Flagellimonas aquimarina sp. nov., and transfer of Spongiibacterium flavum Yoon and Oh 2012 and S. pacificum Gao et al. 2015 to the genus Flagellimonas Bae et al. 2007 as Flagellimonas flava comb. nov. and F. pacifica comb. nov., respectively

Choi, Seon; Lee, Ji Hee; Kang, Joo Won; Choe, Han; Seong, Chi Nam

doi:10.1099/ijsem.0.002975

“…In the light of these results, we propose to include Flagellimonas and Spongiibacterium in Muricauda , which has priority. This solution appears to be preferable compared to a recent proposal that only transferred Spongiibacterium to Flagellimonas (Choi et al, 2018). Additional supermatrix analyses indeed confirmed that Flagellimonas and Spongiibacterium are nested within Muricauda , whereas Croceitalea (Lee et al, 2008; Yoon and Oh, 2012; Su et al, 2017) and Croceivirga (Hu et al, 2017) form independent lineages (Supplementary Data Sheet 1).…”

Section: Resultsmentioning

confidence: 89%

“…The description is as for Flagellimonas aquimarina (Choi et al, 2018). The type strain is ECD12 = KCTC 52351 = JCM 32292.…”

Section: Discussionmentioning

confidence: 99%

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

García-López

¹

,

Meier‐Kolthoff

²

,

Tindall

³

et al. 2019

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Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

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“…parva, small, pertaining to the small colonial morphology on agar medium). The description was given by Choi et al [17]and Gao et al [61].…”

Section: Description Of Muricauda Aurantiaca Nom Novmentioning

confidence: 99%

“…193 [5]. At the time of writing, Muricauda comprises 28 species, which were all isolated from marine environments, such as Muricauda lutaonensis from a coastal hot spring [6], four species from marine tidal flats [7][8][9][10], Muricauda aquimarina and Muricauda flavescens from a salt lake [2], Muricauda amoyensis from coast sand [11], eight species from sea water [3,[12][13][14][15][16], Muricauda koreensis from seaweed [17], five species from sea sediments [1,[18][19][20][21], Muricauda eckloniae from marine alga [22], Muricauda flava and Muricauda hymeniacidonis from marine sponges [23,24], Muricauda marina from marine snow [25], Muricauda amphidinii from dinoflagellate [26], and Muricauda alvinocaridis from shrimp gill [27]. M. eckloniae, M. flava and M. koreensis were described as Flagellimonas eckloniae, Spongiibacterium flavum and Flagellimonas aquimarina, respectively, but García merged Flagellimonas and Spongiibacterium into Muricauda and these three species were transferred to Muricauda.…”

Section: Introductionmentioning

confidence: 99%

Muricauda onchidii sp. nov., isolated from a marine invertebrate from South China Sea, and transfers of Flagellimonas algicola, Flagellimonas pacifica and Flagellimonas maritima to Muricauda algicola comb. nov., Muricauda parva nom. nov. and Muricauda aurantiaca nom. nov., respectively, and emended description of the genus Muricauda

Liang

¹

,

Yin

²

,

Zheng

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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An aerobic, Gram-stain-negative, rod-shaped and non-motile strain (XY-359T) was isolated from the mouth of a marine invertebrate Onchidium species from the South China Sea. It grew at pH 6.0–8.5 (optimum, pH 7.5), at 15−37 °C (optimum, 30 °C) and in the presence of 0.5–4.5 % (w/v) NaCl (optimum, 2.5 %). It could not hydrolyse Tweens 20, 40, 60 or 80 and no flexirubin-type pigments were produced. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, six unidentified phospholipids and two unidentified polar lipids. The major fatty acids were iso-C17:0 3-OH, iso-C15:1 G and iso-C15:0 3-OH. The respiratory quinone was MK-6. Strain XY-359T showed the greatest degree of 16S rRNA sequence similarity to Flagellimonas algicola AsT0115T (96.54 %), followed by Muricauda flava DSM 22638T (96.27 %). Phylogenetic analysis based on 16S rRNA gene sequences and 31 core genes indicated that strain XY-359T belongs to the genus Muricauda . The genome size of strain XY-359T was 4 207 872 bp, with 39.1 mol% of DNA G+C content. The average nucleotide identity and digital DNA–DNA hybridization values between strain XY-359T and F. algicola AsT0115T were 74.58 % and 18.5 %, respectively, and those between strain XY-359T and M. flava DSM 22638T were 74.2 % and 18.3 %. The combined phenotypic, chemotaxonomic and phylogenetic data suggest that strain XY-359T represents a novel species of the genus Muricauda , for which the name Muricauda onchidii sp. nov. is proposed. The type strain is XY-359T (=MCCC 1K03658T =KCTC 72218T). Moreover, based on the proposal of nesting Spongiibacterium and Flagellimonas within Muricauda by García (Validation List No. 193) and the analyses of phylogenetic trees and average amino acid identities in this study, the transfers of F. algicola , F. pacifica and F. maritima to the genus Muricauda as Muricauda algicola comb. nov., Muricauda parva nom. nov. and M. aurantiaca nom. nov., respectively, are proposed, with an emended description of the genus Muricauda .

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“…The strain was routinely cultured on MA at 25 °C and stored as a suspension in skimmed milk (10 %, w/v) at −80 °C. Pseudozobellia thermophila KCTC 22016 T [17] and Flagellimonas flava KCTC 22665 T [18, 19] were obtained from their respective culture collection centres. These two strains were used as reference strains and routinely grown on MA at 25 °C.…”

Section: Isolation and Ecologymentioning

confidence: 99%

Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount

Wang

¹

,

Liu

²

,

Zhang

³

2020

International Journal of Systematic and Evolutionary Microbiology

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The Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7–8, 25–30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C15 : 0 and summed feature 1 (composed of C13 : 03-OH and/or iso-C15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531T (95.1 %) and Flagellimonas flava A11T (93.9 %). Genome sequencing revealed the strain TP-CH-4T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4T represents a novel species of a novel genus of the family Flavobacteriaceae , for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4T (=CGMCC 1.17120T=KCTC 72434T).

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Flagellimonas aquimarina sp. nov., and transfer of Spongiibacterium flavum Yoon and Oh 2012 and S. pacificum Gao et al. 2015 to the genus Flagellimonas Bae et al. 2007 as Flagellimonas flava comb. nov. and F. pacifica comb. nov., respectively

Cited by 26 publications

References 23 publications

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount

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