Chitinophaga dinghuensis sp. nov., isolated from soil

Lv, Ying-ying; Wang, Jia; You, Jichun; Qiu, Lihong

doi:10.1099/ijsem.0.000653

Cited by 18 publications

(7 citation statements)

References 30 publications

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“…The description is as before (Lv et al, 2015) with the following modification. The G+C content of the type-strain genome is 44.7%, its approximate size 7.12 Mbp, its IMG deposit 2731639224.…”

Section: Discussionmentioning

confidence: 99%

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: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…80% of our authors rate our submission process as 'excellent' or 'very good'. 5. Your article will be published on an interactive journal platform with advanced metrics.…”

Section: Funding Informationmentioning

confidence: 99%

“…For the time being, there are 27 species of the genus listed on LPSN (List of Prokaryotic Names with Standing in Nomenclature: www.bacterio.net). Most of the strains of the genus Chitinophaga were isolated from soil, such as forest soil [4,5], mountain soil [6] and plant rhizosphere soil [7][8][9], and they were also found in river sediment [2], wastewater [10], weathered rock [11], vermicompost [12] and plant [13].…”

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confidence: 99%

Chitinophaga alhagiae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia

Zou

Zhang

Song

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, non-flagellated, rod-shaped bacterium, designated strain T22 T , was isolated from rhizosphere soil of Alhagi sparsifolia, collected from Xinjiang, China. Its major fatty acids (>5 %) were iso-C 15 : 0 , C 16 : 1 !5c, iso-C 17 : 0-3OH, summed feature 1 (C 13 : 0 3-OH/iso-C 15 : 1 H) and summed feature 3 (C 16 : 1 !6c/C 16 : 1 !7c). The predominant respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, two aminolipids and four unidentified lipids. The DNA G+C content of the type strain was 53.4 mol%. According to phylogenetic analysis based on 16S rRNA gene sequences, strain T22 T was related most closely to Chitinophaga barathri YLT18 T (=CCTCC AB 2015054 T) with similarity of 97.7 %. However, strain T22 T was clearly distinguished from Chitinophaga barathri YLT18 T using genome-to-genome distance and average nucleotide identity value calculation, as well as a range of physiological and biochemical characteristics comparisons. It is obvious from the genotypic and phenotypic data that strain T22 T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga alhagiae sp. nov., is proposed. The type strain is T22 T (=ACCC 60125 T =KCTC 62518 T).

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“…All listed data were obtained in the present study. Data indicated within parentheses were taken from the appropriate literature [28][29][30]. Fatty acid analyses are presented in % and were conducted in duplicates.…”

Section: Protologuementioning

confidence: 99%

Chitinophaga extrema sp. nov., isolated from subsurface soil and leaf litter in a tropical peat swamp forest

Goh

Wong

Parimannan

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39′ 04.7′ N 101° 17′ 43.7′′ E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA–DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).

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Chitinophaga dinghuensis sp. nov., isolated from soil

Cited by 18 publications

References 30 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

Chitinophaga alhagiae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia

Chitinophaga extrema sp. nov., isolated from subsurface soil and leaf litter in a tropical peat swamp forest

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