scholarly journals Spiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov.

2020 ◽  
Vol 70 (4) ◽  
pp. 2873-2878 ◽  
Author(s):  
María José León ◽  
Cristina Galisteo ◽  
Antonio Ventosa ◽  
Cristina Sánchez-Porro
Keyword(s):  
Type Species ◽  
Single Species ◽  
Amino Acid Identity ◽  
The Other ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Single Genus ◽  
Type Strains

A comparative taxonomic study of Spiribacter and Halopeptonella species was carried out using a phylogenomic approach based on comparison of the core genome, orthologous average nucleotide identity (OrthoANIu), Genome-to-Genome Distance Calculator (GGDC) and average amino acid identity (AAI). Phylogenomic analysis based on 976 core translated gene sequences obtained from their genomes showed that Spiribacter aquaticus SP30T, S. curvatus UAH-SP71T, S. roseus SSL50T, S. salinus M19-40T and Halopeptonella vilamensis DSM 21056T formed a robust cluster, clearly separated from the remaining species of closely related taxa. AAI between H. vilamensis DSM 21056T and the species of the genus Spiribacter was ≥73.1 %, confirming that all these species belong to the same single genus. On the other hand, S. roseus SSL50T and S. aquaticus SP30T showed percentages of OrthoANIu and digital DNA–DNA hybridization of 98.4 % and 85.3 %, respectively, while these values among those strains and the type strains of the other species of Spiribacter and H. vilamensis DSM 21056T were ≤80.8 and 67.8 %, respectively. Overall, these data show that S. roseus SSL50T and S. aquaticus SP30T constitute a single species and thus that S. aquaticus SP30T should be considered as a later, heterotypic synonym of S. roseus SSL50T based on the rules for priority of names. We propose an emended description of S. roseus , including the features of S. aquaticus . We also propose the reclassification of H. vilamensis as Spiribacter vilamensis comb. nov.

Description of Acinetobacter kanungonis sp. nov., based on phylogenomic analysis

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Lipika Das ◽  
Sushanta Deb ◽  
Subrata K. Das
Keyword(s):  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Cellular Components ◽  
Reference Strains ◽  
Type Strains

A novel strain of a member of the genus Acinetobacter, strain PS-1T, was isolated from the skin of fresh water pufferfish (Tetraodon cutcutia) collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. The major cellular fatty acids of PS-1T were C18 : 1ω9c (30.67 %), C16 : 1ω7c (19.54 %), C16 : 0 (15.87 %), C12 : 0 (7.35 %) and C12 : 0 3-OH (6.77 %). The genome size was 3.5 Mbp and the DNA G+C content was 41.97 %. Gene ontology study revealed that the major fraction of genes were associated with biological processes (53.99 %) followed by molecular function (30.42 %) and cellular components (15.58 %). Comparisons of 16S rRNA gene sequences revealed 97.94–97.05 % sequence similarity with the closely related type strains of species of the genus Acinetobacter . The average nucleotide identity (ANI) and average amino acid identity (AAI) of PS-1T with reference strains of species of the genus Acinetobacter with validly published names were bellow 95–96 and the corresponding in-silico DNA–DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of PS-1T indicate that the strain represents a novel species of the genus Acinetobacter and the name Acinetobacter kanungonis sp. nov. is proposed. The type strain is PS-1T (=JCM 34131T=NCIMB 15260T)

scholarly journals Reclassification of Geobacillus galactosidasius and Geobacillus yumthangensis as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov., respectively

2020 ◽  
Vol 70 (12) ◽  
pp. 6518-6523 ◽  
Author(s):  
Ishfaq Nabi Najar ◽  
Sayak Das ◽  
Nagendra Thakur
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Whole Genome ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Genome Analyses ◽  
Type Strains

Members of the genus Geobacillus within the phylum Firmicutes are Gram-stain-positive, aerobic, endospore-forming, obligate thermophiles. In 2016, the genus Geobacillus was subdivided into two genera based on whole-genome approaches. The new genus, Parageobacillus , comprises five genomospecies. In this study, we recommend the reclassification of two Geobacillus species, Geobacillus galactosidasius and Geobacillus yumthangensis , into the genus Parageobacillus . We have applied whole genome approaches to estimate the phylogenetic relatedness among the 18 Geobacillus and Parageobacillus type strains for which genome sequences are currently publicly available. The phylogenomic metrics AAI (average amino acid identity), ANI (average nucleotide identity) and dDDH (digital DNA–DNA hybridization) denoted that the type strains of G. galactosidasius and G. yumthangensis belong to the genus Parageobacillus . Furthermore, a phylogeny based on comparison of the 16S rRNA gene sequences, recN gene sequences and core genes identified from the whole-genome analyses designated that the type strains of G. galactosidasius and G. yumthangensis belong in the genus Parageobacillus . With these findings, we consequently propose that G. galactosidasius and G. yumthangensis should be reclassified as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov.

Aliarcobacter, Halarcobacter, Malaciobacter, Pseudarcobacter and Poseidonibacter are later synonyms of Arcobacter: transfer of Poseidonibacter parvus, Poseidonibacter antarcticus, ‘Halarcobacter arenosus’, and ‘Aliarcobacter vitoriensis’ to Arcobacter as Arcobacter parvus comb. nov., Arcobacter antarcticus comb. nov., Arcobacter arenosus comb. nov. and Arcobacter vitoriensis comb. nov.

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Stephen L. W. On ◽  
William G. Miller ◽  
Patrick J. Biggs ◽  
Angela J. Cornelius ◽  
Peter Vandamme
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Sensu Stricto ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Single Genus ◽  
Phylogenomic Analyses ◽  
High Level

This paper re-examines the taxonomic positions of recently described Poseidonibacter (P. parvum and P. antarcticus ), Aliarcobacter (‘Al. vitoriensis’), Halarcobacter (‘H. arenosus’) and Arcobacter ( A. caeni , A. lacus ) species, and other species proposed to represent novel genera highly related to the genus Arcobacter . Phylogenomic and several overall genome relatedness indices (OGRIs) were applied to a total of 118 representative genomes for this purpose. Phylogenomic analyses demonstrated the Arcobacter clade to be distinct from other Epsilonproteobacteria , clearly defined and containing closely related species. Aliarcobacter butzleri and Malaciobacter pacificus did not cluster with other members of these proposed genera, indicating incoherence of these genera. Every OGRI measure applied indicated a high level of relatedness among all Arcobacter clade species, including the recently described taxa studied here, and substantially lower between type species representatives for other Epsilonproteobacteria. Where published guidelines were available, OGRI values for Arcobacter clade species were either unsupportive of division into other genera or were at the lowest boundary range (for average amino acid identity). We propose that Aliarcobacter , Halarcobacter , Malaciobacter , Pseudarcobacter , Poseidonibacter and Arcobacter sensu stricto be considered members of a single genus, Arcobacter , and subsequently transfer P. parvum, P. antarcticus , ‘ Al. vitoriensis ’ and ‘H. arenosus’ to Arcobacter as Arcobacter parvum comb. nov., Arcobacter antarcticus comb. nov., Arcobacter vitoriensis comb. nov. and Arcobacter arenosus comb. nov.

Genome-based reclassification of Amycolatopsis eurytherma as a later heterotypic synonym of Amycolatopsis thermoflava

2021 ◽  
Author(s):  
Priya Singh ◽  
Princy Hira ◽  
Charu Dogra Rawat ◽  
Rup Lal ◽  
Utkarsh Sood
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Taxonomic Assignment ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity

The present study was carried out to clarify the taxonomic assignment of two closely related Amycolatopsis species. Genomic information for 48 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Amycolatopsis eurytherma Kim et al. 2002 and Amycolatopsis thermoflava Chun et al. 1999, are conspecific. The 16S rRNA gene sequences of the two species possess 98.85 % sequence similarity. Further, whole-genome comparisons showed that A. eurytherma DSM 44348T and A. thermoflava N1165T shared 98.75 % average nucleotide identity, 98.63 % average amino acid identity and 87.8 % digital DNA–DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. eurytherma DSM 44348T and A. thermoflava N1165T formed a monophyletic clade. Based on this evidence we propose the reclassification of Amycolatopsis eurytherma Kim et al. 2002 as a later heterotypic synonym of Amycolatopsis thermoflava Chun et al. 1999.

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Peter Schumann ◽  
Franziska Kalensee ◽  
Jialan Cao ◽  
Alexis Criscuolo ◽  
Dominique Clermont ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Copper Smelter ◽  
Amino Acid Identity ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Emended Description ◽  
Copper Mines

In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300T developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7–8 and with 0.5–2 % (m/v) NaCl. Its peptidoglycan was of type A4α l-Lys–l-Glu (A11.54). The menaquinone profile was dominated by MK-8(II, III-H4) and contained minor amounts of MK-8(H2), MK-8(H6) and MK-9(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, and components that were not fully characterized, including two phospholipids, two glycolipids and an uncharacterized lipid. Major whole-cell sugars were rhamnose and ribose. The fatty acid profile contained mainly iso and anteiso branched fatty acids (anteiso-C15 : 0, iso-C14 : 0) and aldehydes/dimethylacetals (i.e. not fatty acids). Sequence analysis of its genomic DNA and subsequent analysis of the data placed the isolate in the group currently defined by members of the genera Ruania and Haloactinobacterium (family Ruaniaceae , order Micrococcales ) as a sister taxon to the previously described species Haloactinobacterium glacieicola , sharing an average nucleotide identity and average amino acid identity values of 85.3 and 85.7 %, respectively. Genotypic and chemotaxonomic analyses support the view that strain F300T (=DSM 108350T=CIP 111667T) is the type strain of a new genus and new species for which the name Occultella aeris gen. nov., sp. nov. is proposed. Based on revised chemotaxonomic and additional genome based data, it is necessary to discuss and evaluate the results in the light of the classification and nomenclature of members of the family Ruaniaceae , i.e. the genera Haloactinobacterium and Ruania . Consequently, the reclassification of Haloactinobacterium glacieicola as Occultella glacieicola comb. nov. and Haloactinobacterium album as Ruania alba comb. nov., with an emended description of the genus Ruania are proposed.

Acerihabitans arboris gen. nov., sp. nov., a new member of the family Pectobacteriaceae isolated from sap drawn from Acer pictum

2021 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Hanna Choe ◽  
Ji-Sun Kim
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family Pectobacteriaceae and formed a distinct clade between members of the genera Sodalis and Biostraticola with gene support index of 89. The closest phylogenetic neighbours were Biostraticola tofi DSM 19580T (97.3% 16S rRNA gene sequence similarity) and Sodalis praecaptivus HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family Pectobacteriaceae , for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.

Aestuariisphingobium litorale Li et al. 2020 is a later heterotypic synonym of Chakrabartia godavariana Jani et al. 2019

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Peng Wang ◽  
Yuxin Gao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Rrna Gene ◽  
Genomic Comparison ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Chakrabartia godavariana PRB40T was compared with Aestuariisphingobium litorale SYSU M10002T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of C. godavariana PRB40T had high similarity (99.8 %) to that of A. litorale SYSU M10002T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Chakrabartia . A draft genomic comparison between the two strains revealed an average nucleotide identity of 97.3 % and a digital DNA–DNA hybridization estimate of 79.5±2.9 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Aestuariisphingobium litorale is a later heterotypic synonym of Chakrabartia godavariana .

scholarly journals Reclassification of Deinococcus xibeiensis Wang et al. 2010 as a heterotypic synonym of Deinococcus wulumuqiensis Wang et al. 2010

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 1083-1085 ◽  
Author(s):  
Sunhee Hong ◽  
Christine E. Farrance ◽  
Anne Russell ◽  
Hana Yi
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Taxonomic Status ◽  
Single Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

Two species of the genus Deinococcus , namely Deinococcus wulumuqiensis Wang et al. 2010 and Deinococcus xibeiensis Wang et al. 2010, were simultaneously proposed and described in the same publication. However, the identical 16S rRNA gene sequence of the two type strains strongly raised the probability of their relatedness at the species level. Thus, the genomic relatedness of the two species of the genus Deinococcus was investigated here to clarify their taxonomic status. The high (99.9 %) average nucleotide identity (ANI) between the genome sequences of the two type strains suggested that the two species are synonymous. Additional phenotypic data including enzymic activities and substrate-utilization profiles showed no pronounced differences between the type strains of the two species. Data from this study demonstrated that the two taxa constitute a single species. According to Rule 42 of the Bacteriological Code, we propose that D. xibeiensis Wang et al. 2010 should be reclassified as a subjective heterotypic synonym of D. wulumuqiensis Wang et al. 2010.

scholarly journals Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

2021 ◽  
Author(s):  
Torben Sølbeck Rasmussen ◽  
Theresa Streidl ◽  
Thomas C. A. Hitch ◽  
Esther Wortmann ◽  
Paulina Deptula ◽  
...  
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Obese Mouse ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Succinate Production ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
Average Amino Acid Identity

A bacterial strain, designated WCA-9-b2T, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52–74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives ( D. longicatena , Ruminococcus gnavus , C. scindens , Dorea formicigenerans , Ruminococcus lactaris , Clostridium hylemonae , Merdimonas faecis , Faecalicatena contorta and Faecalicatena fissicatena ). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T=CECT 30156T).

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