Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

Arenibacter arenosicollis sp. nov., isolated from a sand dune

2021 ◽  
Author(s):  
Sooyeon Park ◽  
Seo Yeon Lee ◽  
Jung-Sook Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, designated BSSL-BM3T, was isolated from sand collected from a dune near the Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain BSSL-BM3T fell within the clade comprising the type strains of Arenibacter species. Strain BSSL-BM3T exhibited 16S rRNA gene sequence similarity values of 98.0–99.0 % to the type strains of Arenibacter catalasegens , Arenibacter hampyeongensis , Arenibacter echinorum , Arenibacter palladensis and Arenibacter troitsensis and of 94.2–96.7 % to the type strains of the other Arenibacter species. The averagenucleotide identity and digitalDNA–DNA hybridization values between strain BSSL-BM3T and the type strains of A. catalasegens , A. hampyeongensis , A. echinorum , A. palladensis and A. troitsensis were 82.2–88.8 % and 25.0–36.5 %, respectively. The DNA G+C content of strain BSSL-BM3T from genomic sequence data was 38.75 mol%. Strain BSSL-BM3T contained MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and iso-C15 : 1 G as the major fatty acids. The major polar lipids of strain BSSL-BM3T were phosphatidylethanolamine and two unidentified lipids. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain BSSL-BM3T is separated from recognized Arenibacter species. On the basis of the data presented here, strain BSSL-BM3T is considered to represent a novel species of the genus Arenibacter , for which the name Arenibacter arenosicollis sp. nov. is proposed. The type strain is BSSL-BM3T (=KACC 21632T=NBRC 114502T).

scholarly journals Shewanella insulae sp. nov., isolated from a tidal flat

2020 ◽  
Vol 70 (6) ◽  
pp. 3872-3877 ◽  
Author(s):  
Sooyeon Park ◽  
In Kyu Kim ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Genomic Sequence ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M18T, was isolated from tidal-flat sediment collected from the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M18T fell within the clade comprising the type strains of Shewanella species. Strain JBTF-M18T exhibited 16S rRNA gene sequence similarity values of 97.1–98.8 % to the type strains of S. loihica , S. aquimarina , S. waksmanii and S. marisflavi and of less than 96.9 % to the type strains of the other Shewanella species. The average nucleotide identity and digital DNA–DNA hybridization values between strain JBTF-M18T and the type strains of S. waksmanii and S. loihica were 72.0 and 89.5% and 18.9 and 38.1 %, respectively. DNA–DNA relatedness values between strain JBTF-M18T and the type strains of S. aquimarina and S. marisflavi were 14 and 19 %, respectively. The DNA G+C content of strain JBTF-M18T from genomic sequence data was 52.9 %. Strain JBTF-M18Tcontained MK-6 as the predominant menaquinone and Q-7 and Q-8 as the predominant ubiquinones. It had iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain JBTF-M18T were phosphatidylethanolamine and phosphatidylglycerol. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M18T is separated from recognized Shewanella species. On the basis of the data presented, strain JBTF-M18T is considered to represent a novel species of the genus Shewanella , for which the name Shewanella insulae sp. nov. is proposed. The type strain is JBTF-M18T (=KACC 19869T=NBRC 113583T).

Agromyces mariniharenae sp. nov., a novel indole-acetic acid producing actinobacterium isolated from marine sand

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Yuting Zhang ◽  
Junwei Zhao ◽  
Jiangmeihui Hu ◽  
Chuanyu Han ◽  
Bing Yu ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Indole Acetic Acid ◽  
Sequence Data ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Marine Sand ◽  
Pr China ◽  
Distinct Branch ◽  
Type Strains

A Gram-positive, aerobic, heterotrophic, non-endospore-forming, rod-shaped and indole-acetic acid-producing strain, designated NEAU-184T, was isolated from marine sand collected in Sanya, PR China, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain NEAU-184T should be assigned to the genus Agromyces and formed a distinct branch with its closest neighbour, Agromyces iriomotensis NBRC 106452T (99.1 %). 2,4-Diaminobutyric acid, d-alanine, d-glutamic acid and glycine were detected in cell-wall hydrolysate and glucose, rhamnose and xylose were detected in whole-cell hydrolysate. The polar lipids were found to contain diphosphatidylglycerol, glycolipid, phosphatidylglycerol and two unidentified lipids. The major menaquinone was MK-12 and the minor menaquinones were MK-13 and MK-11. The predominant fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 71.5 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA–DNA hybridization results and some phenotypic characteristics. Meanwhile, the strain has the ability to produce indole-acetic acid (0.334mg ml−1). Therefore, strain NEAU-184T represents a novel species of the genus Agromyces , for which the name Agromyces mariniharenae sp. nov. is proposed, with strain NEAU-184T (=CGMCC 4.7505T=JCM 32546T) as the type strain.

Sulfitobacter aestuariivivens sp. nov., isolated from a tidal flat

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Sooyeon Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Genomic Sequence ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-flagellated, coccoid, ovoid or rod-shaped bacterial strain, TSTF-M16T, was isolated from a tidal flat on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain TSTF-M16T fell within a clade comprising the type strains of Sulfitobacter species. Strain TSTF-M16T exhibited 16S rRNA gene sequence similarities of 98.5 and 98.1 % to the type strains of Sulfitobacter mediterraneus and Sulfitobacter sabulilitoris , respectively, and 96.2–97.8 % to the type strains of the other Sulfitobacter species. The average nucleotide identity and digital DNA–DNA hybridization values between the genomic sequences of strain TSTF-M16T and the type strains of 16 Sulfitobacter species were 70.6–74.2 and 17.9–19.0 %, respectively. The DNA G+C content of strain TSTF-M16T from genomic sequence data was 59.26 mol%. Strain TSTF-M16T contained Q-10 as the predominant ubiquinone and C18 : 1  ω7c as the major fatty acid. The major polar lipids of strain TSTF-M16T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Distinguished phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain TSTF-M16T is separated from recognized Sulfitobacter species. On the basis of the data presented here, strain TSTF-M16T is considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter aestuariivivens sp. nov. is proposed. The type strain is TSTF-M16T (=KACC 21645T=NBRC 114501T).

scholarly journals Amycolatopsis granulosa sp. nov., Amycolatopsis ruanii sp. nov. and Amycolatopsis thermalba sp. nov., thermophilic actinomycetes isolated from arid soils

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1245-1251 ◽  
Author(s):  
Tiago Domingues Zucchi ◽  
Geok Yuan Annie Tan ◽  
Avinash Naga Venkata Bonda ◽  
Sarah Frank ◽  
Jenileima Devi Kshetrimayum ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Data ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Thermophilic Actinomycetes ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis . 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA–DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307T = NCIMB 14709T = NRRL B-24844T), Amycolatopsis ruanii sp. nov. (type strain NMG112T = NCIMB 14711T = NRRL B-24848T) and Amycolatopsis thermalba sp. nov. (type strain SF45T = NCIMB 14705T = NRRL B-24845T).

scholarly journals Pseudomonas izuensis sp. nov., a novel species isolated from Izu Oshima, Japan

2020 ◽  
Vol 70 (7) ◽  
pp. 4212-4216 ◽  
Author(s):  
Yu Jie Lu ◽  
Yuh Morimoto ◽  
Mari Tohya ◽  
Tomomi Hishinuma ◽  
Keiichi Hiramatsu ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Whole Genome ◽  
Gram Stain ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Pseudomonas Jessenii ◽  
Type Strains

An aerobic, Gram-stain-negative, rod-shaped bacterial strain, IzPS43_3003T, was isolated from Izu Oshima, an active volcanic island located 22 km east of the Izu Peninsula, Japan. The sequence of its 16S rRNA gene indicated that IzPS43_3003T belongs to the Pseudomonas fluorescens lineage, with its sequence being most similar to that of Pseudomonas vancouverensis DhA-51T (99.79 %). Phylogenetic analysis based on whole genome sequences showed that IzPS43_3003T was a member of the Pseudomonas jessenii subgroup. The average nucleotide identity values and genome-to genome distances between the whole genome sequences of IzPS43_3003T and other type strains showed that the highest correlations were with Pseudomonas moorei DSM 12647T (87.3 and 33.5% respectively). These genotypic and phenotypic analyses indicated that IzPS43_3003T belongs to a novel species, Pseudomonas izuensis sp. nov. Its type strain is IzPS43_3003T (=LMG 31527T,=CECT 9963T).

scholarly journals Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3220-3224 ◽  
Author(s):  
Tiarin Ferreira ◽  
Carol A. van Reenen ◽  
Akihito Endo ◽  
Cathrin Spröer ◽  
Antoinette P. Malan ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Carbohydrate Fermentation ◽  
Type Strains ◽  
Produce Acid

Bacterial strain SF87T, and additional strains SF80, SF362 and 106-C, isolated from the nematode Steinernema khoisanae, are non-bioluminescent Gram-reaction-negative bacteria that share many of the carbohydrate fermentation reactions recorded for the type strains of recognized Xenorhabdus species. Based on 16S rRNA gene sequence data, strain SF87T is shown to be closely related (98 % similarity) to Xenorhabdus hominickii DSM 17903T. Nucleotide sequences of strain SF87 obtained from the recA, dnaN, gltX, gyrB and infB genes showed 96–97 % similarity with Xenorhabdus miraniensis DSM 17902T . However, strain SF87 shares only 52.7 % DNA–DNA relatedness with the type strain of X. miraniensis , confirming that it belongs to a different species. Strains SF87T, SF80, SF362 and 106-C are phenotypically similar to X. miraniensis and X. beddingii , except that they do not produce acid from aesculin. These strains are thus considered to represent a novel species of the genus Xenorhabdus , for which the name Xenorhabdus khoisanae sp. nov. is proposed. The type strain is SF87T ( = DSM 25463T = ATCC BAA-2406T).

scholarly journals Pseudonocardia cypriaca sp. nov., Pseudonocardia salamisensis sp. nov., Pseudonocardia hierapolitana sp. nov. and Pseudonocardia kujensis sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1703-1711 ◽  
Author(s):  
Nevzat Sahin ◽  
Aysel Veyisoglu ◽  
Demet Tatar ◽  
Cathrin Spröer ◽  
Demet Cetin ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Data ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Iv ◽  
Type Strains

The taxonomic positions of four novel actinomycetes isolated from soil samples, designated KT2142T, PM2084T, K236T and A4038T, were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Pseudonocardia . Whole-cell hydrolysates of the four strains contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars (cell-wall type IV). Their predominant menaquinone was found to be MK-8(H4). The major fatty acid was iso-C16 : 0. 16S rRNA gene sequence data supported the classification of the isolates in the genus Pseudonocardia and showed that they formed four distinct branches within the genus. DNA–DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The four isolates were readily distinguished from one another and from the type strains of species classified in the genus Pseudonocardia based on a combination of phenotypic and genotypic properties. In conclusion, it is proposed that the four isolates be classified in four novel species of the genus Pseudonocardia , for which the names Pseudonocardia cypriaca sp. nov. (type strain KT2142T = KCTC 29067T = DSM 45511T = NRRL B-24882T), Pseudonocardia hierapolitana sp. nov. (type strain PM2084T = KCTC 29068T = DSM 45671T = NRRL B-24879T), Pseudonocardia salamisensis sp. nov. (type strain K236T = KCTC 29100T = DSM 45717T) and Pseudonocardia kujensis sp. nov. (type strain A4038T = KCTC 29062T = DSM 45670T = NRRL B-24890T) are proposed.

scholarly journals Amphritea ceti sp. nov., isolated from faeces of Beluga whale (Delphinapterus leucas)

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4068-4072 ◽  
Author(s):  
Young-Ok Kim ◽  
Sooyeon Park ◽  
Doo Nam Kim ◽  
Bo-Hye Nam ◽  
Sung-Min Won ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Beluga Whale ◽  
Delphinapterus Leucas ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Beluga Whale Delphinapterus Leucas ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated RA1T, was isolated from faeces collected from Beluga whale (Delphinapterus leucas) in Yeosu aquarium, South Korea. Strain RA1T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RA1T joins the cluster comprising the type strains of three species of the genus Amphritea , with which it exhibited 95.8–96.0 % sequence similarity. Sequence similarities to the type strains of other recognized species were less than 94.3 %. Strain RA1T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain RA1T were phosphatidylethanolamine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain RA1T was 47.4 mol%. The differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain RA1T is separated from other species of the genus Amphritea . On the basis of the data presented, strain RA1T is considered to represent a novel species of the genus Amphritea , for which the name Amphritea ceti sp. nov. is proposed. The type strain is RA1T ( = KCTC 42154T = NBRC 110551T).

scholarly journals Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3862-3866 ◽  
Author(s):  
Shi Peng ◽  
Dong Dan Hong ◽  
Yang Bing Xin ◽  
Li Ming Jun ◽  
Wei Ge Hong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Physiological And Biochemical Characteristics ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1T showed 96.8 % similarity to Sphingobacterium nematocida CCTCC AB 2010390T and less than 95.2 % similarity to other members of the genus Sphingobacterium . Growth of strain CCNWSP36-1T occurred at 10–40 °C and at pH 5.0–9.0. The NaCl range (w/v) for growth was 0–4 %. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1T ( = ACCC 19328T = JCM 30166T).

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