Reichenbachiella faecimaris sp. nov., isolated from a tidal flat, and emended descriptions of the genus Reichenbachiella and Reichenbachiella agariperforans

Cha, In-Tae; Oh, Yong-Sik; Park, Soo-Je; Park, Byoung-Joon; Lee, Je-Kwan; Lim, Chaesung; Park, A-Rum; Yoo, Jae-Soo; Lee, Dong Hun; Rhee, Sung‐Keun; Roh, Dong-Hyun

doi:10.1099/ijs.0.026849-0

Cited by 19 publications

(12 citation statements)

References 18 publications

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“…et al, 2013) and Ohtaekwangia (Yoon J.et al, 2011), hence a new family can be proposed to accommodate these genera (see also Supplementary Table 1, Supplementary Data Sheet 1). As in the GBDP tree, the 16S rRNA gene trees and the ULT (Supplementary Data Sheet 1) showed Ekhidna lutea in a clade together with Marinoscillum (Seo et al, 2009) and Reichenbachiella (Nedashkovskaya et al, 2005f; Cha et al, 2011), which suggests the classification of these three genera into a new family, which is not precluded by their phenotype (Supplementary Table 1). Roseivirga (Nedashkovskaya et al, 2005a,e, 2008a; Selvaratnam et al, 2016) formed a strongly supported clade together with Fabibacter (Lau et al, 2006a), with which it was even intermixed as discussed below.…”

Section: Resultsmentioning

confidence: 83%

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

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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Section: Resultsmentioning

confidence: 83%

“…The description is as before (Cha et al, 2011) with the following modification. The G+C content of the type-strain genome is 43.4%, its approximate size 5.03 Mbp, its GenBank deposit SAMN04488028.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…nov.; present study); 2 Roseivirga spongicola UST030701-084 T (Lau et al 2006); 3 Roseivirga ehrenbergii KMM 6017 T Nedashkovskaya et al( 2005); 4 Roseivurga echinicomitans KMM 6058 T ; Nedashkovskaya et al (2005); 5 Fabibacter halotolerans UST030701-084 T (Lau et al 2006); 6 Fulvivirga kasyanovii KMM 6220 T (Nedashkovskaya et al 2007); 7 Reichenbachiella agariperformans (Cha et al 2010;Nedashkovskaya et al 2003 Shu-F-UV2-2 T (Yoon et al 2007) 28 Rapidithrix thailandica TISTR 1750 T (Srisukchayakul et al 2007). Values are percentages of total fatty acids; -not detected; tr traces (\1%)…”

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confidence: 52%

Porifericola rhodea gen. nov., sp. nov., a new member of the phylum Bacteroidetes isolated by the bait-streaked agar technique

Yoon

Oku

Park

et al. 2011

Antonie van Leeuwenhoek

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A strictly aerobic, gram-negative, non-motile, reddish-pink pigmented, rod-shaped strain designated N5EA6-3A2B(T), was isolated from an unidentified marine sponge by use of a bait-streaked agar technique. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate represented a distinct and deep evolutionary lineage of descent in the family Flammeovirgaceae within the phylum Bacteroidetes and clustered with as yet uncultured bacteria. The most closely related established species was Roseivirga spongicola UST030701-084(T) (89% sequence similarity) in the family of Flammeovirgaceae. The strain could be differentiated phenotypically and physiologically from recognized members of the family Flammeovirgaceae. The G+C content of DNA was 43 mol%, the major respiratory quinone was menaquinone 7 (MK-7) and iso-C15:0, C16:1ω5c and iso-C17:0 3-OH were the major fatty acids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the name Porifericola rhodea gen. nov., sp. nov. is proposed. The type strain of Porifericola rhodea is N5EA6-3A2B(T) (=MBIC08357(T) = NBRC 107748(T)).

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“…Cha et al (2011). +, Positive reaction; 2, negative reaction; W, weakly positive; ND, not determined.…”

Section: Sporocytophaga Myxococcoides Dsm 11118 T (Aj310654)mentioning

confidence: 99%

Marinoscillum luteum sp. nov., isolated from marine sediment

Cha

Park

Kim

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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A novel strain, designated SJP7 T , was isolated from sediment of the Tofua Arc of the Tonga Trench. The 16S rRNA gene sequence of the isolate showed the highest similarity to that of Marinoscillum pacificum KCCM 42325 T (95.9 %). Phylogenetic analysis revealed that the isolate formed a distinct phyletic line with Marinoscillum pacificum KCCM 42325 T and Marinoscillum furvescens LMG 13023 T within the family Cytophagaceae. Cells of strain SJP7 T were Gramstain-negative and appeared as long rods that were motile by gliding. Growth was observed at 15-40 6C (optimum, 30 6C), at pH 5.5-9.0 (optimum, pH 7.5-8.0) and in the presence of 0.5-7.0 % (w/v) NaCl (optimum, 2.5-3 %). The major respiratory quinone was MK-7. The dominant fatty acids were summed feature 3 (comprising C 16 : 1 v7c and/or C 16 : 1 v6c), iso-C 15 : 0 and C 16 : 1 v5c. The DNA G+C content was 43.5 mol%. These properties support the affiliation of strain SJP7 T with the genus Marinoscillum. Further phenotypic differentiation of strain SJP7 T from other species of the genus Marinoscillum was indicated by the results of physiological and biochemical tests. On the basis of evidence from our polyphasic taxonomic study, strain SJP7

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Reichenbachiella faecimaris sp. nov., isolated from a tidal flat, and emended descriptions of the genus Reichenbachiella and Reichenbachiella agariperforans

Cited by 19 publications

References 18 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

Porifericola rhodea gen. nov., sp. nov., a new member of the phylum Bacteroidetes isolated by the bait-streaked agar technique

Marinoscillum luteum sp. nov., isolated from marine sediment

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