Lutibacter agarilyticus sp. nov., a marine bacterium isolated from shallow coastal seawater

Park, Seong Chan; Choe, Han; Hwang, Yeoung Min; Baik, Keun Sik; Seong, Chi Nam

doi:10.1099/ijs.0.047670-0

Cited by 20 publications

(17 citation statements)

References 23 publications

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“…Annotation of the genome of strain 1KV19 T consisted of 4132 predicted gene sequences and 49 RNA genes. The G+C content of strain 1KV19 T calculated from the draft genome sequence was 29.6 mol%, which is lower than the values given of members of the genus (29.8-41.6 mol%) [1][2][3][4][5][6][7][8][9][10][11]. The ANI values between strain 1KV19 T and the closely related Lutibacter strains were lower than 79.1 % (Table 1), which were lower than the proposed genomic species cut-off of 95 % [22].…”

Section: Genome Featuresmentioning

confidence: 75%

“…During our investigations on the biodiversity of bacteria in the Arctic, strain 1KV19 T was isolated from a surface sediment sample collected in Kongsfjorden, Spitzbergen (78° 59′ 16″ N, 11° 39′ 19″ E) Svalbard in August 2017. The sediment sample was cultivated using an enrichment culture technique at 15 °C while shaking, and the medium was used as previously described [12], which consisted of the following ingredients in seawater: 0.1 % NH 4 Cl, 0.2 % CH 3 COONa, 0.02 % MgSO 4 ·7H 2 O, 0.02 % yeast extract, 0.02 % peptone, 0.1 % EDTA-Na 2 and 0.11 % sodium pyruvate. After cultivating for 7 days, the suspension was serially diluted to 10 -4 with sterilized seawater and 0.1 ml aliquots of each dilution were spread onto marine agar 2216 (MA; BD Difco) plates.…”

Section: Isolation and Culturementioning

confidence: 99%

“…The genus Lutibacter in the family Flavobacteriaceae, phylum Bacteroidetes was first proposed by Choi and Cho [1] with the description of a single recognized species Lutibacter litoralis (type species). By August 2019, the genus Lutibacter comprised 11 species with validly published names: L. litoralis [1], L. maritimus [2], L. aestuarii [3], L. agarilyticus [4], L. flavus [5], L. oricola [6], L. holmesii [7], L. crassostreae [8], L. profundi [9], L. oceani [10] and L. litorisediminis [11]. These members of the genus Lutibacter have been isolated from tidal flat sediments, coastal seawater, sea organisms and a deep-sea hydrothermal vent.…”

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confidence: 99%

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Lutibacter citreus sp. nov., isolated from Arctic surface sediment

Zhou

Wang

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated 1KV19T, was isolated from a surface sediment sample collected near a bay in the Arctic. Growth of strain 1KV19T occurred in 1–4 % (w/v) NaCl (optimum, 2 %), at 4–35 °C (optimum, 25–30 °C) and at pH 6.5–8.0 (optimum, pH 7.0–7.5). The phylogenetic trees based on the 16S rRNA gene sequences showed that strain 1KV19T was associated with the genus Lutibacter and had the highest 16S rRNA gene sequence similarity to Lutibacter oceani 325-5T with 98.1 % similarity. Similarity values between strain 1KV19T and the type strains of other Lutibacter species were in the range 95.9–97.6 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain 1KV19T and related species of the genus Lutibacter were 76.4–79.1 and 19.9–22.3 %, respectively. The major cellular fatty acids of strain 1KV19T were iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 1 H. The respiratory quinone was MK-6. The major polar lipids of strain 1KV19T were phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. The phenotypic, genotypic and chemotaxonomic differences between strain 1KV19T and its phylogenetic relatives indicate that strain 1KV19T should be regarded as representing a novel species in the genus Lutibacter , for which the name Lutibacter citreus sp. nov. is proposed. The type strain is 1KV19T (=KCTC 62595T=MCCC 1H00307T).

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Section: Genome Featuresmentioning

confidence: 75%

Section: Isolation and Culturementioning

confidence: 99%

mentioning

confidence: 99%

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Lutibacter citreus sp. nov., isolated from Arctic surface sediment

Zhou

Wang

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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“…The genus Lutibacter , including L. profundi LP1 T , thus far comprise nine strains which are proposed to represent novel species: L. litoralis CL-TF09 T [25], L. maritimus S7-2 T [26], L. aestuarii MA-My1 T [27], L. flavus T [29] , L. agarilyticus KYW566 T [28], L. oricola UDC377 T [3], L. crassostreae TYO-8 T [30] and L. holmesii KMM 6277 T [31]. The strain L. crassostreae TYO-8 T was isolated from an oyster collected from the South Sea, South Korea [30], whereas L. holmesii KMM 6277 T was isolated from an sea urchin collected from Troitas Bay, Sea of Japan [31].…”

Section: Organism Informationmentioning

confidence: 99%

Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system

Wissuwa

Bauer

Steen

et al. 2017

Stand in Genomic Sci

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Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki’s Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways. However, genes for the oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon sources. In accordance, the genome harbours 130 proteases and 104 carbohydrate-active enzymes, indicating a specialization in degrading organic matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization cluster was identified. Furthermore, a variety of enzymes may be secreted via T9SS and contribute to the hydrolytic variety of the microorganism. Genes for gliding motility are present, which may enable the bacteria to move within the biofilm. A substantial number of genes encoding for extracellular polysaccharide synthesis pathways, curli fibres and attachment to surfaces could mediate adhesion in the biofilm and may contribute to the biofilm formation. In addition to aerobic respiration, the complete denitrification pathway and genes for sulphide oxidation e.g. sulphide:quinone reductase are present in the genome. sulphide:quinone reductase and denitrification may serve as detoxification systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched environment. The information gained from the genome gives a greater insight in the functional role of L. profundi LP1T in the biofilm and its adaption strategy in an extreme environment.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-016-0219-x) contains supplementary material, which is available to authorized users.

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“…In 2006, the genus Lutibacter was proposed along with the isolation and characterization of Lutibacter litoralis (Choi & Cho, 2006). Since then, seven other species have been characterized and the names validly published: Lutibacter maritimus (Park et al, 2010), Lutibacter aestuarii , Lutibacter flavus (Choi et al, 2013), Lutibacter agarilyticus (Park et al, 2013), Lutibacter oricola (Sung et al, 2015), Lutibacter crassostreae (Park et al, 2015), and Lutibacter holmesii (Nedashkovskaya et al, 2015). So far, all species of the genus Lutibacter have been isolated from a tidal area or shallow coastal waters in South Korea and the Sea of Japan.…”

mentioning

confidence: 99%

Lutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter

Bauer

Roalkvam

Steen

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A bacterial strain designated LP1T was isolated from a microbial mat growing on the surface of a black smoker chimney at the Loki's Castle hydrothermal system, which is located on the Arctic Mid-Ocean Ridge. Phylogenetic analyses based on 16S rRNA gene sequences positioned strain LP1 T within the family Flavobacteriaceae with Lutibacter holmesii as the closest relative (97.5 % 16S rRNA gene sequence similarity). Strain LP1 T was rod-shaped, Gram-reaction-negative and non-motile. It grew in a modified artificial seawater medium supplemented with tryptone and vitamins at pH 5.5-7.5 (optimum pH 6.0-6.5), within a temperature range of 13-34 C (optimum 23 C), and under microaerobic conditions. The most abundant fatty acids (>10 %) were iso-C 15 : 0 (25.2 %) and iso-C 15 : 0 3-OH (14.5 %). The genome of strain LP1 T has a DNA G+C content of 29.8 mol%. Based on the results of the polyphasic characterization presented here, strain LP1 T is considered to represent a novel species of the genus Lutibacter, for which the

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Lutibacter agarilyticus sp. nov., a marine bacterium isolated from shallow coastal seawater

Cited by 20 publications

References 23 publications

Lutibacter citreus sp. nov., isolated from Arctic surface sediment

Lutibacter citreus sp. nov., isolated from Arctic surface sediment

Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system

Lutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter

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