scholarly journals Taxono-genomics description of Olsenella lakotia SW165T sp. nov., a new anaerobic bacterium isolated from the cecum of feral chicken

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1103
Author(s):  
Supapit Wongkuna ◽  
Sudeep Ghimire ◽  
Tavan Janvilisri ◽  
Kinchel Doerner ◽  
Surang Chankhamhaengdecha ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Fatty Acid Production ◽  
Gram Staining ◽  
Biochemical Assays ◽  
A Genome ◽  
Culture Identification

Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165T. Methods: For the possible novel strain SW165T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis. Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was Olsenella profusa DSM 13989T (96.33% similarity) within the family Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45oC and pH 6.0-7.5 respectively.  This strain produced acetic acid as the primary fermentation product. Major fatty acids were C12:0, C14:0, C14:0 DMA and summed feature 1 (C13:1 at 12-13 and C14:0 aldehyde). Strain SW165T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165T and DSM 13989T were only 17.6 ± 5.3 and 74.35%, respectively. Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus Olsenella, and name it Olsenella lakotia SW165T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.

scholarly journals Taxono-genomics description of Olsenella lakotia SW165T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1103
Author(s):  
Supapit Wongkuna ◽  
Sudeep Ghimire ◽  
Tavan Janvilisri ◽  
Kinchel Doerner ◽  
Surang Chankhamhaengdecha ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Fatty Acid Production ◽  
Gram Staining ◽  
Biochemical Assays ◽  
A Genome ◽  
Culture Identification

Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165T. Methods: For the possible novel strain SW165T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis. Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was Olsenella profusa DSM 13989T (96.33% similarity) within the family Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45oC and pH 6.0-7.5 respectively.  This strain produced acetic acid as the primary fermentation product. Major fatty acids were C12:0, C14:0, C14:0 DMA and summed feature 1 (C13:1 at 12-13 and C14:0 aldehyde). Strain SW165T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165T and DSM 13989T were only 17.6 ± 5.3 and 74.35%, respectively. Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus Olsenella, and name it Olsenella lakotia SW165T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.

Desulfotomaculum intricatum sp. nov., a sulfate reducer isolated from freshwater lake sediment

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3574-3578 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A novel spore-forming, sulfate-reducing bacterium, strain SR45T, was isolated from sediment of a freshwater lake, Lake Mizugaki, in Japan. Cells of strain SR45 were rod-shaped (1.0–1.5×2.0–5.0 µm) and weakly motile; Gram staining and the KOH lysis test were negative. For growth, the optimum pH was 6.4–6.8 and the optimum temperature was 42–45 °C. Strain SR45T used sulfate, thiosulfate, sulfite and elemental sulfur as electron acceptors but not Fe(III). The G+C content of the genomic DNA was 41.1 mol%. Phylogenetic analyses based on genes for the 16S rRNA and DNA gyrase (gyrB) revealed that the isolated strain belonged to the family Peptococcaceae in the class Clostridia . The closest relative is Desulfotomaculum acetoxidans 5575T, with 16S rRNA gene sequence similarity of 92–94 %. It is suggested that the strain is the second isolated member of Desulfotomaculum subcluster Ie. The isolate had multiple 16S rRNA gene copies, with 13 different sequences. On the basis of phylogenetic and phenotypic characterization, the name Desulfotomaculum intricatum sp. nov. is proposed, with the type strain SR45T ( = NBRC 109411T = DSM 26801T).

Bizionia hallyeonensis sp. nov., isolated from seawater in an oyster farm

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 685-690 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Chul-Hyung Kang ◽  
Yong-Taek Jung ◽  
So-Jung Kang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Oyster Farm

A Gram-staining-negative, non-spore-forming, aerobic, non-flagellated, non-gliding, rod-shaped bacterium, designated strain T-y7T, was isolated from seawater collected in an oyster farm in the South Sea, South Korea, and subjected to a polyphasic study. Strain T-y7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, strain T-y7T fell within a clade comprising Bizionia species. It formed a coherent cluster with the type strains of Bizionia algoritergicola , B. argentinensis , B. echini and B. myxarmorum , with which it exhibited 16S rRNA gene sequence similarities of 97.4–98.9 % and mean DNA–DNA relatedness values of 11–27 %. Strain T-y7T had MK-6 as its predominant menaquinone and iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH as its major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The genomic DNA G+C content was 37.1 mol%. Its phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain T-y7T does not belong to any established Bizionia species. On the basis of the data presented, strain T-y7T is considered to represent a novel species of the genus Bizionia , for which the name Bizionia hallyeonensis sp. nov. is proposed. The type strain is T-y7T ( = KCTC 23881T  = CCUG 62110T).

scholarly journals Luteimonas lutimaris sp. nov., isolated from a tidal flat

2011 ◽  
Vol 61 (11) ◽  
pp. 2729-2733 ◽  
Author(s):  
Youn-Je Park ◽  
Moon Su Park ◽  
Seung Hyeon Lee ◽  
Woojun Park ◽  
Kangseok Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Gram Staining ◽  
Optimum Ph

A Gram-staining-negative, strictly aerobic bacterium, designated strain G3T, was isolated from a tidal flat of the Taean coast in South Korea. Cells were moderately halotolerant and non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain G3T was observed between 15 and 40 °C (optimum 30 °C) and between pH 5.5 and 9.0 (optimum pH 6.5–7.5). Strain G3T contained Q-8 as the predominant lipoquinone and iso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0 and iso-C11 : 0 as the major fatty acids. The G+C content of the genomic DNA was 69.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain G3T formed a tight phylogenetic lineage with Luteimonas mephitis B1953/27.1T within the genus Luteimonas and was most closely related to L. mephitis B1953/27.1T with 98.0 % 16S rRNA gene sequence similarity. The DNA–DNA relatedness between strain G3T and L. mephitis B1953/27.1T was 35.2±3.3 %. On the basis of chemotaxonomic data and molecular properties, strain G3T represents a novel species of the genus Luteimonas, for which the name Luteimonas lutimaris sp. nov. is proposed. The type strain is G3T ( = KACC 14929T = JCM 16916T).

scholarly journals Massilia norwichensis sp. nov., isolated from an air sample

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 56-64 ◽  
Author(s):  
Ivana Orthová ◽  
Peter Kämpfer ◽  
Stefanie P. Glaeser ◽  
René Kaden ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9T, isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9T identified Massilia haematophila CCUG 38318T, M. niastensis 5516S-1T (both 97.7 % similarity), M. aerilata 5516S-11T (97.4 %) and M. tieshanensis TS3T (97.4 %) as the next closest relatives. In partial gyrB and lepA sequences, NS9T shared the highest similarities with M. haematophila CCUG 38318T (94.5 %) and M. aerilata 5516-11T (94.3 %), respectively. These sequence data demonstrate the affiliation of NS9T to the genus Massilia . The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9T to the genus Massilia . Major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C10 : 0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA–DNA hybridizations demonstrate that strain NS9T is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9T ( = CCUG 65457T = LMG 28164T).

scholarly journals Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces

2011 ◽  
Vol 61 (11) ◽  
pp. 2610-2615 ◽  
Author(s):  
Hidetoshi Morita ◽  
Akiyo Nakano ◽  
Hiromi Onoda ◽  
Hidehiro Toh ◽  
Kenshiro Oshima ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequencing ◽  
Healthy Infant ◽  
16S Rrna Gene Sequence ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Strains HM2-1 and HM2-2T were isolated from the faeces of a healthy infant and were characterized by determining their phenotypic and biochemical features and phylogenetic positions based on partial 16S rRNA gene sequence analysis. They were Gram-positive, obligately anaerobic, non-spore-forming, non-gas-producing, and catalase-negative non-motile rods. They did not grow at 15 or 45 °C in anaerobic bacterial culture medium, and their DNA G+C content was in the range 56–59 mol%. In enzyme activity tests, strains HM2-1 and HM2-2T were positive for α/β-galactosidases and α/β-glucosidases but negative for β-glucuronidase and cystine arylamidase. An analysis of the cell-wall composition of strains HM2-1 and HM2-2T revealed the presence of glutamic acid, alanine and lysine. The presence of fructose-6-phosphate phosphoketolase shows that isolates HM2-1 and HM2-2T are members of the genus Bifidobacterium. These two isolates belong to the same species of the genus Bifidobacterium. Strain HM2-2T was found to be related to Bifidobacterium catenulatum JCM 1194T (97.4 % 16S rRNA gene sequence identity: 1480/1520 bp), Bifidobacterium pseudocatenulatum JCM 1200T (97.2 %: 1472/1514 bp), Bifidobacterium dentium ATCC 27534T (96.7 %: 1459/1509 bp) and Bifidobacterium angulatum ATCC 27535T (96.5 %: 1462/1515 bp). The predominant cellular fatty acids of strains HM2-1 and HM2-2T were 16 : 0 and 18 : 1ω9c, with proportions greater than 18 % of the total. Phylogenetic analyses involving phenotypic characterization, DNA–DNA hybridization and partial 16S rRNA gene sequencing proves that the strains represent a novel species of the genus Bifidobacterium, for which the name Bifidobacterium kashiwanohense sp. nov. is proposed. The type strain is HM2-2T ( = JCM 15439T  = DSM 21854T).

scholarly journals Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum

2007 ◽  
Vol 57 (10) ◽  
pp. 2284-2288 ◽  
Author(s):  
Seo-Youn Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rhizosphere Soil ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains

Two Gram-negative, milky-white-pigmented, motile, slightly curved rod-shaped bacterial isolates, UMS-37T and UMS-40, were isolated from rhizosphere soil of wild edible greens cultivated on Ulleung island, Korea, and their taxonomic positions were investigated by a polyphasic approach. They grew optimally at 25–30 °C and contained Q-8 as the predominant ubiquinone. The major cellular fatty acids (>10 % of total fatty acids) were C16 : 0, cyclo C17 : 0 and C16 : 1 ω7c and/oriso-C15 : 0 2-OH. The DNA G+C contents of the two isolates were 59.8 and 60.0 mol%. Isolates UMS-37T and UMS-40 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 94 %; they exhibited 16S rRNA gene sequence similarity levels of 96.8–98.2 % to the type strains of recognized Herbaspirillum species. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolates UMS-37T and UMS-40 formed a distinct phylogenetic lineage within the genus Herbaspirillum. DNA–DNA relatedness levels between isolates UMS-37T and UMS-40 and the type strains of some phylogenetically related Herbaspirillum species were in the range 3–56 %. On the basis of differences in phenotypic properties and phylogenetic distinctiveness and genomic data, isolates UMS-37T and UMS-40 were classified in the genus Herbaspirillum within a novel species, for which the name Herbaspirillum rhizosphaerae sp. nov. is proposed, with the type strain UMS-37T (=KCTC 12558T =CIP 108917T).

scholarly journals Rhizobium vallis sp. nov., isolated from nodules of three leguminous species

2011 ◽  
Vol 61 (11) ◽  
pp. 2582-2588 ◽  
Author(s):  
Fang Wang ◽  
En Tao Wang ◽  
Li Juan Wu ◽  
Xin Hua Sui ◽  
Ying Li ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains

Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7T (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570T (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA–DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T m). The type strain of R. vallis sp. nov. is CCBAU 65647T ( = LMG 25295T  = HAMBI 3073T), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.

scholarly journals Sphingomonas montanisoli sp. nov., isolated from mountain soil

2020 ◽  
Vol 70 (6) ◽  
pp. 3606-3613 ◽  
Author(s):  
Zixiao Xu ◽  
Yuxiao Zhang ◽  
Yasir Muhammad ◽  
Gejiao Wang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
A Genome

A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of Sphingomonas crocodyli CCP-7T (97.0%), Sphingomonas jatrophae S5-249T (96.6%) and Sphingomonas starnbergensis 382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with S. crocodyli CCP-7T, S. jatrophae S5-249T and S. starnbergensis 382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains ( S. crocodyli BCRC 81096T and S. jatrophae DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA–DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with S. crocodyli BCRC 81096T and S . jatrophae DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).

scholarly journals Humicoccus flavidus gen. nov., sp. nov., isolated from soil

2007 ◽  
Vol 57 (1) ◽  
pp. 56-59 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Seo-Youn Jung ◽  
Tae-Kwang Oh
Keyword(s):  
Fatty Acids ◽  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Diamino Acid

A Gram-positive, non-motile, spherical, non-spore-forming bacterial strain, DS-52T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and pH 6.0–7.0. Strain DS-52T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and galactose, mannose, xylose and rhamnose as whole-cell sugars. It contained MK-8(H4) and MK-9(H4) as the predominant menaquinones and anteiso-C15 : 0, iso-C15 : 0 and C17 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyldimethylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-52T is most closely related to the genus Nakamurella of the suborder Frankineae. Strain DS-52T exhibited 16S rRNA gene sequence similarity values of 96.5 % to Nakamurella multipartita JCM 9543T and 92.0–93.9 % to other members of the suborder Frankineae. The diagnostic diamino acid type and polar lipid profile of strain DS-52T were the same as those of the genus Nakamurella. However, strain DS-52T could be clearly distinguished from the genus Nakamurella by differences in predominant menaquinones, major fatty acids and cell-wall sugars. Accordingly, based on combined phenotypic, chemotaxonomic and phylogenetic data, strain DS-52T (=KCTC 19127T=CIP 108919T) is proposed as the type strain of a novel species in a new genus, Humicoccus flavidus gen. nov., sp. nov.

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