Pustulibacterium marinum gen. nov., sp. nov., a member of the family 
               
                  Flavobacteriaceae
               
             isolated from the Bashi Channel

Wang, Guanghua; Zhou, Deng; Dai, Shikun; Tian, Xinpeng; Li, Jie; Chen, Wen; Xiang, Wenzhou; Li, Xiang

doi:10.1099/ijs.0.048413-0

Cited by 11 publications

(4 citation statements)

References 24 publications

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“…The description is as before (Wang G. et al, 2013) with the following modification. The genomic G+C content is c. 35–40%, the genome size is c. 4.0–4.5 Mbp.…”

Section: Discussionmentioning

confidence: 99%

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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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“…The description is as before (Wang G. et al, 2013) with the following modification. The genomic G+C content is c. 35–40%, the genome size is c. 4.0–4.5 Mbp.…”

Section: Discussionmentioning

confidence: 99%

“…The description is as before (Wang G. et al, 2013) with the following modification. The G+C content of the type-strain genome is 35.4%, its approximate size 4.21 Mbp, its GenBank deposit SAMN05216480.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…Moreover, minor proportions of genes (53) assigned to COG functional categories (Table S4) are involved in the transport and metabolism of carbohydrates. This is different from the general preference for the metabolism of carbohydrates in members of the Flavobacteriaceae, which are often specialized in the degradation of recalcitrant polysaccharides and biomacromolecules [7]. In addition, a large number of genes were found to be involved in inorganic ion transport and metabolism (110) and signal transduction mechanisms (56) thereby indicating a high capacity of this strain to respond to environmental stimuli.…”

Section: Genome Featuresmentioning

confidence: 89%

“…At the time of writing, this family contains about 163 recognized genera according to the List of Prokaryotic Names with Standing in Nomenclature (LPSN) [6]. It has been reported that more than one-quarter of the members of this family are marine-related [7]. The members of the family Flavobacteriaceae play an important role in the uptake and degradation of dissolved and particulate organic matter and digest complex polysaccharides and other biomacromolecules [8].…”

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confidence: 99%

Haloflavibacter putidus gen. nov., sp. nov., isolated from coastal seawater

Feng

Zou

Zhang

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, aerobic, gliding, rod-shaped (0.2–0.5×1.0-13.0 µm) and yellow-pigmented bacterium, designated PLHSN227T, was isolated from seawater collected near the coast of Yantai, PR China. PLHSN227T was found to grow at 15–37 °C (optimum, 28–30 °C) and pH 6.0–8.5 (optimum, 6.5–7.5) in the presence of 2–14 % (w/v) NaCl (optimum, 5.0 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that PLHSN227T represented a member of the family Flavobacteriaceae and exhibited the highest sequence similarity (94.6 %) to the type strain Salegentibacter holothuriorum NBRC 100249T. The chemotaxonomic analysis revealed that the sole respiratory quinone was menaquinone 6 (MK-6) and the major fatty acids included C19 : 0ω8c cyclo, iso-C15 : 0, anteiso-C15 : 0, C18 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids included phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The DNA G+C content of PLHSN227T was 35.6 mol%. PLHSN227T showed the highest average amino acid identity value of 67.2 %, the average nucleotide identity value of 75.6 and 14.5 % digital DNA–DNA hybridization identity with Mesonia algae DSM 15361T. According to the phylogenetic data, PLHSN227T formed a distinct clade in the phylogenetic tree. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is considered that PLHSN227T represents a novel genus within the family Flavobacteriaceae , for which the name Haloflavibacter putidus gen. nov., sp. nov. is proposed. The type strain is PLHSN227T (=KCTC 72159T=MCCC 1H00371T).

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Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov.

Yoon

Adachi

Kasai

2014

Antonie van Leeuwenhoek

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A facultatively anaerobic, Gram-stain negative, golden-yellow pigmented, non-motile and rod-shaped bacterium, designated strain A5Q-67(T) was isolated from leaf litter collected at the mangrove estuary of Nakama River, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (94.2 %) to Imtechella halotolerans K1(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain A5Q-67(T) were identified as iso-C17:0 3-OH, summed feature 1 (iso-C15:1 H and/or C13:0 3-OH) and iso-C15:0 as defined by the MIDI system. The DNA G+C content was determined to be 36.7 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Frondibacter aureus gen. nov., sp. nov. is proposed. The type strain of F. aureus is A5Q-67(T) (=KCTC 32991(T) = NBRC 110021(T)).

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Pustulibacterium marinum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Bashi Channel

Cited by 11 publications

References 24 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

Haloflavibacter putidus gen. nov., sp. nov., isolated from coastal seawater

Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov.

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