Labilibacter aurantiacus gen. nov., sp. nov., isolated from sea squirt (Styela clava) and reclassification of Saccharicrinis marinus as Labilibacter marinus comb. nov.

Lü, Dan; Zhao, Jinxin; Wang, Fengqing; Xie, Zhihong; Du, Zong‐Jun

doi:10.1099/ijsem.0.001649

Cited by 24 publications

(6 citation statements)

References 21 publications

(26 reference statements)

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“…Moreover, the fatty acid pro le showed differences of the major cellular fatty acids of strain Ai-910 T with its closest reference strains (Table S6). The respiratory quinone of strain Ai-910 T was MK-7, similar to other members in the family Marinilabiliaceae (Miyazaki et al 2012;Lu et al 2017).…”

Section: Biochemical and Chemotaxonomic Characterizationsupporting

confidence: 54%

Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales

Huang,

Zhang,

Sun

et al. 2024

Arch Microbiol

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A strictly anaerobic, motile bacterium, designated as strain Ai-910 T , was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gramstain-negative rods. Optimal growth was observed at 38°C (growth range 25-42°C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C 15 : 0 and anteiso-C 15 : 0 . The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain Ai-910 T formed a distinct phylogenetic lineage that re ects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkali exus imshenetskii Z-7010 T (92.78%), Alkalitalea saponilacus SC/BZ-SP2 T (92.51%), and Geo lum rubicundum JAM-BA0501 T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910 T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910 T represented a novel species. The average amino acid identity between strain Ai-910 T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910 T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%.Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910 T from its close relatives suggest that strain Ai-910 T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910 T (= CGMCC 1.17893 T = KCTC 25304 T ).

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Section: Biochemical and Chemotaxonomic Characterizationsupporting

confidence: 54%

Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales

Huang,

Zhang,

Sun

et al. 2024

Arch Microbiol

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“…Labilibacter (Lu et al, 2017) appeared as paraphyletic in the GBDP and rRNA gene trees (Figure 5, Supplementary Data Sheet 1) because Saccharicrinis (Liu et al, 2014b; Yang S.-H. et al, 2014) formed the sister group of L. marinus (Lu et al, 2017) with high support. While originally placed in Saccharicrinis as S. marinus (Liu Q.-Q.…”

Section: Resultsmentioning

confidence: 99%

“…et al, 2015), it had been reclassified in Labilibacter in a study in which a 16S rRNA gene tree showed it to form a clade together with the type species of Labilibacter , in contrast to our phylogenetic analyses. Some phenotypic differences such as temperature range for growth and fatty acids (Supplementary Table 1) were proposed as suggestive of separating the two genera (Lu et al, 2017) but it was not clarified which character states were apomorphies of which taxon. The known polar-lipid spectra are basically identical between the two genera.…”

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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“…The strain AAT T contains 14 SusC protein genes and 6 SusD protein genes (Supplementary Table 1). (Lu et al, 2017).…”

Section: Carbohydrate-active Enzymes and Analysis Of Susc And Susd Genesmentioning

confidence: 99%

Characterization of Plebeiobacterium marinum gen. nov., sp. nov. and Plebeiobacterium sediminum sp. nov., revealing the potential nitrogen fixation capacity of the order Marinilabiliales

Liang

et al. 2023

Front. Mar. Sci.

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Biological nitrogen fixation plays a crucial role in the marine nitrogen cycle, impacting global marine productivity and related carbon fluxes. The strains were analyzed by gene annotation, growth conditions and phylogenetic analysis of 16S rRNA gene sequences.These two strains were isolated from the coastal sediment at Xiaoshi Island in Weihai, China. The strains were analyzed by gene annotation, growth conditions and phylogenetic analysis of 16S rRNA gene sequences. It was revealed that strains D04T and AATT contain a set of nif gene clusters responsible for nitrogen fixation. Cell are yellow-colored, Gram-stain-negative, facultatively anaerobic, and rod-shaped bacteria. The optimal growth conditions for strain D04T were found to be at 33 °C, pH 7.0, and in 2% (w/v) NaCl, while strain AATT prefers growth conditions at 33 °C, pH 6.5, and in 3% (w/v) NaCl. The highest similarity of strains D04T and AATT was to Saccharicrinis fermentans NBRC 15936T, with a similarity of 94.1% and 94.8%, respectively. The 16S rRNA gene sequence similarity between the two strains was 96.6%. These novel strains were found to represent new taxa of the Marinilabiliaceae family, and we propose the names Plebeiobacterium marinum gen. nov., sp. nov. and Plebeiobacterium sediminum sp. nov. with type strains D04T (MCCC 1H00493T = KCTC 92026T) and AATT (MCCC 1H00485T = KCTC 92028T), respectively. In this study, nitrogen fixation genes were predicted for 53 strains from the whole order Marinilabiliales and it was found that nitrogen fixation gene clusters were present in 26 strains. These gene clusters were found in every family in the order, highlighting that the presence of nitrogen-fixing gene clusters in the order is common. Nitrogen-fixing bacteria in sediments play an important role in various biogeochemical cycles. Thus, understanding the oceanic nitrogen cycle can provide insights into the energy flow of marine systems.

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Labilibacter aurantiacus gen. nov., sp. nov., isolated from sea squirt (Styela clava) and reclassification of Saccharicrinis marinus as Labilibacter marinus comb. nov.

Cited by 24 publications

References 21 publications

Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales

Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales

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

Characterization of Plebeiobacterium marinum gen. nov., sp. nov. and Plebeiobacterium sediminum sp. nov., revealing the potential nitrogen fixation capacity of the order Marinilabiliales

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