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PubMed2026

Genomic evidence that Shouchella miscanthi (Shin et al. 2020) Joshi et al. 2022 is a later heterotypic synonym of Shouchella hunanensis (Patel and Gupta 2020) Joshi et al. 2022.

Shouchella hunanensis DSM 23008T and Shouchella miscanthi AK13T were originally described from forest soil and the rhizosphere of Miscanthus sacchariflorus, respectively. The two strains share closely similar phenotypic properties, and their 16S rRNA gene sequences show 99.5% similarity. Phylogenetic analysis of all 16S rRNA gene copies revealed copy-dependent placements, whereas the phylogenomic analysis placed the two type strains and three additional genomes in a strongly supported, short-branched cluster. Eight 16S rRNA gene copies were identified in each genome, with detectable intragenomic heterogeneity, particularly in AK13ᵀ. Pairwise average nt identity among the two type-strain genomes and three additional publicly available genomes ranged from 99.0% to 99.3%, clearly above the accepted species boundary. The digital DNA-DNA hybridization value between strains S. hunanensis DSM 23008T and S. miscanthi AK13T was 92.5%. On the basis of the combined phylogenetic, genomic and phenotypic evidence, S. miscanthi (Shin et al. 2020) Joshi et al. 2022 is proposed as a later heterotypic synonym of S. hunanensis (Patel and Gupta 2020) Joshi et al. 2022.

Phylogeny↗

PubMed2006

Lactobacillus cypricasei Lawson et al. 2001 is a later heterotypic synonym of Lactobacillus acidipiscis Tanasupawat et al. 2000.

The applicability of a multilocus sequence analysis (MLSA)-based identification system for lactobacilli was evaluated. Two housekeeping genes that code for the phenylalanyl-tRNA synthase alpha-subunit (pheS) and RNA polymerase alpha-subunit (rpoA) were sequenced and analysed for members of the Lactobacillus salivarius species group. The type strains of Lactobacillus acidipiscis and Lactobacillus cypricasei were investigated further using a third gene that encodes the alpha-subunit of ATP synthase (atpA). The MLSA data revealed close relatedness between L. acidipiscis and L. cypricasei, with 99.8-100 % pheS, rpoA and atpA gene sequence similarities. Comparison of the 16S rRNA gene sequences of the type strains of the two species confirmed the close relatedness (99.8 % gene sequence similarity) between the two taxa. Similar phenotypes and high DNA-DNA binding values in the range of 84 to 97.5 % confirmed that L. acidipiscis and L. cypricasei are synonymous species. On the basis of the present study, it is proposed that Lactobacillus cypricasei is a later heterotypic synonym of Lactobacillus acidipiscis.

Bacterial Proteins↗

PubMed2006

Reclassification of Roseomonas fauriae Rihs et al. 1998 as a later heterotypic synonym of Azospirillum brasilense Tarrand et al. 1979.

The relatedness of Roseomonas fauriae and Azospirillum brasilense was investigated using phenotypic methods and DNA-DNA hybridization. Conventional biochemical tests did not differentiate between the two taxa. DNA-DNA hybridization experiments revealed high values for relatedness between the type strains of these species and suggest that these two taxa constitute a single species. Strains previously identified as R. fauriae should be reclassified as A. brasilense, with the name Roseomonas fauriae as a later heterotypic synonym of Azospirillum brasilense.

Alphaproteobacteria↗

PubMed2005

Lactobacillus arizonensis is a later heterotypic synonym of Lactobacillus plantarum.

The 'Lactobacillus plantarum group' encompasses the taxa Lactobacillus plantarum subsp. plantarum, Lactobacillus plantarum subsp. argentoratensis, Lactobacillus paraplantarum, Lactobacillus pentosus and Lactobacillus arizonensis. In this study, the phylogenetic position of L. arizonensis was examined using 16S rRNA gene-specific methodologies (16S rRNA sequencing and ribotyping) and genomic DNA-based investigations [repetitive extragenic palindromic DNA (rep)-PCR and DNA-DNA hybridization]. Our results show that the L. arizonensis type strain could not be distinguished from the type strain of L. plantarum or from various L. plantarum reference strains. Therefore, it is proposed that the species L. arizonensis should be reclassified as a heterotypic synonym of L. plantarum.

DNA, Bacterial↗

PubMed2006

Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983.

The taxonomic status of the species Lactobacillus durianis and Lactobacillus vaccinostercus is briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1,523 bp), partial recA gene sequences (99.5 % similarity over 600 bp) and partial hsp60 gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA-DNA binding level (87 %) and similar genomic DNA G+C contents (41-44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of the Bacteriological Code, the name Lactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the name Lactobacillus durianis should be considered a later heterotypic synonym.

Bacterial Proteins↗

PubMed2003

Emended description of Janibacter terrae, including ten dibenzofuran-degrading strains and Janibacter brevis as its later heterotypic synonym.

Ten Gram-positive strains that degraded dibenzofuran belonged to one homogeneous cluster with common biochemical and chemotaxonomic properties. The strains included the previously described strains [Terrabacter sp.] DPO 360 and DPO 1361 and were isolated from different locations in central Europe. They all shared menaquinone MK-8(H(4)) and meso-diaminopimelic acid in the cell wall and showed the same cellular fatty acid, polar lipid and RiboPrint patterns. Chemotaxonomic properties, as well as DNA G+C content (72.8 mol%), were consistent with those described for the genus Janibacter. Analysis of 16S rDNA sequences suggested a close relationship to Janibacter terrae and Janibacter brevis. DNA-DNA hybridization of two dibenzofuran-degrading strains (DPO 360 and DPO 1361) and the type strains of J. terrae and J. brevis revealed that these strains belong to the same species. An emended description of the species J. terrae is given. J. brevis is a later heterotypic synonym of J. terrae.

Actinomycetales↗

PubMed2005

Corynebacterium mooreparkense, a later heterotypic synonym of Corynebacterium variabile.

Strains of a Gram-positive bacterium were isolated from the Irish smear-ripened cheese Gubbeen, and assigned to a new species, Corynebacterium mooreparkense, in 2001. During a further study on the same cheese, no additional isolates from this species could be found. Instead, multiple isolates of its nearest phylogenetic neighbour, Corynebacterium variabile, were found. A first screening with rep-PCR and SDS-PAGE pointed to a similarity between C. mooreparkense and C. variabile. Following this peculiar result, attempts were made to collect all type strains deposited at different culture collections and all strains described by Brennan et al. [Int J Syst Evol Microbiol (2001) 51, 843-852]. Subsequently, 16S rRNA gene sequencing and DNA-DNA hybridizations were performed. All C. mooreparkense strains had a 16S rRNA gene sequence similarity of at least 99.5 % with C. variabile and the DNA-DNA relatedness was 95 %. On the basis of these results, it is concluded that C. mooreparkense is a later heterotypic synonym of C. variabile.

Bacterial Proteins↗

PubMed2002

Helicobacter nemestrinae ATCC 49396T is a strain of Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989, and Helicobacter nemestrinae Bronsdon et al. 1991 is therefore a junior heterotypic synonym of Helicobacter pylori.

Helicobacter nemestrinae Bronsdon et al. 1991, a gastric helicobacter species isolated from a pigtailed macaque, is thought to be the species most closely related to the important human pathogen Helicobacter pylori. The only available strain of this taxon is the type strain, ATCC 49396T. We sequenced seven housekeeping genes and two flagellin genes for H. nemestrinae ATCC 49396T. If ATCC 49396T were a separate species, these sequences should have been distinct from those of H. pylori. Instead, all sequences clustered together with sequences obtained previously for 20 or more H. pylori isolates from diverse geographical locations. The 16S rDNA sequence differed from that reported previously for this strain by 38 nucleotides and was most similar to that of H. pylori 85D08 (accession no. U00769), which was isolated from a rhesus macaque. It differed by less than 1% from 16S rDNA sequences of numerous other H. pylori strains, including the type strain, NCTC 11637T (= ATCC 43504T). These data indicate that the strain currently distributed as H. nemestrinae ATCC 49396T is really a strain of H. pylori and that H. nemestrinae Bronsdon et al. 1991 is a junior heterotypic synonym of Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989.

Animals↗

PubMed2004

Genetic evidence that Weissella kimchii Choi et al. 2002 is a later heterotypic synonym of Weissella cibaria Björkroth et al. 2002.

The taxonomic positions of Weissella kimchii and Weissella cibaria were examined using phenotypic tests, 16S rRNA gene sequencing and DNA-DNA hybridization. The two species displayed very similar sugar-fermentation patterns and produced the D-form of lactic acid. Phylogenetic analysis showed that W. cibaria is the closest neighbour of W. kimchii, sharing about 99.7 % similarity in the 16S rRNA gene sequence. DNA-DNA hybridization experiments further reinforced these results, demonstrating a 98.2 % reassociation level between W. cibaria LMG 17699(T) and W. kimchii DSM 14295(T). On the other hand, strain RO5, an isolate from paddy rice silage, exhibited 99.4 % 16S rRNA gene sequence similarity and a DNA reassociation level of more than 97 % with both type strains. Therefore, it is proposed that the species W. kimchii should be reclassified as W. cibaria.

Bacillus↗

PubMed2005

Clostridium sardiniense Prévot 1938 and Clostridium absonum Nakamura et al. 1973 are heterotypic synonyms: evidence from phylogenetic analyses of phospholipase C and 16S rRNA sequences, and DNA relatedness.

Clostridium sardiniense Prévot 1938 and Clostridium absonum Nakamura et al. 1973 have long been considered similar in terms of their biological and biochemical properties, but their taxonomic positions have not been clarified by DNA-DNA hybridization studies or rigorous analysis of 16S rRNA genes. In the present study, DNA-DNA hybridization analysis revealed that C. absonum strains DSM 599(T), DSM 600 and KZ 1544 shared 83.0-86.3 % DNA relatedness with C. sardiniense DSM 2632(T). 16S rRNA gene sequence analysis showed that the C. absonum strains also shared high identity with C. sardiniense DSM 2632(T) (99.7, 99.3 and 99.8 % for DSM 599(T), DSM 600 and KZ 1544, respectively), implying that C. absonum and C. sardiniense are synonyms. In addition, alignment of the inferred amino acid sequences for phospholipase C (PLC) indicated 96.5 % identity between PLCs from C. sardiniense and C. absonum, but relatively low identity with other clostridial species. These results strongly suggest that the species C. sardiniense and C. absonum should be united, with the name C. sardiniense having priority.

Bacterial Proteins↗

PubMed2005

Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 and Marinobacter aquaeolei Nguyen et al. 1999 are heterotypic synonyms.

The genus Marinobacter was described with a single species, Marinobacter hydrocarbonoclasticus Gauthier et al. 1992, to place a hydrocarbon-degrading marine bacterium belonging to the gamma-subclass of the Proteobacteria. Marinobacter aquaeolei Nguyen et al. 1999, the second described species of the genus, was proposed for a strain isolated from an oil-producing well on an offshore platform in southern Vietnam, on the basis of differences in the whole-cell protein pattern and lipopolysaccharide composition, although its phenotypic and genotypic characteristics were very similar to those of the type species, M. hydrocarbonoclasticus. In the present paper, literature data concerning the two species were reviewed. Fatty acid composition, G+C content and DNA-DNA hybridization studies were performed in order to clarify the taxonomic positions of these two species. Based on the results obtained in this study and phenotypic and phylogenetic traits available from the literature, it is proposed that the two species should be united under the same name; according to the rules of priority, M. hydrocarbonoclasticus, the first described species, is the earlier synonym and M. aquaeolei is the later synonym.

Alteromonadaceae↗

PubMed2005

Reclassification of Lactobacillus ferintoshensis as a later heterotypic synonym of Lactobacillus parabuchneri.

Lactobacillus ferintoshensis has recently been described as a novel species, distinct from its close phylogenetic neighbours Lactobacillus buchneri, Lactobacillus kefiri and Lactobacillus hilgardii. Two highly related species with validly published names, Lactobacillus parakefiri and Lactobacillus parabuchneri, were not considered in the study due to the lack of 16S rRNA gene sequence data at that time. Since the publication of the study, the sequences have become available and have revealed that L. ferintoshensis and L. parabuchneri share 99.7% 16S rRNA gene sequence similarity. Further genomic and phenotypic data, derived from fluorescent amplified fragment length polymorphism, DNA-DNA hybridization and API 50 CHL analyses, have demonstrated that the species are synonymous.

Alcoholic Beverages↗

PubMed2003

The nomenclatural type of the genus Deleya and the consequences of Deleya aesta and Alcaligenes aquamarinus being synonyms.

The genus Deleya was created to encompass a number of marine organisms that had previously been classified in diverse genera. Deleya aesta was designated as the type species of the genus. Subsequent work indicated that Deleya aesta, Alcaligenes aquamarinus and Alcaligenes faecalis subsp. homari were heterotypic synonyms. Consequently, Akagawa & Yamasato (Int J Syst Bacteriol 39, 462-466, 1989) concluded that, based on Rules 23a and 51b of the Bacteriological Code (1975 Revision), the oldest legitimate species epithet was aquamarinus and the type species of the genus Deleya should therefore be changed to Deleya aquamarina. Dobson & Franzmann (Int J Syst Bacteriol 46, 550-558, 1996) concluded that it was not possible to distinguish between members of the genus Deleya and members of the genus Halomonas Vreeland et al. 1980, leading them to transfer members of the genus Deleya to the genus Halomonas and resulting in the creation of a new combination, Halomonas aquamarina. Closer examination of some of these changes indicates that they are not all in accordance with the Rules of the Bacteriological Code (1975 or 1990 Revisions).

Alcaligenes↗

PubMed2006

Reclassification of Lactobacillus thermotolerans Niamsup et al. 2003 as a later synonym of Lactobacillus ingluviei Baele et al. 2003.

The relatedness of the species Lactobacillus ingluviei and Lactobacillus thermotolerans was investigated by comparing partial sequences of the 16S rRNA gene (99.9 % similarity over 1504 bp), the hsp60 gene (98.8 % similarity over 954 bp) and the recA gene (98.5 % similarity over 452 bp) and by determining DNA-DNA binding levels (79+/-3 %) and genomic DNA G+C contents (50 and 49 mol%, respectively). These data, in addition to their similar biochemical characteristics, suggest that the two taxa constitute a single species. According to Rules 38 and 42 of the Bacteriological Code, they should be united under the name Lactobacillus ingluviei, with the name Lactobacillus thermotolerans as a later heterotypic synonym.

Lactobacillus↗

PubMed2003

The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination "Sinorhizobium adhaerens" (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion.

The synonymy of the genera Ensifer and Sinorhizobium was recently reported, but it was proposed that the later-named genus, Sinorhizobium, take priority in nomenclature. There is no justification in the International Code of Nomenclature of Bacteria (Prokaryotes) for this step; Ensifer is the correct name of the genus, with Ensifer adhaerens as the type species. Species previously allocated to Sinorhizobium are here proposed as the new combinations Ensifer arboris, Ensifer fredii, Ensifer kostiensis, Ensifer kummerowiae, Ensifer medicae, Ensifer meliloti, Ensifer saheli, Ensifer terangae and Ensifer xinjiangensis. Sinorhizobium morelense was proposed in 2002 [Wang, E. T., Tan, Z. Y., Willems, A., Fernández-López, M., Reinhold-Hurek, B. & Martínez-Romero, E., Int J Syst Evol Microbiol 52, 1687-1693, 2002], but a consideration of all published data indicate that it is a nitrogen-fixing genomovar and later heterotypic synonym of Ensifer adhaerens. A Request for an Opinion is made as to whether or not the combination "Sinorhizobium adhaerens" (Casida 1982) Willems et al. 2003 is legitimate.

Phylogeny↗

PubMed2005

Phylogenetic relationships of the genus Kluyvera: transfer of Enterobacter intermedius Izard et al. 1980 to the genus Kluyvera as Kluyvera intermedia comb. nov. and reclassification of Kluyvera cochleae as a later synonym of K. intermedia.

In order to assess the relationship between the genus Kluyvera and other members of the family Enterobacteriaceae, the 16S rRNA genes of type strains of the recognized Kluyvera species, Kluyvera georgiana, Kluyvera cochleae, Kluyvera ascorbata and Kluyvera cryocrescens, were sequenced. A comparative phylogenetic analysis based on these 16S rRNA gene sequences and those available for strains belonging to several genera of the family Enterobacteriaceae showed that members of the genus Kluyvera form a cluster that contains all the known Kluyvera species. However, the type strain of Enterobacter intermedius (ATCC 33110T) was included within this cluster in a very close relationship with the type strain of K. cochleae (ATCC 51609T). In addition to the phylogenetic evidence, biochemical and DNA-DNA hybridization analyses of species within this cluster indicated that the type strain of E. intermedius is in fact a member of the genus Kluyvera and, within it, of the species Kluyvera cochleae. Therefore, following the current rules for bacterial nomenclature and classification, the transfer of E. intermedius to the genus Kluyvera as Kluyvera intermedia comb. nov. is proposed (type strain, ATCC 33110T=CIP 79.27T=LMG 2785T=CCUG 14183T). Biochemical analysis of four E. intermedius strains and one K. cochleae strain independent of the respective type strains further indicated that E. intermedius and K. cochleae represent the same species and are therefore heterotypic synonyms. Nomenclatural priority goes to the oldest legitimate epithet. Consequently, Kluyvera cochleae Muller et al. 1996 is a later synonym of Kluyvera intermedia (Izard et al. 1980) Pavan et al. 2005.

Bacterial Typing Techniques↗

PubMed2001

A taxonomic note on the authorship and date of valid publication of Rhodococcus sputi.

Authorship of the name Rhodococcus sputi is variously attributed to Tsukamura 1978 or Tsukamura and Yano 1985. DNA-DNA binding data indicate that this species and Rhodococcus obuensis Tsukamura 1983 and Rhodococcus chubuensis Tsukamura 1983 are subjective (heterotypic) synonyms. Although these organisms have been placed in the genus Gordonia as Gordonia sputi, the correct name of the taxon created by unification of these three species is directly affected by the date of valid publication of these species as members of the genus Rhodococcus. Thus, the name R. sputi only has priority if the authorship is attributed to Tsukamura 1978. The question of authorship and priority is clarified in the present work.

Authorship↗

PubMed2005

Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1.

Recent studies on the occurrence of (per)chlorate-reducing bacteria have resulted in the characterization of strains capable of dissimilatory (per)chlorate reduction. Phylogenetic analysis has shown that these bacteria are members of the Proteobacteria. Strains have been isolated from polluted and pristine sites, but only strains from polluted sites have been characterized in detail and deposited in culture collections. Herein we describe the isolation and characterization of perchlorate-reducing bacterium strain MA-1(T) and chlorate-reducing bacterium strain ASK-1, respectively isolated from a pristine and a chlorate-polluted site. Both isolates are members of the Proteobacteria. The 16S rRNA gene sequence similarity of MA-1(T) to Dechloromonas agitata DSM 13637(T) is 97.6%, but the relatedness in DNA-DNA reassociation is only 37%. Therefore, we propose to classify strain MA-1(T) (=DSM 15637(T)=ATCC BAA-776(T)) as the type strain of a novel species, Dechloromonas hortensis sp. nov. Strain ASK-1 and a previously described strain GR-1 show 100 and 99% 16S rRNA gene sequence similarity to Pseudomonas chloritidismutans DSM 13592(T) and Dechlorosoma suillum DSM 13638(T), respectively. DNA-DNA hybridization studies indicated that strains ASK-1 and GR-1 are related at the species level to P. chloritidismutans DSM 13592(T) (79%) and Dechlorosoma suillum DSM 13638(T) (85%), respectively. As suggested previously, Dechlorosoma suillum appears to be a later heterotypic synonym of Azospira oryzae. Although strain ASK-1 is identified as P. chloritidismutans, its morphology and growth requirements are different from those of the type strain.

Chlorates↗