Zooshikella harenae sp. nov., Isolated from Pacific Oyster Crassostrea gigas, and Establishment of Zooshikella ganghwensis subsp. marina subsp. nov. and Zooshikella ganghwensis subsp. ganghwensis subsp. nov.

Here, we describe the polyphasic taxonomy of a novel isolated strain WH53T from the genus Zooshikella isolated from the sand sediment located between the lumen of the Crassostrea gigas From Germany. Phylogenetic analysis determined that the strain WH53T had a high similarity to Zooshikella ganghwensis JC2044T (99.57%) and Zooshikella marina LMG 28823T (99.36%). Strain WH53T contained ubiquinone-9 (Q-9) as the predominant menaquinone, and the major fatty acids were C16:0, C16:1ω7c, and C18:1ω7c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, amino phospholipids, and unidentified phospholipids were identified as their polar lipid composition. The DNA G+C content and genome size of strain WH53T were 40.08 mol% and 5,914,969 bp, respectively. Digital DNA–DNA hybridisation (dDDH) for strain WH53T against Z. ganghwensis JC2044T and Z. marina LMG 28823T showed low relatedness values of 26.3% and 26.1%, respectively. The extract of strain WH53T exhibited antimicrobial property. Strain WH53T represents a novel species in the genus Zooshikella. We propose the name of Zooshikella harenae sp. nov., with the type strain WH53T (= DSM 111628T = NCCB 100808T). Furthermore, the dDDH, average nucleotide identity (ANI), percentage of conserved proteins (POCP), and amino acid identity (AAI) value between Z. marina LGM 28823T and Z. ganghwensis DSM 15267T were 79.9%, 97.84%, 76.08%, and 87.01%, respectively, suggesting that both of them should be reclassified as Z. ganghwensis subsp. marina subsp. nov. and Z. ganghwensis subsp. ganghwensis DSM 15267 subsp. nov.

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Phylogenetic relationships among haloalkaliphilic archaea of the family Natrialbaceae

10.1101/2020.01.20.913392 ◽

2020 ◽

Author(s):

Shivakumara Siddaramappa

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Novel Species ◽

Single Species ◽

Amino Acid Identity ◽

Average Nucleotide Identity ◽

Acid Identity ◽

Average Amino Acid Identity ◽

The Family ◽

Clade 1

ABSTRACTThe family Natrialbaceae is a member of the class Halobacteria of the archaeal phylum Euryarchaeota. Seventeen genera with validly or effectively published names are currently included within this family. In this study, using pairwise average nucleotide identity and average amino acid identity comparisons in conjunction with phylogenetic analysis, it has been shown that the family Natrialbaceae is highly diverse and contains several potentially novel species and genera that are yet to be fully characterized. The deduced proteome sequence-based phylogenetic tree, constructed using the alignment- and parameter-free method CVTree3, contained six major clades, with Salinarchaeum sp. Harcht-Bsk1 being the only representative within clade 1. Furthermore, Haloterrigena daqingensis was found to be closely related to Natronorubrum sediminis, and it is proposed that these archaea together represent a novel genus. Interestingly, Haloterrigena jeotgali, Haloterrigena thermotolerans, and Natrinema pellirubrum were found to be very closely related to each other, and it is proposed that they be merged into a single species. Notably, the type genus Natrialba itself appeared to be heterogenous and contains species that could be broadly classified among two genera. Likewise, the genus Natrinema is also heterogenous and contains species that could be classified among six genera. Altogether, 19 novel genera have been proposed to be created, and four haloalkaliphilic archaea hitherto recognized only using genus names are confirmed to represent novel species.

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

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004814 ◽

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.

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Ignicoccus hospitalis sp. nov., the host of ‘Nanoarchaeum equitans’

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64721-0 ◽

2007 ◽

Vol 57 (4) ◽

pp. 803-808 ◽

Cited By ~ 64

Author(s):

Walter Paper ◽

Ulrike Jahn ◽

Michael J. Hohn ◽

Michaela Kronner ◽

Daniela J. Näther ◽

...

Keyword(s):

Type Strain ◽

Novel Species ◽

Protein Composition ◽

High Similarity ◽

The North ◽

Physiological Properties ◽

Cell Architecture ◽

Ignicoccus Hospitalis ◽

Nanoarchaeum Equitans ◽

Unique Cell

A novel chemolithoautotrophic and hyperthermophilic member of the genus Ignicoccus was isolated from a submarine hydrothermal system at the Kolbeinsey Ridge, to the north of Iceland. The new isolate showed high similarity to the two species described to date, Ignicoccus islandicus and Ignicoccus pacificus, in its physiological properties as well as in its unique cell architecture. However, phylogenetic analysis and investigations on the protein composition of the outer membrane demonstrated that the new isolate was clearly distinct from I. islandicus and I. pacificus. Furthermore, it is the only organism known so far which is able to serve as a host for ‘Nanoarchaeum equitans’, the only cultivated member of the ‘Nanoarchaeota’. Therefore, the new isolate represents a novel species of the genus Ignicoccus, which we name Ignicoccus hospitalis sp. nov. (type strain KIN4/IT=DSM 18386T=JCM 14125T).

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Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes.

F1000Research ◽

10.12688/f1000research.14566.1 ◽

2018 ◽

Vol 7 ◽

pp. 521 ◽

Cited By ~ 9

Author(s):

Granger G. Sutton ◽

Lauren M. Brinkac ◽

Thomas H. Clarke ◽

Derrick E. Fouts

Keyword(s):

Type Strain ◽

Computational Analysis ◽

Novel Species ◽

Average Nucleotide Identity ◽

Genome Sequences ◽

Predominant Species ◽

Enterobacter Hormaechei ◽

Enterobacter Asburiae ◽

Type Strains ◽

Strain Genome

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp. oharae, E. hormaechei subsp. steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E. hormaechei subsp. hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI’s RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.

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Prevotella hominis sp. nov., isolated from human faeces

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004342 ◽

2020 ◽

Vol 70 (8) ◽

pp. 4767-4773 ◽

Cited By ~ 4

Author(s):

Jong-Shian Liou ◽

Chien-Hsun Huang ◽

Nao Ikeyama ◽

Ai-Yun Lee ◽

I-Ching Chen ◽

...

Keyword(s):

Type Strain ◽

Type Species ◽

Novel Species ◽

Genomic Analysis ◽

Amino Acid Identity ◽

Strictly Anaerobic ◽

Content Type ◽

Link Type ◽

Predominant Bacterium ◽

Species Specific

A strictly anaerobic predominant bacterium, designated as strain gm001T, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001T was identified as a member of the genus Prevotella , and a comparison of 16S rRNA and hsp60 gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of Prevotella copri . Phylogenomic tree analysis indicated that the gm001T cluster is an independent lineage of P. copri DSM 18205T. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001T and P. copri DSM 18205T were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C15 : 0, C15 : 0 and iso-C15 : 0. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001T represents a novel species of the genus Prevotella , for which the name Prevotella hominis sp. nov. is proposed. The type strain is gm001T (=BCRC 81118T=JCM 33280T).

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Maricaulis alexandrii sp. nov., a novel dimorphic prosthecate and active bioflocculants-bearing bacterium isolated from phycosphere microbiota of laboratory cultured highly-toxic Alexandrium catenella LZT09

10.21203/rs.3.rs-265494/v1 ◽

2021 ◽

Author(s):

Xiao-ling Zhang ◽

Min Qi ◽

Qiu-hong Li ◽

Zhen-dong Cui ◽

Qiao Yang

Keyword(s):

Genomic Dna ◽

Type Strain ◽

Novel Species ◽

Average Nucleotide Identity ◽

Gram Stain ◽

Unidentified Phospholipid ◽

Alexandrium Catenella ◽

Sulfoquinovosyl Diacylglycerol ◽

Curved Rods ◽

Prosthecate Bacterium

Abstract An aerobic, Gram-stain-negative, straight or curved rods, prosthecate bacterium designated as LZ-16-1T was isolated from phycosphere microbiota of highly-toxic and laboratory cultured dinoflagellate Alexandrium catenella LZT09. This new isolate produces active bioflocculanting exopolysaccharides (EPS). Cells were dimorphic with non-motile prostheca, or non-stalked and motile by a single polar flagellum. Growth occurred at 10-40 °C, pH 5–9 and 1–8 % (w/v) NaCl, with optimum growth at 25 °C, pH 7–8 and 2-4 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA indicated that strain LZ-16-1T was affiliated to the genus Maricaulis, and closely related to Maricaulis parjimensis MCS 25T (99.48%) and M. virginensis VC-5T (99.04%),. However, based on genome sequencing and phylogenomic calculations, the average nucleotide identity (ANI) and digtal DNA-DNA genome hybridization (dDDH) values between the two strains were only 85.0 and 20.9%, respectively. Strain LZ-16-1T owned Q-10 as predominant isoprenoid quinone; summed feature 8, C16:0, C17:0, C18:0, C18:1 ω9c and summed feature 9 as dominant fatty acids; and sulfoquinovosyl diacylglycerol, glycolipids and unidentified phospholipid as major polar lipids. The genomic DNA G+C content is 63.6 mol%. Physiological and chemotaxonomic characterization further confirmed the distinctiveness of strain LZ-16-1T from other Maricaulis members. Thus, strain LZ-16-1T represents a novel species of the genus Maricaulis, for which the name Maricaulis alexandrii sp. nov. (type strain LZ-16-1T=KCTC 72194T=CCTCC AB 2019006T) is proposed .

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Carboxylicivirga marinus sp. nov., Isolated From Marine Sediment, and Genome Insight of the Genus Carboxylicivirga

Frontiers in Marine Science ◽

10.3389/fmars.2021.731212 ◽

2021 ◽

Vol 8 ◽

Author(s):

Tian-Shu Zhang ◽

Ya-Ning Zhang ◽

De-Chen Lu ◽

Ya Gong ◽

Zong-Jun Du

Keyword(s):

Type Strain ◽

Novel Species ◽

Sequence Similarity ◽

Rrna Gene ◽

Average Nucleotide Identity ◽

Gram Stain ◽

16S Rrna Gene Sequences ◽

Respiratory Quinone ◽

The 16S Rrna Gene ◽

Optimal Ph

A Gram-stain-negative, facultatively aerobic, beige and slender bacterium, designed N1Y132T, was isolated from a sediment sample taken from coastal zone of Weihai, China (37°34′31.44″ N, 122°9′15″ E). Growth occurred at 15-33°C (optimal 25–28°C), at pH 6.5–8.5 (optimal pH 7.5), in 0–9% (w/v) NaCl (optimal 2.0–2.5%). According to the phylogenetic analysis based on the 16S rRNA gene sequences, strain N1Y132T showed the highest sequence similarity (97.9%) with Carboxylicivirga taeanensis JCM 19490T, followed by C. sediminis JR1T (97.4%), C. mesophila JCM 18290T (96.4%) and C. linearis FB218T (95.1%). Thus, strain N1Y132T was a member of the genus Carboxylicivirga. The average nucleotide identity (ANI) values between strain N1Y132T and C. sediminis JR1T, C. linearis FB218T and C. mesophila JCM 18290T were 74.8%, 71.1%, and 74.9%, respectively. Chemotaxonomic analysis showed that the sole respiratory quinone was MK-7 and the major fatty acids (> 5.0%) included iso-C15:0, anteiso-C15:0, iso-C13:0, iso-C14:0, iso-C15:0 3-OH, and C15:1ω6c. The polar lipids were consisted of a phosphatidylethanolamine, two phosphoaminolipids and six unidentified lipids. The DNA G + C content was 38.1 mol%. Based on the evidence presented in this study, strain N1Y132T represents a novel species of the genus Carboxylicivirga, for which the name Carboxylicivirga marinus sp. nov. is proposed. The type strain is N1Y132T (= KCTC 72934T = MCCC 1H00431T).

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Leptospira dzianensis and Leptospira putramalaysiae are later heterotypic synonyms of Leptospira yasudae and Leptospira stimsonii

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004713 ◽

2021 ◽

Author(s):

Arnau Casanovas-Massana ◽

Antony T. Vincent ◽

Pascale Bourhy ◽

Vasantha Kumari Neela ◽

Frederic J. Veyrier ◽

...

Keyword(s):

Type Strain ◽

Type Species ◽

Novel Species ◽

Nucleotide Identity ◽

Average Nucleotide Identity ◽

Content Type ◽

Link Type ◽

Genome Comparisons

Leptospira dzianensis and Leptospira putramalaysiae were recently described as novel species and published almost concurrently with Leptospira yasudae and Leptospira stimsonii . Genome comparisons based on average nucleotide identity of the type strain genomes indicate that L. dzianensis and L. putramalaysiae are conspecific with L. yasudae and L. stimsonii , respectively. Based on the rules of priority, L. dzianensis should be reclassified as a later heterotypic synonym of L. yasudae , and L. putramalaysiae should be reclassified as a later heterotypic synonym of L. stimsonii .

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Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes.

F1000Research ◽

10.12688/f1000research.14566.2 ◽

2018 ◽

Vol 7 ◽

pp. 521 ◽

Cited By ~ 30

Author(s):

Granger G. Sutton ◽

Lauren M. Brinkac ◽

Thomas H. Clarke ◽

Derrick E. Fouts

Keyword(s):

Type Strain ◽

Computational Analysis ◽

Novel Species ◽

Average Nucleotide Identity ◽

Genome Sequences ◽

Predominant Species ◽

Enterobacter Hormaechei ◽

Enterobacter Asburiae ◽

Type Strains ◽

Strain Genome

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Comparative genomics ofSynechococcusand proposal of the new genusParasynechococcus

PeerJ ◽

10.7717/peerj.1522 ◽

2016 ◽

Vol 4 ◽

pp. e1522 ◽

Cited By ~ 26

Author(s):

Felipe Coutinho ◽

Diogo Antonio Tschoeke ◽

Fabiano Thompson ◽

Cristiane Thompson

Keyword(s):

Primary Productivity ◽

New Genus ◽

Core Genome ◽

Amino Acid Identity ◽

Average Nucleotide Identity ◽

Acid Identity ◽

Average Amino Acid Identity ◽

Protein Encoding ◽

Genomic Taxonomy ◽

Encoding Genes

Synechococcusis among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study ofSynechococcusgenomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division ofSynechococcusin two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwaterSynechococcusand determine the genotypic traits that differentiate these lineages.

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