Flavobacterium
               
            
            hauense sp. nov., isolated from soil and emended descriptions of 
               
                  Flavobacterium subsaxonicum
               
            , 
               
                  Flavobacterium beibuense
               
             and 
               
                  Flavobacterium rivuli

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

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“…The description is as given by Dong et al (2013b) with the following modification. The genomic G+C content of the type strain is 41.6%.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…Antibiotic sensitivity tests were performed using the diffusion method (Fraser & Jorgensen, 1997) on LB agar and MuellerHinton agar with filter-paper discs (8 mm diameter) containing one of the following antibiotics: ampicillin (10 mg), amoxicillin (10 mg), bacitracin (0.04 U), carbenicillin (100 mg), cefradine (30 mg), chloromycetin (30 mg), erythromycin (15 mg), gentamicin (10 mg), kanamycin (30 mg), lincomycin (2 mg), novobiocin (30 mg), penicillin G (10 U), polymyxin (300 I), rifampicin (5 mg), roxithromycin (15 mg), spectinomycin (100 mg), streptomycin (Ali et al, 2009). Data for columns 1-6 marked with an asterisk were taken from Zhang et al (2015a), Dong et al (2013b), Fu et al (2011), Kaur et al (2012) and Yang et al (2015). The data for columns 1-6 were from this study.…”

Section: Flavobacterium Dongtanense Lw30 T (Gu073293)mentioning

confidence: 99%

Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata

Sun

Liu

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…lacus , and F . faecale have been released (Dong et al 2013; Fujii et al 2014; Jin et al 2014; Kim et al 2011, 2012, 2014; Lee et al 2013; Li et al 2014; Liu et al 2008; Subhash et al 2013; Xin et al 2009). In addition, papers describing the isolation of new Lysobacter strains including L .…”

Section: Introductionmentioning

confidence: 99%

Antibacterial activity of aquatic gliding bacteria

2016

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The study aimed to screen and isolate strains of freshwater aquatic gliding bacteria, and to investigate their antibacterial activity against seven common pathogenic bacteria. Submerged specimens were collected and isolated for aquatic gliding bacteria using four different isolation media (DW, MA, SAP2, and Vy/2). Gliding bacteria identification was performed by 16S rRNA gene sequencing and phylogenetic analysis. Crude extracts were obtained by methanol extraction. Antibacterial activity against seven pathogenic bacteria was examined by agar-well diffusion assay. Five strains of aquatic gliding bacteria including RPD001, RPD008, RPD018, RPD027 and RPD049 were isolated. Each submerged biofilm and plastic specimen provided two isolates of gliding bacteria, whereas plant debris gave only one isolate. Two strains of gliding bacteria were obtained from each DW and Vy/2 isolation medium, while one strain was obtained from the SAP2 medium. Gliding bacteria strains RPD001, RPD008 and RPD018 were identified as Flavobacterium anhuiense with 96, 82 and 96 % similarity, respectively. Strains RPD049 and RPD027 were identified as F. johnsoniae and Lysobacter brunescens, respectively, with similarity equal to 96 %. Only crude extract obtained from RPD001 inhibited growth of Listeria monocytogenes (MIC 150 µg/ml), Staphylococcus aureus (MIC 75 µg/ml) and Vibrio cholerae (MIC 300 µg/ml), but showed weak inhibitory effect on Salmonella typhimurium (MIC > 300 µg/ml). Gliding bacterium strain RPD008 should be considered to a novel genus separate from Flavobacterium due to its low similarity value. Crude extract produced by RPD001 showed potential for development as a broad antibiotic agent.

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Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum , Flavobacterium beibuense and Flavobacterium rivuli

Cited by 33 publications

References 33 publications

Genome-Based Taxonomic Classification of Bacteroidetes

Genome-Based Taxonomic Classification of Bacteroidetes

Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata

Antibacterial activity of aquatic gliding bacteria

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