Flavobacterium cloacae sp. nov., isolated from waste water

Li, Hongming; Lu, Peng; Zhu, Guoping

doi:10.1099/ijsem.0.001684

Cited by 16 publications

(5 citation statements)

References 21 publications

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“…The ULT confirmed Flavobacterium as paraphyletic (Supplementary Data Sheet 1). In the CCT, F. anatoliense (Kacagan et al, 2013) , F. ceti (Vela et al, 2007; Lata et al, 2012; Kacagan et al, 2013), and F. cloacae (Liu et al, 2017) were also more closely related to Myroides than to the type species, F. aquatile . When the species F. anatoliense, F. marinum , and F. ummariense were proposed, Myroides was not considered in the phylogenetic analysis.…”

Section: Resultsmentioning

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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Section: Resultsmentioning

confidence: 99%

“…The description is as for Flavobacterium cloacae (Liu et al, 2017). The type strain is wh15 = CCTCC AB 2015420 = JCM 31173.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…at 18.578%-19.575%, followed by the family Rhodocyclaceae at 12.960%-19.813%, and order Burkholderiales members at 7.266%-10.564%. Flavobacterium has been previously reported as an abundant member in wastewater effluent in springtime from a site in Korea (Chen et al, 2019); Flavobacterium has also been extensively documented in wastewater (Ryu et al, 2007;Fujii et al, 2014;Liu et al, 2017). Rhodocyclaceae is also a dominant member of wastewater microbiomes such as in poultry, cattle, and pigs WWTPs (Boukerb et al, 2021).…”

Section: Resultsmentioning

confidence: 99%

16S metabarcoding of the bacterial community of a poultry wastewater treatment plant in the Philippines

Relucio-San Diego,

Gloria,

Obusan

2024

Front. Environ. Sci.

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“…The description is as for Flavobacterium cloacae [45]. The type strain is wh15 T =CCTCC AB 2015420 T =JCM 31173 T .…”

Section: Description Of Paenimyroides Cloacae Comb Novmentioning

confidence: 99%

Paenimyroides aestuarii gen. nov. sp. nov., a novel bacterium isolated from sediment in the Pearl River Estuary and reclassification of five Flavobacterium and four Myroides species

Zhang,

Cui,

Zeng

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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An aerobic, Gram-negative, non-motile, yellow-to-orange pigmented and round bacterium, designated strain SCSIO 72103T, was isolated from sediment collected in the Pearl River Estuary, Guangdong Province, PR China and subjected to a polyphasic taxonomic study. Growth occurred at 20–37 °C (optimum, 28 °C), pH 6–8 (optimum, pH 7) and with 1–5.5% NaCl (optimum, 1–3 %). Comparative 16S rRNA gene analysis indicated that strain SCSIO 72103T had the highest similarities to Flavobacterium baculatum SNL9T (94.7 %) and Myroides aquimaris SW105T (94.2 %). Phylogenetic analysis based 16S rRNA gene sequences showed that strain SCSIO 72103T formed a single clade with M. aquimaris SW105T. Strain SCSIO 72103T contained iso-C15 : 0 as the major fatty acid and the predominant respiratory quinone was menaquinone MK-6. These characteristics are consistent with those of F. baculatum SNL9T and M. aquimaris SW105T. Phosphatidylethanolamine, most notably, unidentified aminolipid and unidentified aminophospholipid were major polar lipids. Strain SCSIO 72103T had a single circular chromosome of 2.96 Mb with a DNA G+C content of 35.1 mol%. The average nucleotide identity, average amino acid identity (AAI) and digital DNA–DNA hybridization values showed that the pairwise similarities between SCSIO 72103T and the type strains of F. baculatum SNL9T and M. aquimaris SW105T were 78.5–80.5 %, 79.0–81.4 % and 22.7–22.8 %, respectively. The AAI values between species in this clade and the type species of Flavobacterium and Myroides were below the 65 % threshold, indicating that these species belong to a novel genus. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain SCSIO 72103T represents a new species of a novel genus, for which the name Paenimyroides aestuarii gen. nov. sp. nov. is proposed. The type strain is SCSIO 72103T (=KCTC 92043T=MCCC 1K06659T). It is also proposed that nine known species in the genera Flavobacterium and Myroides are reclassified as Paenimyroides species.

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Flavobacterium cloacae sp. nov., isolated from waste water

Cited by 16 publications

References 21 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

16S metabarcoding of the bacterial community of a poultry wastewater treatment plant in the Philippines

Paenimyroides aestuarii gen. nov. sp. nov., a novel bacterium isolated from sediment in the Pearl River Estuary and reclassification of five Flavobacterium and four Myroides species

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