Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.

2021 ◽  
Author(s):  
Undine Behrendt ◽  
Sonja Wende ◽  
Steffen Kolb ◽  
Andreas Ulrich
Keyword(s):  
Type Species ◽  
Taxonomic Status ◽  
Amino Acid Identity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Status ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
A Genome

The genera Proteus and Cosenzaea are closely related members of the family Morganellaceae . The genus Cosenzaea consists of the species Cosenzaea myxofaciens originally separated from the genus Proteus by rpoB gene analysis. Due to the high similarity of the 16S rRNA genes between species of both genera, the taxonomic status is here re-evaluated by a genome-based approach. Based on a core genome phylogeny and genome relatedness indices, it is shown that the taxonomy and nomenclature given for the basonym Proteus myxofaciens is more appropriate. Therefore, we propose to use this name in preference. Furthermore, the species status of Proteus terrae and Proteus cibarius was reassessed. Both species are related at subspecies level by digital DNA–DNA hybridization (dDDH) analysis. Additionally, average amino acid identity (AAI) and average nucleotide identity (ANI) do not support a separate species status, and therefore it is proposed to classify P. cibarius as a subspecies of P. terrae . Consequently, both species are being renamed Proteus terrae subsp. cibarius subsp. nov. and Proteus terrae subsp. terrae subsp. nov., respectively. The genome relatedness indices revealed a close relationship of the Proteus genomospecies 5 with P. terrae subsp. terrae. Thus, it has been assigned to the same subspecies.

Classification of Pasteurella species B as Pasteurella oralis sp. nov.

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1396-1401 ◽  
Author(s):  
Henrik Christensen ◽  
Mads F. Bertelsen ◽  
Anders Miki Bojesen ◽  
Magne Bisgaard
Keyword(s):  
Related Species ◽  
Sequence Comparison ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Species Status ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
A Genome

Pasteurella species B has so far only been reported from the oral cavity of dogs, cats and a ferret. In the present study, information from 15 recent isolates from different sources, including African hedgehogs (Atelerix albiventris), banded mongoose (Mungos mungo), Moholi bushbabies (Galago moholi) and pneumonia of a cat, were compared to five strains investigated previously from bite wounds in humans inflicted by a cat and dog and from gingiva of a cat. rpoB gene sequence comparison showed that 17 isolates, including the reference strain (CCUG 19794T), had identical sequences, whereas two were closely related and demonstrated 97.9 and 99.6 % similarity to strain CCUG 19794T, respectively; the type strain of Pasteurella stomatis was the most closely related strain, with 92.3 % similarity. This is within the mean range (76–100 %) of rpoB gene sequence similarity between species of the same genus within the family Pasteurellaceae . 16S rRNA gene sequencing of four strains selected based on rpoB sequence comparison showed at least 99.7 % similarity between strains of Pasteurella species B, with 96.2 % similarity to the type strain of the closest related species ( Pasteurella canis ), indicating that Pasteurella species B should have separate species status. Separate species status was also documented when recN sequence comparisons were converted to a genome similarity of 93.7 % within Pasteurella species B and 59.0 % to the type strain of the closest related species ( P. canis ). Based on analysis of the phylogenetic and phenotypic data, and since most isolates originate from the oral cavities of a diverse group of animals, it is suggested that these bacteria be classified as Pasteurella oralis sp. nov.; the type strain is P683T ( = CCUG 19794T = CCM 7950T = strain 23193T = MCCM 00102T), obtained from a cat. Previous reports of the type strain have shown ubiquinone-8, demethylmenaquinone-8 and menaquinone-8 as the major quinones. Polyamines in the type strain were reported as diaminopropane, putrescine, cadaverine, sym-norspermidine, spermidine and spermine in a previous investigation, and the major fatty acids of the type strain were reported to be C16 : 0, C16 : 1ω7c and C14 : 0, with minor amounts of C18 : 0 and C18 : 1ω9c. The DNA G+C content of the type strain has been reported to be 40.0 mol%.

scholarly journals Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1501-1506 ◽  
Author(s):  
Bacem Mnasri ◽  
Tian Yan Liu ◽  
Sabrine Saidi ◽  
Wen Feng Chen ◽  
Wen Xin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Root Nodules ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Microbial Strains ◽  
Type Strains

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum , are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of R. loessense , R. mongolense , R. gallicum and R. yanglingense ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.

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.

Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 861-866 ◽  
Author(s):  
Hirokazu Shimoshige ◽  
Tomoaki Yamada ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
...  
Keyword(s):  
Type Species ◽  
Lipid Analysis ◽  
Halophilic Archaea ◽  
Single Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Low Levels

Two extremely halophilic archaea, strains MGY-184T and MGY-205, were isolated from sea salt produced in Japan and rock salt imported from Bolivia, respectively. Both strains were pleomorphic, non-motile, Gram-negative and required more than 5 % (w/v) NaCl for growth, with optimum at 9–12 %, in the presence of 2 % (w/v) MgCl2 . 6H2O. In the presence of 18 % (w/v) MgCl2 . 6H2O, however, both strains showed growth even at 1.0 % (w/v) NaCl. Both strains possessed two 16S rRNA genes (rrnA and rrnB), and they revealed closest similarity to Halobaculum gomorrense JCM 9908T, the single species with a validly published name of the genus Halobaculum , with similarity of 97.8 %. The rrnA and rrnB genes of both strains were 100 % similar. The rrnA genes were 97.6 % similar to the rrnB genes in both strains. DNA G+C contents of strains MGY-184T and MGY-205 were 67.0 and 67.4 mol%, respectively. Polar lipid analysis revealed that the two strains contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester derived from C20C20 archaeol. The DNA–DNA hybridization value between the two strains was 70 % and both strains showed low levels of DNA–DNA relatedness (48–50 %) with Halobaculum gomorrense JCM 9908T. Physiological and biochemical characteristics allowed differentiation of strains MGY-184T and MGY-205 from Halobaculum gomorrense JCM 9908T. Therefore, strains MGY-184T and MGY-205 represent a novel species of the genus Halobaculum , for which the name Halobaculum magnesiiphilum sp. nov. is proposed; the type strain is MGY-184T ( = JCM 17821T = KCTC 4100T).

scholarly journals Mucilaginibacter koreensis sp. nov., isolated from leaf mould

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2274-2279 ◽  
Author(s):  
Cheol Su Park ◽  
Kyudong Han ◽  
Tae-Young Ahn
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-staining-negative, strictly aerobic, rod-shaped, pale-pink pigmented bacterial strain, designated TF8T, was isolated from leaf mould in Cheonan, Republic of Korea. Its taxonomic position was determined through a polyphasic approach. Optimal growth occurred on R2A agar without NaCl supplementation, at 25–28 °C and at pH 6.0–7.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TF8T belongs to the genus Mucilaginibacter in the family Sphingobacteriaceae . The sequence similarity between 16S rRNA genes of strain TF8T and the type strains of other species of the genus Mucilaginibacter ranged from 92.1 to 94.7 %. The closest relatives of strain TF8T were Mucilaginibacter lutimaris BR-3T (94.7 %), M. soli R9-65T (94.5 %), M. litoreus BR-18T (94.5 %), M. rigui WPCB133T (94.0 %) and M. daejeonensis Jip 10T (93.8 %). The major isoprenoid quinone was MK-7 and the major cellular fatty acids were iso-C15 : 0 (33.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 24.8 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 13.0 %). The major polar lipids of TF8T were phosphatidylethanolamine and three unidentified aminophospholipids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of the data presented here, strain TF8T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter koreensis sp. nov. is proposed. The type strain is TF8T ( = KACC 17468T = JCM 19323T).

scholarly journals Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.

scholarly journals Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India

2020 ◽  
Author(s):  
Kuppusamy Pandiyan ◽  
Prity Kushwaha ◽  
Samadhan Y. Bagul ◽  
Hillol Chakdar ◽  
Munusamy Madhaiyan ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Moderately Halophilic ◽  
Link Type ◽  
Moderately Halophilic Bacterium

A moderately halophilic, Gram-stain-negative, aerobic bacterium, strain D1-1T, belonging to the genus Halomonas , was isolated from soil sampled at Pentha beach, Odisha, India. Phylogenetic trees reconstructed based on 16S rRNA genes and multilocus sequence analysis of gyrB and rpoD genes revealed that strain D1-1T belonged to the genus Halomonas and was most closely related to Halomonas alimentaria YKJ-16T (98.1 %) followed by Halomonas ventosae Al12T (97.5 %), Halomonas sediminicola CPS11T (97.5 %), Halomonas fontilapidosi 5CRT (97.4 %) and Halomonas halodenitrificans DSM 735T (97.2 %) on the basis of 16S rRNA gene sequence similarity. Sequence identities with other species within the genus were lower than 97.0 %. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of 22.4–30 % and 79.5–85.4 % with close relatives of H. halodenitrificans DSM 735T, H . alimentaria YKJ-16T, H. ventosae Al12T and H. fontilapidosi 5CRT were lower than the threshold recommended for species delineation (70 % and 95–96 % for dDDH and ANI, respectively). Further, strain D1-1T formed yellow-coloured colonies; cells were rod-shaped, motile with optimum growth at 30 °C (range, 4–45 °C) and 2–8 % NaCl (w/v; grew up to 24 % NaCl). The major fatty acids were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) and C16 : 0 and the main respiratory quinone was ubiquinone Q-9 in line with description of the genus. Based on its chemotaxonomic and phylogenetic characteristics and genome uniqueness, strain D1-1T represents a novel species in the genus Halomonas , for which we propose the name Halomonas icarae sp. nov., within the family Halomonadaceae . The type strain is D1-1T (=JCM 33602T=KACC 21317T=NAIMCC-B-2254T).

Phylogenomic analysis of Anabaenopsis elenkinii (Nostocales, Cyanobacteria)

2021 ◽  
Author(s):  
Endrews Delbaje ◽  
Ana Paula D. Andreote ◽  
Thierry A. Pellegrinetti ◽  
Renata B. Cruz ◽  
Luis H. Z. Branco ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Soda Lakes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

The saline-alkaline lakes (soda lakes) are the habitat of the haloalkaliphilic cyanobacterium Anabaenopsis elenkinii, the type species of this genus. To obtain robust phylogeny of this type species, we have generated whole-genome sequencing of the bloom-forming Anabaenopsis elenkinii strain CCIBt3563 isolated from a Brazilian soda lake. This strain presents the typical morphology of A. elenkinii with short and curved trichomes with apical heterocytes established after separation of paired intercalary heterocytes and also regarding to cell dimensions. Its genome size is 4 495 068 bp, with a G+C content of 41.98 %, a total of 3932 potential protein coding genes and four 16S rRNA genes. Phylogenomic tree inferred by RAxML based on the alignment of 120 conserved proteins using GTDB-Tk grouped A. elenkinii CCIBt3563 together with other genera of the family Aphanizomenonaceae. However, the only previous available genome of Anabaenopsis circularis NIES-21 was distantly positioned within a clade of Desikacharya strains, a genus from the family Nostocaceae. Furthermore, average nucleotide identity values from 86–98 % were obtained among NIES-21 and Desikacharya genomes, while this value was 76.04 % between NIES-21 and the CCIBt3563 genome. These findings were also corroborated by the phylogenetic tree of 16S rRNA gene sequences, which also showed a strongly supported subcluster of A. elenkinii strains from Brazilian, Mexican and Kenyan soda lakes. This study presents the phylogenomics and genome-scale analyses of an Anabaenopsis elenkinii strain, improving molecular basis for demarcation of this species and framework for the classification of cyanobacteria based on the polyphasic approach.

Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

2021 ◽  
Author(s):  
Sinchan Banerjee ◽  
András Táncsics ◽  
Erika Tóth ◽  
Fruzsina Révész ◽  
Károly Bóka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Enrichment Culture ◽  
Draft Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Para Xylene

A benzene, para- and meta-xylene-degrading Gram-stain-negative, aerobic, yellow-pigmented bacterium, designated as D2P1T, was isolated from a para-xylene-degrading enrichment culture. Phylogenetic analyses based on 16S rRNA genes showed that D2P1T shares a distinct phyletic lineage within the genus Hydrogenophaga and shows highest 16S rRNA gene sequence similarity to Hydrogenophaga taeniospiralis NBRC 102512T (99.2 %) and Hydrogenophaga palleronii NBRC 102513T (98.3 %). The draft genome sequence of D2P1T is 5.63 Mb long and the genomic DNA G+C content is 65.5 %. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed low genomic relatedness to its closest relatives (OrthoANI <86 %; dDDH <30 %). D2P1T contains ubiquinone 8 (Q-8) as the only respiratory quinone and phospholipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol as major polar lipids. The main whole-cell fatty acids of D2P1T are summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). The polyphasic taxonomic results indicated that strain D2P1T represents a novel species of the genus Hydrogenophaga , for which the name Hydrogenophaga aromaticivorans sp. nov. is proposed. The type strain is D2P1T (=LMG 31780T=NCAIM B 02655T).

Microbacterium paulum sp. nov., isolated from microfiltered milk

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Paolo Bellassi ◽  
Alessandra Fontana ◽  
Maria Luisa Callegari ◽  
Fabrizio Cappa ◽  
Lorenzo Morelli
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Type Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Aerobic ◽  
Species Definition ◽  
Content Type ◽  
Link Type

A novel Gram-stain-positive, strictly aerobic, short rod-shaped bacterium, designated 2CT, was isolated from freshly packaged microfiltered milk. This strain was able to grow within the NaCl concentration range of 0–5 % (w/v), temperature range of 8–37 °C (optimally at 30 °C) and at pH 6.0–10.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2CT was closely related to species of the genus Microbacterium , with the highest sequence similarity (99.2 %) to Microbacterium lacticum DSM 20427T as well as Microbacterium flavum DSM 18909T (=YM18-098T). The phylogenetic tree based on 16S rRNA genes showed that strain 2CT clustered with M. flavum DSM 18909T. However, the phylogenetic tree based on concatenated 16S rRNA and four housekeeping genes showed that strain 2CT clustered with M. lacticum DSM 20427T. Furthermore, the phylogenomic tree showed that strain 2CT clustered with M. lacticum DSM 20427T and M. flavum DSM 18909T. The major respiratory quinones were MK-10, MK-11 and MK-12. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipid composition of strain 2CT consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified glycolipids and two unidentified lipids. The cell-wall peptidoglycan type was a variant of B1α {Gly} [l-Lys] d-Glu-l-Lys, with the amino acids lysine, glycine, alanine and glutamic acid. The whole-cell sugars consisted of galactose, glucose, ribose and minor amounts of rhamnose. In addition, strain 2CT showed a glycolyl-type cell wall. The genomic DNA G+C content was 69.8mol%, while the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the closely related Microbacterium species were below the recognized thresholds of 95–96 % ANI and 70 % DDH for species definition. Based on the phenotypic and genotypic data, strain 2CT (=LMG 32277T=CECT 30329T) is considered to represent a new species, for which the name Microbacterium paulum sp. nov. is proposed.

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