scholarly journals Phylogenomic Analyses of Bradyrhizobium Reveal Uneven Distribution of the Lateral and Subpolar Flagellar Systems, Which Extends to Rhizobiales

2019 ◽  
Vol 7 (2) ◽  
pp. 50 ◽  
Author(s):  
Daniel Garrido-Sanz ◽  
Miguel Redondo-Nieto ◽  
Elías Mongiardini ◽  
Esther Blanco-Romero ◽  
David Durán ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Uneven Distribution ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Simultaneous Presence ◽  
Lateral Flagellum ◽  
Phylogenomic Analyses

Dual flagellar systems have been described in several bacterial genera, but the extent of their prevalence has not been fully explored. Bradyrhizobium diazoefficiens USDA 110T possesses two flagellar systems, the subpolar and the lateral flagella. The lateral flagellum of Bradyrhizobium displays no obvious role, since its performance is explained by cooperation with the subpolar flagellum. In contrast, the lateral flagellum is the only type of flagella present in the related Rhizobiaceae family. In this work, we have analyzed the phylogeny of the Bradyrhizobium genus by means of Genome-to-Genome Blast Distance Phylogeny (GBDP) and Average Nucleotide Identity (ANI) comparisons of 128 genomes and divided it into 13 phylogenomic groups. While all the Bradyrhizobium genomes encode the subpolar flagellum, none of them encodes only the lateral flagellum. The simultaneous presence of both flagella is exclusive of the B. japonicum phylogenomic group. Additionally, 292 Rhizobiales order genomes were analyzed and both flagellar systems are present together in only nine genera. Phylogenetic analysis of 150 representative Rhizobiales genomes revealed an uneven distribution of these flagellar systems. While genomes within and close to the Rhizobiaceae family only possess the lateral flagellum, the subpolar flagellum is exclusive of more early-diverging families, where certain genera also present both flagella.

scholarly journals Genome Sequence of the Alphaproteobacterium Blastochloris sulfoviridis DSM 729, Which Requires Reduced Sulfur as a Growth Supplement and Contains Bacteriochlorophyll b

2020 ◽  
Vol 9 (18) ◽  
Author(s):  
John A. Kyndt ◽  
Dayana Montano Salama ◽  
Terry E. Meyer
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequence ◽  
Gc Content ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Growth Supplement ◽  
Bacteriochlorophyll B ◽  
Reduced Sulfur

The genome sequence of Blastochloris sulfoviridis is 3.85 Mb with a GC content of 68%. Its nearest relative is B. tepida (average nucleotide identity [ANI], 91.5%), followed by B. viridis (ANI, 83%). According to ANI and whole-genome-based phylogenetic analysis, the nearest relatives of Blastochloris are Rhodoplanes and Rhodopseudomonas, confirming the recognition of distinct genera.

A large-scale evaluation of algorithms to calculate average nucleotide identity

2017 ◽  
Vol 110 (10) ◽  
pp. 1281-1286 ◽  
Author(s):  
Seok-Hwan Yoon ◽  
Sung-min Ha ◽  
Jeongmin Lim ◽  
Soonjae Kwon ◽  
Jongsik Chun
Keyword(s):  
Large Scale ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Scale Evaluation

scholarly journals Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov

2019 ◽  
Author(s):  
Cristina Merla ◽  
Carla Rodrigues ◽  
Virginie Passet ◽  
Marta Corbella ◽  
Harry A. Thorpe ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Type Strain ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Mass Spectrometry Analysis ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Single Strain ◽  
Spectrometry Analysis

AbstractKlebsiella oxytoca causes opportunistic human infections and post-antibiotic haemorrhagic diarrhoea. This Enterobacteriaceae species is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4, Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from, Klebsiella michiganensis (Ko1), Klebsiella oxytoca (Ko2), K. huaxiensis (Ko8) and K. grimontii (Ko6). The average nucleotide identity of Ko3 and Ko4 were 90.7% with K. huaxiensis and 95.5% with K. grimontii, respectively. In addition, three strains of K. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human faeces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4 and Ko8 from the other K. oxytoca species. Based on these results, we propose the names Klebsiella spallanzanii for the Ko3 phylogroup, with SPARK_775_C1T (CIP 111695T, DSM 109531T) as type strain, and Klebsiella pasteurii for Ko4, with SPARK_836_C1T (CIP 111696T, DSM 109530T) as type strain. Strains of K. spallanzanii were isolated from human urine, cow faeces and farm surfaces, while strains of K. pasteurii were found in faecal carriage from humans, cows and turtles.Accession numbersThe nucleotide sequences generated in this study were deposited in ENA and are available through the INSDC databases under accession numbers MN091365 (SB6411T = SPARK775C1T), MN091366 (SB6412 T = SPARK836C1T) and MN104661 to MN104677 (16S rRNA), MN076606 to MN076643 (gyrA and rpoB), and MN030558 to MN030567 (blaOXY). Complete genomic sequences were submitted to European Nucleotide Archive under the BioProject number PRJEB15325.AbbreviationsANI, average nucleotide identity; HCCA, a-cyano-4-hydroxycinnamic acid; isDDH, in silico DNA-DNA hybridization; SCAI, Simmons citrate agar with inositol; MALDI57 ToF MS: Matrix-assisted laser desorption/ionization time of flight mass spectrometry

Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Inhyup Kim ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Minchung Kang ◽  
Yoonseop So ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Bacterial Species ◽  
Jeju Island ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.

scholarly journals Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments

2019 ◽  
Vol 8 (18) ◽  
Author(s):  
Gordon Webster ◽  
Alex J. Mullins ◽  
Andrew J. Watkins ◽  
Edward Cunningham-Oakes ◽  
Andrew J. Weightman ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Dna Hybridization ◽  
In Silico ◽  
Methanogenic Archaea ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

The genomes of two Methanococcoides spp. that were isolated from marine sediments and are capable of carrying out methanogenesis from choline and other methylotrophic substrates were sequenced. The average nucleotide identity and in silico DNA-DNA hybridization analyses demonstrate that they represent species different from those previously described.

scholarly journals Draft Genome Sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor, Purple Sulfur Photosynthetic Bacteria in the Gammaproteobacterial Family Chromatiaceae

2020 ◽  
Vol 9 (14) ◽  
Author(s):  
Fabiola A. Aviles ◽  
Terry E. Meyer ◽  
John A. Kyndt
Keyword(s):  
Photosynthetic Bacteria ◽  
Draft Genome ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

We have determined the draft genome sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor for comparison with those of T. drewsii and Imhoffiella purpurea. According to average nucleotide identity (ANI) and whole-genome phylogenetic comparisons, these two species are clearly distinct from the Imhoffiella species and T. drewsii.

scholarly journals Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3146-3152 ◽  
Author(s):  
Sylvain Brisse ◽  
Virginie Passet ◽  
Patrick A. D. Grimont
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Carbon Sources ◽  
Biochemical Properties ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Human Infections ◽  
Human Blood Cultures

Strains previously classified as members of Klebsiella pneumoniae phylogroups KpI, KpII-A, KpII-B and KpIII were characterized by 16S rRNA (rrs) gene sequencing, multilocus sequence analysis based on rpoB, fusA, gapA, gyrA and leuS genes, average nucleotide identity and biochemical characteristics. Phylogenetic analysis demonstrated that KpI and KpIII corresponded to K. pneumoniae and Klebsiella variicola , respectively, whereas KpII-A and KpII-B formed two well-demarcated sequence clusters distinct from other members of the genus Klebsiella . Average nucleotide identity between KpII-A and KpII-B was 96.4 %, whereas values lower than 94 % were obtained for both groups when compared with K. pneumoniae and K. variicola . Biochemical properties differentiated KpII-A, KpII-B, K. pneumoniae and K. variicola , with acid production from adonitol and l-sorbose and ability to use 3-phenylproprionate, 5-keto-d-gluconate and tricarballylic acid as sole carbon sources being particularly useful. Based on their genetic and phenotypic characteristics, we propose the names Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and K. quasipneumoniae subsp. similipneumoniae subsp. nov. for strains of KpII-A and KpII-B, respectively. The type strain of K. quasipneumoniae sp. nov. and of K. quasipneumoniae subsp. quasipneumoniae subsp. nov. is 01A030T ( = SB11T = CIP 110771T = DSM 28211T). The type strain of K. quasipneumoniae subsp. similipneumoniae subsp. nov. is 07A044T ( = SB30T = CIP 110770T = DSM 28212T). Both strains were isolated from human blood cultures. This work also showed that Klebsiella singaporensis is a junior heterotypic synonym of K. variicola .

scholarly journals Rhodospirillum centenum Utilizes Separate Motor and Switch Components To Control Lateral and Polar Flagellum Rotation

2002 ◽  
Vol 184 (9) ◽  
pp. 2429-2438 ◽  
Author(s):  
Jonathan McClain ◽  
David R. Rollo ◽  
Brenda G. Rushing ◽  
Carl E. Bauer
Keyword(s):  
Phylogenetic Analysis ◽  
Microscopic Analysis ◽  
Photosynthetic Bacterium ◽  
Duplication Event ◽  
Viscous Medium ◽  
Polar Flagellum ◽  
Electron Microscopic ◽  
Transfer Event ◽  
Rhodospirillum Centenum ◽  
Lateral Flagellum

ABSTRACT Rhodospirillum centenum is a purple photosynthetic bacterium that is capable of differentiating from vibrioid swimming cells that contain a single polar flagellum into rod-shaped swarming cells that have a polar flagellum plus numerous lateral flagella. Microscopic studies have demonstrated that the polar flagellum is constitutively present and that the lateral flagella are found only when the cells are grown on solidified or viscous medium. In this study, we demonstrated that R. centenum contains two sets of motor and switch genes, one set for the lateral flagella and the other for the polar flagellum. Electron microscopic analysis indicated that polar and lateral flagellum-specific FliG, FliM, and FliN switch proteins are necessary for assembly of the respective flagella. In contrast, separate polar and lateral MotA and MotB motor subunits are shown to be required for motility but are not needed for the synthesis of polar and lateral flagella. Phylogenetic analysis indicates that the polar and lateral FliG, FliM, and FliN switch proteins are closely related and most likely arose as a gene duplication event. However, phylogenetic analysis of the MotA and MotB motor subunits suggests that the polar flagellum may have obtained a set of motor genes through a lateral transfer event.

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