scholarly journals Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3507-3510 ◽  
Author(s):  
Christopher A. Dunlap
Keyword(s):  
Dna Hybridization ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Sequencing Analysis ◽  
Emended Description ◽  
Type Strains

‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

scholarly journals Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena

2021 ◽  
Vol 12 ◽  
Author(s):  
Rafael R. de la Haba ◽  
Hiroaki Minegishi ◽  
Masahiro Kamekura ◽  
Yasuhiro Shimane ◽  
Antonio Ventosa
Keyword(s):  
Genomic Analysis ◽  
Single Copy ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Orthologous Genes ◽  
Additional Species ◽  
Representative Species ◽  
Single Genus ◽  
Type Strains

The haloarchaeal genera Natrinema and Haloterrigena were described almost simultaneously by two different research groups and some strains studied separately were described as different species of these genera. Furthermore, the description of additional species were assigned to either Natrinema or Haloterrigena, mainly on the basis of the phylogenetic comparative analysis of single genes (16S rRNA gene and more recently rpoB’ gene), but these species were not adequately separated or assigned to the corresponding genus. Some studies suggested that the species of these two genera should be unified into a single genus, while other studies indicated that the genera should remain but some of the species should be reassigned. In this study, we have sequenced or collected the genomes of the type strains of species of Natrinema and Haloterrigena and we have carried out a comparative genomic analysis in order to clarify the controversy related to these two genera. The phylogenomic analysis based on the comparison of 525 translated single-copy orthologous genes and the Overall Genome Relatedness Indexes (i.e., AAI, POCP, ANI, and dDDH) clearly indicate that the species Haloterrigena hispanica, Haloterrigena limicola, Haloterrigena longa, Haloterrigena mahii, Haloterrigena saccharevitans, Haloterrigena thermotolerans, and Halopiger salifodinae should be transferred to the genus Natrinema, as Natrinema hispanicum, Natrinema limicola, Natrinema longum, Natrinema mahii, Natrinema saccharevitans, Natrinema thermotolerans, and Natrinema salifodinae, respectively. On the contrary, the species Haloterrigena turkmenica, Haloterrigena salifodinae, and Haloterrigena salina will remain as the only representative species of the genus Haloterrigena. Besides, the species Haloterrigena daqingensis should be reclassified as a member of the genus Natronorubrum, as Natronorubrum daqingense. At the species level, Haloterrigena jeotgali and Natrinema ejinorense should be considered as a later heterotypic synonyms of the species Haloterrigena (Natrinema) thermotolerans and Haloterrigena (Natrinema) longa, respectively. Synteny analysis and phenotypic features also supported those proposals.

Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status

2021 ◽  
Author(s):  
Scott Van Nguyen ◽  
Scott A. Cunningham ◽  
Patricio Jeraldo ◽  
Anthony Tran ◽  
Robin Patel
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Average Nucleotide Identity ◽  
Species Status ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA–DNA hybridization values, and phylogenetic analyses of the type strains indicate that Y. kristensenii subsp. rochesterensis and Y. occitanica are the same genospecies. Additionally, the overall genomic relatedness index (OGRI) values reveal that Y. kristensenii subsp. rochesterensis should be elevated to species status as Yersinia rochesterensis sp. nov.

scholarly journals Phylogenomic analysis of the genus Pseudomonas and reclassification of P. humi, P. zeshuii, P. psychrotolerans, P. nitritireducens, P. pharmacofabricae and P. panacis are later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively

2021 ◽  
Author(s):  
Ritu Rani Kujur ◽  
Sushanta Deb ◽  
Subrata K Das
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Taxonomic Assignment ◽  
Genome Database ◽  
Average Amino Acid Identity ◽  
Genome Comparisons

The present study described the comparative genomic analysis of the validly named species of the genus Pseudomonas to define the taxonomic assignment. Genomic information for 208 type strains was available in the NCBI genome database at the time of conducting this analysis. The ANI, AAI and in silico DNA DNA hybridization (isDDH) data were higher than the threshold values for the twelve strains with their closely related type species. Whole genome comparisons shared 97 - 99 % average nucleotide identity, 97.85 to 99.19 % average amino acid identity and 72.80 to 90.40 % digital DNA DNA hybridization values. Further, the phylogenomic analysis based on the core genome confirmed that P. humi CCA1 and P. citronellolis LMG 18378, P. zeshuii KACC 15471 and P. luteola NBRC 103146, P. oryzihabitans DSM 6835 and P. psychrotolerans DSM 15758, P. nitroreducens DSM 14399 and P. nitritireducens WZBFD3-5A2, P. fluvialis CCM 8778 and P. pharmacofabricae ZYSR67-Z, P. panacis DSM 18529 and P. marginalis DSM 13124 formed a monophyletic clade. Thus, we proposed six type species viz., P. humi CCA1, P. zeshuii KACC 15471, P. psychrotolerans DSM 15758, P. nitritireducens WZBFD3 5A2, P. pharmacofabricae ZYSR67 Z and P. panacis DSM 18529 are the later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively considering the priority date of publication.

scholarly journals Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1790-1798 ◽  
Author(s):  
V. Venkata Ramana ◽  
S. Kalyana Chakravarthy ◽  
P. Shalem Raj ◽  
B. Vinay Kumar ◽  
E. Shobha ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rhodopseudomonas Palustris ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Geographical Regions ◽  
Emended Description ◽  
Type Strains

Four strains (JA310T, JA531T, JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310T and JA531T was C18 : 1ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA531T, JA447 and JA490 were genotypically (>80 % related based on DNA–DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310T (33 % related). Furthermore, all four strains had less than 48 % relatedness (DNA–DNA hybridization) with type strains of members of the genus Rhodopseudomonas , i.e. Rhodopseudomonas palustris ATCC 17001T, Rhodopseudomonas faecalis JCM 11668T and Rhodopseudomonas rhenobacensis DSM 12706T. The genomic DNA G+C contents of strains JA310T and JA531T were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310T ( = NBRC 106083T = KCTC 5839T) and JA531T ( = NBRC 107575T = KCTC 5841T) be classified as the type strains of two novel species of the genus Rhodopseudomonas , Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123T ( = NBRC 100419T) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001T and other members of the genus Rhodopseudomonas . An emended description of R. palustris is also provided.

Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete

2011 ◽  
Vol 61 (3) ◽  
pp. 482-486 ◽  
Author(s):  
Sung M. Kim ◽  
Sae W. Park ◽  
Sang T. Park ◽  
Young M. Kim
Keyword(s):  
Carbon Monoxide ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A bacterial strain, PY2T, capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2T was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26T (99.1 % similarity). Strain PY2T was characterized chemotaxonomically as having iso-C15 : 0 as the predominant fatty acid, MK-8(H4) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA–DNA relatedness values between strain PY2T and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA–DNA hybridization experiments, it is proposed that strain PY2T represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2T (=KCCM 42922T=JCM 16259T).

scholarly journals Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

mSystems ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Roshan Kumar ◽  
Helianthous Verma ◽  
Shazia Haider ◽  
Abhay Bajaj ◽  
Utkarsh Sood ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Core Genome ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Genomic Analysis ◽  
Specific Protein ◽  
Comparative Genomic ◽  
Ecological Groups ◽  
Functional And Phylogenetic Diversity

ABSTRACT This study highlights the significant role of the genetic repertoire of a microorganism in the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits for Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium. Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups—rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats—freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism’s genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

scholarly journals Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family ‘Thermoactinomycetaceae’ isolated from compost

2005 ◽  
Vol 55 (5) ◽  
pp. 2101-2104 ◽  
Author(s):  
Kouta Hatayama ◽  
Hirofumi Shoun ◽  
Yasuichi Ueda ◽  
Akira Nakamura
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Type Strains

Four thermophilic, Gram-positive strains, designated H0165T, 500275T, C0170 and 700375, were isolated from a composting process in Japan. The isolates grew aerobically at about 65 °C on a solid medium with formation of substrate mycelia; spores were produced singly along the mycelia. These morphological characters resembled those of some type strains of species belonging to the family ‘Thermoactinomycetaceae’, except that aerial mycelia were not formed. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest related species to the isolates were members of the family ‘Thermoactinomycetaceae’, but that the isolates formed an independent phylogenetic lineage. Some chemotaxonomic characters of the isolates, such as DNA G+C contents of 58·7–60·3 mol%, MK-7 as the major menaquinone and cellular fatty acid profiles, differed from those of members of the family ‘Thermoactinomycetaceae’. DNA–DNA hybridization showed that the isolates could be divided into two genomic groups, strain H0165T and the other three strains. These results indicated that the four isolates should be classified into two species of a novel genus in the family ‘Thermoactinomycetaceae’, for which the names Planifilum fimeticola gen. nov., sp. nov. (type strain H0165T=ATCC BAA-969T=JCM 12507T) and Planifilum fulgidum sp. nov. (type strain 500275T=ATCC BAA-970T=JCM 12508T) are proposed.

scholarly journals Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov., motile purple sulfur bacteria isolated from the chemocline of a meromictic lake

2011 ◽  
Vol 61 (7) ◽  
pp. 1682-1687 ◽  
Author(s):  
Sandro Peduzzi ◽  
Allana Welsh ◽  
Antonella Demarta ◽  
Paola Decristophoris ◽  
Raffaele Peduzzi ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Meromictic Lake ◽  
Purple Sulfur Bacteria ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Sulfur Bacteria ◽  
Type Strains ◽  
Sequence Similarities

Two isolates, designated CadH11T and Cad448T, representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.2 % between CadH11T and Cad448T, and similarities of 97.7 and 98.5 %, respectively, with their closest cultured relative Thiocystis gelatinosa DSM 215T, as well as differences in DNA G+C content and carbon source utilization suggested that the isolates belonged to two distinct species. DNA–DNA hybridization of CadH11T and Cad448T with T. gelatinosa DSM 215T showed relatedness values of 46.4 and 60.8 %, respectively; the relatedness value between CadH11T and Cad448T was 59.2 %. Based on this evidence, strains CadH11T and Cad448T represent two novel species within the genus Thiocystis, for which the names Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov. are proposed, respectively. The type strains of T. chemoclinalis sp. nov. and T. cadagnonensis sp. nov. are CadH11T ( = JCM 15112T  = KCTC 5954T) and Cad448T ( = JCM 15111T  = KCTC 15001T), respectively.

scholarly journals Reclassification of Thermoterrabacterium ferrireducens as Carboxydothermus ferrireducens comb. nov., and emended description of the genus Carboxydothermus

2006 ◽  
Vol 56 (10) ◽  
pp. 2349-2351 ◽  
Author(s):  
A. I. Slobodkin ◽  
T. G. Sokolova ◽  
A. M. Lysenko ◽  
J. Wiegel
Keyword(s):  
Electron Acceptor ◽  
Dna Hybridization ◽  
Anaerobic Bacteria ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Acetate Production ◽  
Physiological Properties ◽  
Emended Description ◽  
Metabolic Properties ◽  
Type Strains

Similarities in phylogeny and metabolic properties between the type species of two monospecific genera of thermophilic anaerobic bacteria, Carboxydothermus hydrogenoformans and Thermoterrabacterium ferrireducens, and analysis of their recently available 16S rRNA gene sequences warranted clarification of their taxonomic positions. We have determined that the value of DNA–DNA hybridization between the type strains is 53 %. Additional physiological studies revealed that C. hydrogenoformans Z-2901T is capable of Fe(III) reduction with H2 as an electron donor and ferrihydrite as an electron acceptor. T. ferrireducens JW/AS-Y7T is able to grow and utilize CO with ferrihydrite as an electron acceptor without hydrogen or acetate production. We therefore reclassify Thermoterrabacterium ferrireducens as Carboxydothermus ferrireducens comb. nov. (type strain JW/AS-Y7T=DSM 11255T=VKM B-2392T). The description of the genus Carboxydothermus is emended to include such important physiological properties as growth on organic compounds and capacity for Fe(III) reduction.

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