scholarly journals Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014

2020 ◽  
Vol 70 (5) ◽  
pp. 3572-3576 ◽  
Author(s):  
José A. Vázquez-Boland ◽  
Mariela Scortti ◽  
Wim G. Meijer
Keyword(s):  
Type Species ◽  
Medical Literature ◽  
Original Description ◽  
Rhodococcus Equi ◽  
Reasonable Assumption ◽  
Taxonomic Study ◽  
Human Pathogen ◽  
Content Type ◽  
Link Type ◽  
Nomenclatural Change

A recent taxonomic study confirmed the synonymy of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and Corynebacterium hoagii (Morse 1912) Eberson 1918. As a result, both R. equi and C. hoagii were reclassified as Rhodococcus hoagii comb. nov. in application of the principle of priority of the Prokaryotic Code. Because R. equi is a well-known animal and zoonotic human pathogen, and a bacterial name solidly established in the veterinary and medical literature, we and others argued that the nomenclatural change may cause error and confusion and be potentially perilous. We have now additionally found that the nomenclatural type of the basonym C. hoagii , ATCC 7005T, does not correspond with the original description of the species C. hoagii in the early literature. Its inclusion as the C. hoagii type on the Approved Lists 1980 results in a change in the characters of the taxon and in C. hoagii designating two different bacteria. Moreover, ATCC 7005, the only strain in circulation under the name C. hoagii , does not have a well documented history; it is unclear why it was deposited as C. hoagii and a possible mix-up with a Corynebacterium ( Rhodococcus ) equi isolate is a reasonable assumption. We therefore request the rejection of Rhodococcus hoagii as a nomen ambiguum, nomen dubium and nomen perplexum in addition to nomen periculosum, and conservation of the name Rhodococcus equi , according to Rules 56ab of the Code.

Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3280-3286 ◽  
Author(s):  
Iris Kuo ◽  
Jimmy Saw ◽  
Durrell D. Kapan ◽  
Stephanie Christensen ◽  
Kenneth Y. Kaneshiro ◽  
...  
Keyword(s):  
Type Species ◽  
Original Description ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Whole Cells ◽  
Link Type ◽  
Decaying Wood ◽  
Type Strains

Strain IK-1T was isolated from decaying tissues of the shrub Wikstroemia oahuensis collected on O‘ahu, Hawai‘i. Cells were rods that stained Gram-negative. Gliding motility was not observed. The strain was oxidase-negative and catalase-positive. Zeaxanthin was the major carotenoid. Flexirubin-type pigments were not detected. The most abundant fatty acids in whole cells of IK-1T grown on R2A were iso-C15 : 0 and one or both of C16 : 1ω7c and C16 : 1ω6c. Based on comparisons of the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strains were Flavobacterium rivuli WB 3.3-2T and Flavobacterium subsaxonicum WB 4.1-42T, with which IK-1T shares 93.84 and 93.67 % identity, respectively. The G+C content of the genomic DNA was 44.2 mol%. On the basis of distance from its nearest phylogenetic neighbours and phenotypic differences, the species Flavobacterium akiainvivens sp. nov. is proposed to accommodate strain IK-1T ( = ATCC BAA-2412T = CIP 110358T) as the type strain. The description of the genus Flavobacterium is emended to reflect the DNA G+C contents of Flavobacterium akiainvivens IK-1T and other species of the genus Flavobacterium described since the original description of the genus.

scholarly journals Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature

2021 ◽  
Vol 7 (7) ◽  
Author(s):  
Prashant P. Patil ◽  
Sanjeet Kumar ◽  
Amandeep Kaur ◽  
Samriti Midha ◽  
Kanika Bansal ◽  
...  
Keyword(s):  
Body Temperature ◽  
Human Body ◽  
Transcriptome Analysis ◽  
Stenotrophomonas Maltophilia ◽  
Type Species ◽  
Human Pathogen ◽  
Content Type ◽  
Link Type ◽  
Human Body Temperature ◽  
Opportunistic Human Pathogen

Stenotrophomonas maltophilia is a typical example of an environmental originated opportunistic human pathogen, which can thrive at different habitats including the human body and can cause a wide range of infections. It must cope with heat stress during transition from the environment to the human body as the physiological temperature of the human body (37 °C) is higher than environmental niches (22–30 °C). Interestingly, S. rhizophila a phylogenetic neighbour of S. maltophilia within genus Stenotrophomonas is unable to grow at 37 °C. Thus, it is crucial to understand how S. maltophilia is adapted to human body temperature, which could suggest its evolution as an opportunistic human pathogen. In this study, we have performed comparative transcriptome analysis of S. maltophilia grown at 28 and 37 °C as temperature representative for environmental niches and the human body, respectively. RNA-Seq analysis revealed several interesting findings showing alterations in gene-expression levels at 28 and 37 °C, which can play an important role during infection. We have observed downregulation of genes involved in cellular motility, energy production and metabolism, replication and repair whereas upregulation of VirB/D4 type IV secretion system, aerotaxis, cation diffusion facilitator family transporter and LacI family transcriptional regulators at 37 °C. Microscopy and plate assays corroborated altered expression of genes involved in motility. The results obtained enhance our understanding of the strategies employed by S. maltophilia during adaptation towards the human body.

Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil

2021 ◽  
Author(s):  
Chatsuda Sakdapetsiri ◽  
Aunchisa Kuntaveesuk ◽  
Wipaporn Ngaemthao ◽  
Chanwit Suriyachadkun ◽  
Chanokporn Muangchinda ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Growth Cycle ◽  
Rrna Gene ◽  
Taxonomic Study ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
Southwestern Area

A novel bacterium, designated strain ANT13_2T, was isolated from a phenanthrene-degrading consortium enriched from a soil sample collected near the Great Wall Station located in the southwestern area of King George Island, Antarctica. Following a polyphasic taxonomic study, a novel species belonging to the genus Paeniglutamicibacter was described. The strain was a Gram-stain-positive bacterium that exhibited a rod–coccus growth cycle. Strain ANT13_2T grew aerobically at an optimum temperature of 20–25 °C and at pH 7.0–8.0. Ribose, arabinose and glucose were detected as whole-cell sugars. The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C15 : 0 (67.7 %) and anteiso-C17 : 0 (11.2 %). The DNA G+C content of the genomic DNA was 60.6 mol%. Based on 16S rRNA gene sequence analysis, strain ANT13_2T showed the highest similarities to Paeniglutamicibacter antarcticus SPC26T (98.9 %) followed by Paeniglutamicibacter gangotriensis Lz1yT (98.4 %), Paeniglutamicibacter sulfureus DSM 20167T (98.3%) and Paeniglutamicibacter kerguelensis KGN15T (97.9 %). The average nucleotide identity values between strain ANT13_2T and the type strains of P. antarcticus SPC26T and P. gangotriensis Lz1yT were 73.8 and 77.5 %, respectively, which are well below the 95–96 % species circumscription threshold. On the basis of this polyphasic taxonomic study, strain ANT13_2T is proposed to represent a novel species to be named Paeniglutamicibacter terrestris sp. nov. The type strain is ANT13_2T (=TBRC 11756T=NBRC 114615T).

Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Corynebacterium hoagii (Morse 1912) Eberson 1918

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 311-312 ◽  
Author(s):  
George M. Garrity
Keyword(s):  
Type Species ◽  
Rhodococcus Equi ◽  
International Code ◽  
Content Type ◽  
Zoonotic Pathogen ◽  
Link Type ◽  
Code Of Nomenclature ◽  
History Of ◽  
International Code Of Nomenclature

A recent review of the nomenclatural history of Rhodococcus equi and its heterotypic synonyms reveals a situation in which the strict application of the Rules of the International Code of Nomenclature of Prokaryotes have resulted in the renaming of this known zoonotic pathogen, which may be reasonably viewed as a perilous name. This situation can be remedied only by the Judicial Commission rendering an opinion to conserve the name Rhodococcus equi and to reject its earlier heterotypic synonym, Corynebacterium hoagii .

scholarly journals Emended description of the genus Methylophaga Janvier et al. 1985

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1644-1646 ◽  
Author(s):  
Rich Boden
Keyword(s):  
Type Species ◽  
Original Description ◽  
The Other ◽  
Content Type ◽  
Link Type ◽  
Emended Description

The genus Methylophaga Janvier et al. 1985 comprises eight species with validly published names at the time of writing. The original description of the genus was published over 26 years ago and was based on only two species, namely Methylophaga marina and Methylophaga thalassica – as such, the description of the genus requires updating to take into account the other six known species. Based on literature concerning the eight species of Methylophaga published over the last 26 years, an emended description of the genus is presented, taking into account properties of all members of the species with validly published names.

The correct name of the taxon that contains the type strain of Rhodococcus equi

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 302-308 ◽  
Author(s):  
B. J. Tindall
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Rhodococcus Equi ◽  
Point Of View ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Concept

Based on a nomenclatural point of view, the name Rhodococcus equi is associated, as required by the Bacteriological Code, with a defined position, rank and circumscription. A search of the literature indicates that the name Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 has also been shown to be a synonym of Corynebacterium equi Magnusson 1923, Corynebacterium hoagii (Morse 1912) Eberson 1918 and Nocardia restricta (Turfitt 1944) McClung 1974. Application of the rules of the Bacteriological Code together with the currently inferred taxonomic concept associated with the species bearing the name Rhodococcus equi indicates that this is not the correct name of this taxon and the use of that name in the context of a circumscription that includes the type strain of the species Corynebacterium hoagii is contrary to the Rules of the Code.

scholarly journals Taxonomic study of the genera Halogeometricum and Halosarcina : transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3915-3919 ◽  
Author(s):  
Xing-Xing Qiu ◽  
Mei-Lin Zhao ◽  
Dong Han ◽  
Wen-Jiao Zhang ◽  
Mike L. Dyall-Smith ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Taxonomic Study ◽  
Content Type ◽  
Link Type

Members of the haloarchaeal genera Halosarcina and Halogeometricum (family Halobacteriaceae ) are closely related to each other and show 96.6–98 % 16S rRNA gene sequence similarity. This is higher than the accepted threshold value (95 %) to separate two genera, and a taxonomic study using a polyphasic approach of all four members of the two genera was conducted to clarify their relationships. Polar lipid profiles indicated that Halogeometricum rufum RO1-4T, Halosarcina pallida BZ256T and Halosarcina limi RO1-6T are related more to each other than to Halogeometricum borinquense CGMCC 1.6168T. Phylogenetic analyses using the sequences of three different genes (16S rRNA gene, rpoB′ and EF-2) strongly supported the monophyly of these four species, showing that they formed a distinct clade, separate from the related genera Halopelagius , Halobellus , Haloquadratum , Haloferax and Halogranum . The results indicate that the four species should be assigned to the same genus, and it is proposed that Halosarcina pallida and Halosarcina limi be transferred to the genus Halogeometricum as Halogeometricum pallidum comb. nov. (type strain, BZ256T = KCTC 4017T = JCM 14848T) and Halogeometricum limi comb. nov. (type strain, RO1-6T = CGMCC 1.8711T = JCM 16054T).

Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov.

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 755-761 ◽  
Author(s):  
P. Kämpfer ◽  
W. Dott ◽  
K. Martin ◽  
S. P. Glaeser
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Rhodococcus Equi ◽  
Rhodococcus Opacus ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-positive, non-endospore-forming rod-shaped bacterium, strain Ca11T, was isolated from a bioreactor with extensive phosphorus removal and was studied in detail for its taxonomic allocation. 16S rRNA gene sequence analysis revealed closest sequence similarity of the strain to type strains of [ Corynebacterium hoagii ] and Rhodococcus equi (98.9 %), Rhodococcus koreensis and Rhodococcus wratislaviensis (both 98.4 %), Rhodococcus opacus and Rhodococcus canchipurensis (both 98.0 %) followed by Rhodococcus kunmingensis and Rhodococcus imtechensis (97.7 %). Phylogenetic trees showed a distinct clustering of strain Ca11T with the type strains of [ C. hoagii ], R. equi , and R. kunmingensis separate to all other species of the genus Rhodococcus . The quinone system of strain Ca11T was composed of dihydrogenated menaquinones with 8 (major amount) as well as 7 and 6 isoprenoid units [MK-8(H2), MK-7(H2), MK-6(H2)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phospholipid and an unidentified glycolipid. The fatty acid profile was similar to that reported for R. equi and contained major amounts of C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0, supporting the allocation of the strain to the genus Rhodococcus . Physiological and biochemical characterization and DNA–DNA hybridization with type strains of the most closely related species allowed clear phenotypic and genotypic differentiation of the isolate. On the basis of these results, strain Ca11T ( = DSM 45893T = LMG 27563T) represents a novel species of the genus Rhodococcus , with the proposed name Rhodococcus defluvii sp. nov. In addition, a polyphasic taxonomic analysis of [ Corynebacterium hoagii ] DSM 20295T and Rhodococcus equi DSM 20307T indicated that the two strains belong to the same species, for which the name Rhodococcus hoagii comb. nov. takes priority, according to the Rules of the Bacteriological Code.

scholarly journals Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1160-1166 ◽  
Author(s):  
Lingfang Zhu ◽  
Meiru Si ◽  
Changfu Li ◽  
Kaiyun Xin ◽  
Chaoqiong Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Shaanxi Province ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Taxonomic Study ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A yellow-pigmented bacterium, designated strain ZFGT-11T, was isolated from roots of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain ZFGT-11T were Gram-stain-negative, strictly aerobic rods that were surrounded by a thick capsule and were motile by means of a single polar flagellum. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFGT-11T was a member of the genus Sphingomonas and was closely related to Sphingomonas naasensis KACC 16534T (97.6 % similarity), Sphingomonas kyeonggiense JCM 18825T (96.8 %), Sphingomonas asaccharolytica IFO 15499T (96.7 %) and Sphingomonas leidyi DSM 4733T (96.6 %). The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major cellular fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C17 : 1ω6c, C14 : 0 2-OH, C16 : 0 and C15 : 0 2-OH. The major polyamine of strain ZFGT-11T was sym-homospermidine. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, two unidentified aminoglycolipids, two unidentified phospholipids and two unidentified lipids were detected in the polar lipid profile. The DNA G+C content was 66.8 mol%. DNA–DNA relatedness for strain ZFGT-11T with respect to its closest phylogenetic relative S. naasensis KACC 16534T was 26.2±4.8 % (mean±sd). On the basis of data from the present polyphasic taxonomic study, strain ZFGT-11T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas gei sp. nov. is proposed. The type strain is ZFGT-11T ( = CCTCC AB 2013306T = KCTC 32449T = LMG 27608T).

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

Sign in / Sign up

Export Citation Format

Share Document