scholarly journals 16SpeB: Towards defining bacterial species boundaries by intra-species gene sequence identity

2016 ◽  
Author(s):  
Adam Chun-Nin Wong ◽  
Patrick Ng ◽  
Angela E. Douglas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Species ◽  
Region Of Interest ◽  
Supplementary Information ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Link Type ◽  
V Region ◽  
The Relationship

ABSTRACTSummary16SpeB (16S rRNA-based Species Boundary) is a package of Perl programs that evaluates total sequence variation of a bacterial species at the levels of the whole 16S rRNA sequences or single hypervariable (V) regions, using publicly-available sequences. The 16SpeB pipelines filter sequences from duplicated strains and of low quality, extracts a V region of interest using general primer sequences, and calculates sequence percentage identity (%ID) through all possible pairwise alignments.ResultsThe minimum %ID of 16S rRNA gene sequences for 15 clinically-important bacterial species, as determined by 16SpeB, ranged from 82.6% to 99.8%. The relationship between minimum %ID of V2/V6 regions and full-gene sequences varied among species, indicating that %ID species limits should be resolved independently for each region of the 16S rRNA gene and bacterial species.Availability16SpeB and user manual are freely available for download from: https://github.com/pnpnpn/16SpeB. A video tutorial is available at: https://youtu.be/[email protected] informationSupplementary data are available at Bioinformatics online.

Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

Sphingobium fontiphilum sp. nov., isolated from a freshwater spring

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1906-1911 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Yan-Ting Wei ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

To investigate the biodiversity of bacteria in the spring water of the Chengcing Lake Park in Taiwan, a Gram-stain-negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated strain Chen16-4T, was isolated and characterized in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain Chen16-4T were Sphingobium amiense YTT, Sphingobium yanoikuyae GIFU 9882T and Sphingobium scionense WP01T, with sequence similarities of 97.6, 97.1 and 97.0 %, respectively. A phylogenetic tree obtained with 16S rRNA gene sequences indicated that strain Chen16-4T and these three closest relatives formed an independent phylogenetic clade within the genus Sphingobium . The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of C18 : 1ω7c in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium . The DNA–DNA relatedness of strain Chen16-4T with respect to recognized species of the genus Sphingobium was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Chen16-4T represents a novel species in the genus Sphingobium , for which the name Sphingobium fontiphilum sp. nov. is proposed. The type strain is Chen16-4T ( = BCRC 80308T = LMG 26342T = KCTC 23559T).

scholarly journals ‘Candidatus Phytoplasma sudamericanum’, a novel taxon, and strain PassWB-Br4, a new subgroup 16SrIII-V phytoplasma, from diseased passion fruit (Passiflora edulis f. flavicarpa Deg.)

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 984-989 ◽  
Author(s):  
Robert E. Davis ◽  
Yan Zhao ◽  
Ellen L. Dally ◽  
Rasa Jomantiene ◽  
Ing-Ming Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Passion Fruit ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Sequence Alignments ◽  
Passiflora Edulis ◽  
Content Type ◽  
Link Type

Symptoms of abnormal proliferation of shoots resulting in formation of witches’-broom growths were observed on diseased plants of passion fruit (Passiflora edulis f. flavicarpa Deg.) in Brazil. RFLP analysis of 16S rRNA gene sequences amplified in PCRs containing template DNAs extracted from diseased plants collected in Bonito (Pernambuco) and Viçosa (Minas Gerais) Brazil, indicated that such symptoms were associated with infections by two mutually distinct phytoplasmas. One phytoplasma, PassWB-Br4 from Bonito, represents a new subgroup, 16SrIII-V, in the X-disease phytoplasma group (‘Candidatus Phytoplasma pruni’-related strains). The second phytoplasma, PassWB-Br3 from Viçosa, represents a previously undescribed subgroup in group 16SrVI. Phylogenetic analyses of 16S rRNA gene sequences were consistent with the hypothesis that strain PassWB-Br3 is distinct from previously described ‘Ca. Phytoplasma ’ species. Nucleotide sequence alignments revealed that strain PassWB-Br3 shared less than 97.5 % 16S rRNA gene sequence similarity with previously described ‘Ca. Phytoplasma ’ species. The unique properties of its DNA, in addition to natural host and geographical occurrence, support the recognition of strain PassWB-Br3 as a representative of a novel taxon, ‘Candidatus Phytoplasma sudamericanum’.

Rhizobium halophytocola sp. nov., isolated from the root of a coastal dune plant

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1997-2003 ◽  
Author(s):  
Fehmida Bibi ◽  
Eu Jin Chung ◽  
Ajmal Khan ◽  
Che Ok Jeon ◽  
Young Ryun Chung
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Coastal Dune ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

During a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881T, was isolated from the root of Rosa rugosa collected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881T grew at temperatures of 4–37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0), and at NaCl concentrations in the range of 0–7.5 % (w/v) (optimum, 4–5 % NaCl). Strain YC6881T was catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881T belonged to the genus Rhizobium and showed the highest 16S rRNA gene sequence similarity of 96.9 % to Rhizobium rosettiformans , followed by Rhizobium borbori (96.3 %), Rhizobium radiobacter (96.1 %), Rhizobium daejeonense (95.9 %), Rhizobium larrymoorei (95.6 %) and Rhizobium giardinii (95.4 %). Phylogenetic analysis of strain YC6881T by recA, atpD, glnII and 16S–23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881T was a symbiotic bacterium that nodulated Vigna unguiculata and Pisum sativum. The major components of the cellular fatty acids were C18 : 1ω7c (53.7 %), C19 : 0 cyclo ω8c (12.6 %) and C12 : 0 (8.1 %). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genes recA, atpD and glnII, and fatty acid composition could be used to discriminate strain YC6881T from other species of the genus Rhizobium in the same sublineage. Based on the results obtained in this study, strain YC6881T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium halophytocola sp. nov. is proposed. The type strain is YC6881T ( = KACC 13775T = DSM 21600T).

scholarly journals 16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds

2021 ◽  
Author(s):  
Antti Juhani Rissanen ◽  
Moritz Buck ◽  
Sari Peura
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Stratified Lakes ◽  
Link Type

A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds of boreal and subarctic area. However, it has probably escaped detection in many previous studies using 16S rRNA gene amplicon sequencing due to insufficient database coverage, which is because Ca. Methylumidiphilus lacks cultured representatives and previously analysed metagenome assembled genomes (MAGs) affiliated with it do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG dataset. Among 66 MAGs classified as Ca. Methylumidiphilus (with completeness over 40% and contamination less than 5%) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we could find 5 MAGs each containing one 1532 bp long sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in two unique 16S rRNA gene sequences. These sequences represented two different putative species, i.e. Ca. Methylumidiphilus alinenensis (Genbank accession: OK236221) as well as another so far unnamed species of Ca. Methylumidiphilus (Genbank accession: OK236220). We suggest that including these two sequences in reference databases will enhance 16S rRNA gene - based detection of members of this genus from environmental samples.

scholarly journals Poritiphilus flavus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coral Porites lutea

2020 ◽  
Vol 70 (11) ◽  
pp. 5620-5626 ◽  
Author(s):  
Guanghua Wang ◽  
Shuailiang Xu ◽  
Ge Dang ◽  
Jianfeng Liu ◽  
Hongfei Su ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Porites Lutea ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, non-endospore-forming, non-motile, aerobic bacterium (strain R33T) was isolated from coral Porites lutea and subjected to a polyphasic taxonomic study. The G+C content was 44.5 mol%. The only detected respiratory quinone was menaquinone 6 (MK-6). The major cellular fatty acids were iso-C15 : 0 and iso-C15 : 1 ω6c. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Global alignment based on 16S rRNA gene sequences indicated that strain R33T shares the highest sequence identity of 93.2 % with Muriicola marianensis A6B8T in the family Flavobacteriaceae . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R33T forms a distinct branch in a stable clade comprising strain R33T and members of the genera Muriicola , Robiginitalea , Eudoraea and Zeaxanthinibacter . The phylogenomic analysis also supported this 16S rRNA gene-based phylogenetic result. Comparative genomic analysis indicated that strain R33T is rich in AraC-type DNA-binding domain-containing protein-coding genes, which means the regulation of carbon utilization is very complex. Low 16S rRNA gene identity, different polar lipids and/or cellular fatty acid profiles could readily distinguish strain R33T from any validly published type strains. Therefore, strain R33T is suggested to represent a new species in a new genus, for which the name Poritiphilus flavus gen. nov., sp. nov. is proposed. The type strain is R33T (=MCCC 1K03853T=KCTC 72443T).

Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Huibin Lu ◽  
Zhipeng Cai ◽  
Tongchu Deng ◽  
Youfeng Qian ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus . YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus . The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus , for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.

Flammeovirga pacifica sp. nov., isolated from deep-sea sediment

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 937-941 ◽  
Author(s):  
Hui Xu ◽  
Yuanyuan Fu ◽  
Ning Yang ◽  
Zhixin Ding ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Strain WPAGA1T was isolated from marine sediment of the west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Flammeovirga . Strain WPAGA1T exhibited highest 16S rRNA gene sequence similarity with Flammeovirga yaeyamensis NBRC 100898T (98.1 %) and lower sequence similarity with Flammeovirga arenaria IFO 15982T (94.6 %) and other members of the genus Flammeovirga (<94.2 %). DNA–DNA relatedness studies showed that strain WPAGA1T was distinct from F. yaeyamensis NBRC 100898T and F. arenaria NBRC 15982T (43±4 % and 32±2 % relatedness values, respectively). Strain WPAGA1T could be distinguished from all known members of the genus Flammeovirga by a number of phenotypic features. However, the dominant fatty acids of strain WPAGA1T (iso-C15 : 0, C16 : 0 and C20 : 4ω6,9,12,15c), the major polyamine (cadaverine) and the G+C content of the chromosomal DNA (32.9 mol%) were consistent with those of members of the genus Flammeovirga . Based on phenotypic and chemotaxonomic features and 16S rRNA gene sequences, strain WPAGA1T can be assigned to the genus Flammeovirga as a representative of a novel species, for which the name Flammeovirga pacifica sp. nov. is proposed; the type strain is WPAGA1T ( = CCTCC AB 2010364T = LMG 26175T = DSM 24597T = MCCC 1A06425T).

scholarly journals Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3804-3809 ◽  
Author(s):  
Samantha J. Stropko ◽  
Shannon E. Pipes ◽  
Jeffrey D. Newman
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Emended Description

While characterizing a related strain, it was noted that there was little difference between the 16S rRNA gene sequences of Bacillus indicus LMG 22858T and Bacillus cibi DSM 16189T. Phenotypic characterization revealed differences only in the utilization of mannose and galactose and slight variation in pigmentation. Whole genome shotgun sequencing and comparative genomics were used to calculate established phylogenomic metrics and explain phenotypic differences. The full, genome-derived 16S rRNA gene sequences were 99.74 % similar. The average nucleotide identity (ANI) of the two strains was 98.0 %, the average amino acid identity (AAI) was 98.3 %, and the estimated DNA–DNA hybridization determined by the genome–genome distance calculator was 80.3 %. These values are higher than the species thresholds for these metrics, which are 95 %, 95 % and 70 %, respectively, suggesting that these two strains should be classified as members of the same species. We propose reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and an emended description of Bacillus indicus .

Allonocardiopsis opalescens gen. nov., sp. nov., a new member of the suborder Streptosporangineae , from the surface-sterilized fruit of a medicinal plant

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 900-904 ◽  
Author(s):  
Hui-Jing Du ◽  
Yu-Qin Zhang ◽  
Hong-Yu Liu ◽  
Jing Su ◽  
Yu-Zhen Wei ◽  
...  
Keyword(s):  
16S Rrna ◽  
Medicinal Plant ◽  
16S Rrna Gene ◽  
Type Species ◽  
Minor Amount ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

An endophytic actinomycete, designated strain I10A-01259T, was isolated from a surface-sterilized fruit of Lonicera maackii (Rupr.) Maxim., a medicinal plant, which was collected from a suburb of Beijing, China. Whole-cell hydrolysates of the isolate contained galactose and meso-diaminopimelic acid. The predominant phospholipids were phosphatidylglycerol and diphosphatidylglycerol; the menaquinones consisted mainly of MK-9, MK-11 and MK-12, with a minor amount of MK-10. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Comparative analysis of 16S rRNA gene sequences indicated that strain I10A-01259T was most closely related to Nocardiopsis arabia S186T (93.2 % sequence similarity), Thermobifida halotolerans YIM 90462T (93.0 %) and other strains of genera within the families Nocardiopsaceae and Thermomonosporaceae . On the phylogenetic tree based on 16S rRNA gene sequences, strain I10A-01259T fell within the radius of the suborder Streptosporangineae , in which the strain formed a distinct lineage next to the genera of the families Nocardiopsaceae and Thermomonosporaceae . Based on the data from our polyphasic taxonomic study, a novel genus and species, Allonocardiopsis opalescens gen. nov., sp. nov., are proposed within the suborder Streptosporangineae . The type strain of Allonocardiopsis opalescens is strain I10A-01259T ( = CPCC 203428T  = DSM 45601T  = KCTC 19844T).

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