kumar Gupta ◽  
Ho Jun Kim ◽  
Keun Sik Baik ◽  
...  
Keyword(s):  
Type Strain ◽  
Arabian Sea ◽  
Novel Species ◽  
Optimum Growth ◽  
Positive Bacterium ◽  
Gram Negative ◽  
Dna Relatedness ◽  
Sequence Identity ◽  
Shewanella Algae ◽  
Relatedness Data

A Gram-negative, facultatively anaerobic, rod-shaped, catalase- and oxidase-positive bacterium, motile by means of a single polar flagellum and designated strain KJW27T, was isolated from the marine sediment of Karwar jetty, west coast of India. The strain was β-haemolytic and grew with 0–10 % (w/v) NaCl, at 10–45 °C and at pH 6.5–10, with optimum growth with 2 % (w/v) NaCl, at 37 °C and at pH 7.5. The major fatty acids were iso-C15 : 0 (22.2 %), C17 : 1ω8c (21 %), summed feature 3 (comprising C16 : 1ω7c and/or C16:1ω6c; 10.2 %), C16 : 0 (7.1 %), iso-C13 : 0 (5.6 %) and C17 : 0 (4.4 %). The DNA G+C content was 51.2 mol%. Phylogenetic analysis based on 16S rRNA and gyrB gene sequences showed that strain KJW27T forms a lineage within the genus Shewanella and is closely related to Shewanella algae ATCC 51192T (98.8 %), Shewanella haliotis DW01T (98.8 %) and Shewanella chilikensis JC5T (98.2 %). Sequence identity with other members of this genus ranges from 92.2 to 96.4 %. The DNA–DNA relatedness of strain KJW27T with S. algae ATCC 51192T, S. haliotis DW01T and S. chilikensis JC5T was 52, 44 and 33 %, respectively. The phenotypic, genotypic and DNA–DNA relatedness data indicate that strain KJW27T should be distinguished from S. algae ATCC 51192T, S. haliotis DW01T and S. chilikensis JC5T. On the basis of the data presented in this study, strain KJW27T represents a novel species, for which the name Shewanella indica sp. nov. is proposed. The type strain is KJW27T ( = KCTC 23171T  = BCC 41031T  = NCIM 5388T).

scholarly journals Ferrimonas senticii sp. nov., a novel gammaproteobacterium isolated from the mucus of a puffer fish caught in Kaneohe Bay, Hawai'i

2007 ◽  
Vol 57 (11) ◽  
pp. 2670-2673 ◽  
Author(s):  
Sonia Campbell ◽  
Renee M. Harada ◽  
Qing X. Li
Keyword(s):  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Marine Agar ◽  
Gram Negative ◽  
Kaneohe Bay ◽  
Puffer Fish ◽  
Sequence Similarities ◽  
Added Salt

A novel species, strain P2S11T, was isolated from the mucus of a puffer fish caught off the coast of Kaneohe Bay, O'ahu, Hawai'i. A phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was most closely related to Ferrimonas marina DSM 16917T and Ferrimonas balearica DSM 9799T with 93.5 % and 82.9 % sequence similarities, respectively, which established the novel strain as belonging to the genus Ferrimonas. The strain formed off-white coloured colonies on marine agar and cells were Gram-negative, non-motile rods. H2S was produced when strain P2S11T was grown on TSI medium with added salt. Strain P2S11T had a DNA G+C content of 54.9 mol% and the dominant fatty acids were C16 : 1 ω9c, C16 : 0 and C17 : 1 ω8c. On the basis of this polyphasic study, strain P2S11T (=ATCC BAA-1480T=DSM 18821T) represents a novel species of the genus Ferrimonas, for which the name Ferrimonas senticii sp. nov. is proposed.

scholarly journals A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
David Wylensek ◽  
Thomas C. A. Hitch ◽  
Thomas Riedel ◽  
Afrizal Afrizal ◽  
Neeraj Kumar ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bile Acids ◽  
Sequence Data ◽  
Novel Species ◽  
Meta Analysis ◽  
Gene Clusters ◽  
In Vitro Assays ◽  
The Novel ◽  
Strain Collection

AbstractOur knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

scholarly journals Mucilaginibacter frigoritolerans sp. nov., Mucilaginibacter lappiensis sp. nov. and Mucilaginibacter mallensis sp. nov., isolated from soil and lichen samples

2010 ◽  
Vol 60 (12) ◽  
pp. 2849-2856 ◽  
Author(s):  
Minna K. Männistö ◽  
Marja Tiirola ◽  
Jennifer McConnell ◽  
Max M. Häggblom
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Optimum Growth ◽  
Respiratory Quinone ◽  
Finnish Lapland ◽  
Solid Media ◽  
Major Respiratory Quinone

Five cold-adapted bacteria belonging to the genus Mucilaginibacter were isolated from lichen and soil samples collected from Finnish Lapland and investigated in detail by phenotypic and phylogenetic analyses. Based on 16S rRNA gene phylogeny, the novel strains represent three new branches within the genus Mucilaginibacter. The strains were aerobic, chemo-organotrophic, non-motile rods and formed pigmented, smooth, mucoid colonies on solid media. The strains grew between 0 and 33 °C (optimum growth at 25 °C) and at pH 4.5–8.0 (optimum growth at pH 6.0). The main cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH) and iso-C17 : 0 3-OH and the major respiratory quinone was MK-7. The DNA G+C contents were 44.0–46.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic data, the strains represent three novel species of the genus Mucilaginibacter for which the names Mucilaginibacter frigoritolerans sp. nov. (type strain FT22T =ATCC BAA-1854T =LMG 25359T), Mucilaginibacter lappiensis sp. nov. (type strain ANJLI2T =ATCC BAA-1855T =LMG 25358T) and Mucilaginibacter mallensis sp. nov. (type strain MP1X4T =ATCC BAA-1856T =LMG 25360T) are proposed.

scholarly journals Hymenobacter xinjiangensis sp. nov., a radiation-resistant bacterium isolated from the desert of Xinjiang, China

2007 ◽  
Vol 57 (8) ◽  
pp. 1752-1756 ◽  
Author(s):  
Qiuju Zhang ◽  
Cong Liu ◽  
Yali Tang ◽  
Guoling Zhou ◽  
Ping Shen ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Gram Negative ◽  
Radiation Resistant ◽  
Rrna Gene Sequencing ◽  
Sequence Similarities

A Gram-negative, non-motile, rod-shaped and pink-pigmented bacterium, designated strain X2-1gT, was isolated from a mixture of sand samples collected from the desert of Xinjiang, China, after exposure of the sand to 8 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter, with low sequence similarities (<97 %) to recognized Hymenobacter species. Biolog GN2 assays supported this conclusion. Optimum growth was observed at pH 7 and 28 °C. The strain contained MK-7 as the predominant menaquinone and the major fatty acids were iso-C15 : 0 (19.5 %), C16 : 1 ω7c/iso-C15 : 0 2-OH (20.2 %), C16 : 1 ω5c (10.6 %), C16 : 0 (6.2 %), anteiso-C17 : 1 B/iso-C17 : 1 I (8.5 %) and C18 : 0 (6.5 %). The DNA G+C content was 54 mol% (T m). On the basis of the polyphasic evidence presented, it is proposed that strain X2-1gT represents a novel species of the genus Hymenobacter, for which the name Hymenobacter xinjiangensis sp. nov. is proposed. The type strain is X2-1gT (=CCTCC AB 206080T =IAM 15452T).

scholarly journals Pseudoxanthomonas yeongjuensis sp. nov., isolated from soil cultivated with Korean ginseng

2007 ◽  
Vol 57 (3) ◽  
pp. 646-649 ◽  
Author(s):  
Seung-Hee Yoo ◽  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Jin-Ho Kim ◽  
Youn-Kyung Baek ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Optimum Growth ◽  
Isoprenoid Quinone ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
Korean Ginseng

A Gram-negative, strictly aerobic, non-spore-forming bacterium, motile by means of single polar flagellum and rod-shaped, designated strain GR12-1T, was isolated from soil of a ginseng field in Yeongju region, Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is related to members of the genus Pseudoxanthomonas, showing sequence similarity values ranged from 92.3 to 96.2 %. This organism grew at 5–33 °C, with optimum growth at 28 °C. Strain GR12-1T grew optimally in the presence of 0–2 % NaCl. The whole-cell fatty acid profile included iso-C15 : 0, iso-C17 : 1 ω9c, iso-C16 : 0, iso-C11 : 0 3-OH and iso-C17 : 0 as major components. The only isoprenoid quinone was ubiquinone 8 (Q-8). The DNA G+C content was 63.4 mol%. On the basis of phenotypic, genetic and phylogenetic data, strain GR12-1T should be classified as a member of a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas yeongjuensis sp. nov. is proposed, with strain GR12-1T (=KACC 11580T=DSM 18204T) as the type strain.

scholarly journals Prevotella nanceiensis sp. nov., isolated from human clinical samples

2007 ◽  
Vol 57 (10) ◽  
pp. 2216-2220 ◽  
Author(s):  
C. Alauzet ◽  
F. Mory ◽  
J.-P. Carlier ◽  
H. Marchandin ◽  
E. Jumas-Bilak ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Novel Species ◽  
Clinical Samples ◽  
The Novel ◽  
Gram Negative ◽  
End Products ◽  
Type Strains

Three strains of anaerobic, non-pigmented, Gram-negative bacilli isolated from various human clinical samples were characterized in terms of phenotypic and genotypic tests, including sequence analysis of 16S rRNA and rpoB genes. The strains were most closely related to the type strains of Prevotella marshii and Prevotella shahii on the basis of both 16S rRNA (89.8 and 89.0 % identity, respectively) and rpoB gene sequences (83.1 and 82.8 % identity, respectively). Phylogenetic analysis showed that the isolates constituted a robust homogeneous group distinct from known species in the genus Prevotella. The rrn skeleton (as determined by PFGE) and the DNA G+C content, determined to be 39.4 mol% for strain LBN 293T, distinguished the novel isolates from the type strains of P. marshii and P. shahii. The three strains were saccharolytic and produced acetic, lactic and succinic acids as major metabolic end products. Polyphasic investigations supported the proposal of a novel species, Prevotella nanceiensis sp. nov., with LBN 293T (=AIP 261.03T =CIP 108993T =CCUG 54409T) as the type strain.

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