Strain identifier

BacDive ID: 166258

Type strain: Yes

Species: Confluentibacter sediminis

Strain Designation: DSL-48

NCBI tax ID(s): 2219045 (species)

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General

@ref: 68224

BacDive-ID: 166258

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Confluentibacter sediminis DSL-48 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 2219045
  • Matching level: species

doi: 10.13145/bacdive166258.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Confluentibacter
  • species: Confluentibacter sediminis
  • full scientific name: Confluentibacter sediminis Wei et al. 2019

@ref: 68224

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Confluentibacter

species: Confluentibacter sediminis

strain designation: DSL-48

type strain: yes

Morphology

cell morphology

  • @ref: 68224
  • gram stain: negative
  • cell length: 1.9-4.0 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 68224
  • colony size: 0.5-1.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Marine agar (MA)

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
68224positivegrowth4-37
68224positiveoptimum35mesophilic

culture pH

@refabilitytypepHPH range
68224positivegrowth5-10alkaliphile
68224positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 68224
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
68224NaClpositivegrowth0-7 %(w/v)
68224NaClpositiveoptimum4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
682244853esculin+hydrolysis
6822428017starch+hydrolysis
682245291gelatin+hydrolysis
6822417634D-glucose+fermentation
6822417632nitrate-reduction
6822417634D-glucose+assimilation
6822430849L-arabinose+assimilation
6822416024D-mannose+assimilation
6822416899D-mannitol-assimilation
6822459640N-acetylglucosamine-assimilation
6822417306maltose-assimilation
6822432032potassium gluconate-assimilation
6822417120hexanoate-assimilation
6822417128adipate-assimilation
6822425115malate-assimilation
6822453258sodium citrate-assimilation
6822418401phenylacetate-assimilation
6822430796(R)-malic acid-carbon source
6822416651(S)-lactate-carbon source
6822430797(S)-malic acid-carbon source
68224645522-hydroxybutyrate-carbon source
68224167632-oxobutanoate-carbon source
68224168102-oxoglutarate-carbon source
68224370543-hydroxybutyrate-carbon source
68224739183-O-methyl-D-glucose-carbon source
68224181014-hydroxyphenylacetic acid-carbon source
6822416411acetic acid-carbon source
6822413705acetoacetate-carbon source
6822417925alpha-D-glucose+carbon source
6822436219alpha-lactose+carbon source
6822473706bromosuccinate-carbon source
6822416947citrate-carbon source
6822418333D-arabitol-carbon source
6822429990D-aspartate-carbon source
6822417057cellobiose+carbon source
6822415824D-fructose+carbon source
6822478697D-fructose 6-phosphate-carbon source
6822428847D-fucose+carbon source
6822412936D-galactose+carbon source
6822418024D-galacturonic acid+carbon source
6822430612D-glucarate-carbon source
682248391D-gluconate-carbon source
6822414314D-glucose 6-phosphate+carbon source
6822415748D-glucuronate+carbon source
6822417306maltose-carbon source
6822416899D-mannitol-carbon source
6822416024D-mannose+carbon source
6822428053melibiose-carbon source
6822416634raffinose-carbon source
6822416523D-serine-carbon source
6822417924D-sorbitol-carbon source
6822416551D-trehalose-carbon source
6822432528turanose-carbon source
6822415740formate-carbon source
6822416537galactarate-carbon source
6822416865gamma-aminobutyric acid-carbon source
682245291gelatin+carbon source
6822428066gentiobiose-carbon source
6822432323glucuronamide-carbon source
6822417754glycerol-carbon source
6822470744glycine-proline+carbon source
6822417596inosine-carbon source
6822416977L-alanine-carbon source
6822416467L-arginine-carbon source
6822429991L-aspartate+carbon source
6822418287L-fucose-carbon source
6822417464L-galactonic acid gamma-lactone+carbon source
6822429988L-glutamate+carbon source
6822415971L-histidine-carbon source
6822457606L-pyroglutamate-carbon source
6822462345L-rhamnose+carbon source
6822417115L-serine-carbon source
6822474611methyl (R)-lactate-carbon source
68224320055methyl beta-D-glucopyranoside-carbon source
6822451850methyl pyruvate-carbon source
6822417268myo-inositol-carbon source
6822463153N-acetyl-D-mannosamine-carbon source
6822428800N-acetylgalactosamine-carbon source
6822459640N-acetylglucosamine-carbon source
6822435418n-acetylneuraminate-carbon source
6822417309pectin+carbon source
6822417272propionate-carbon source
6822426490quinate-carbon source
6822417814salicin-carbon source
6822417164stachyose-carbon source
6822417992sucrose+carbon source
6822453423tween 40-carbon source
682241 % sodium lactate+carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
6822429673rifamycin svyesyes
6822448607lithium chlorideyesyes
6822475248potassium telluriteyesyes
68224161680aztreonamyesyes

metabolite production

  • @ref: 68224
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68224catalase-1.11.1.6
68224cytochrome oxidase+1.9.3.1
68224urease-3.5.1.5
68224arginine dihydrolase-3.5.3.6
68224alkaline phosphatase+3.1.3.1
68224lipase (C 14)+
68224leucine arylamidase+3.4.11.1
68224valine arylamidase+
68224cystine arylamidase+3.4.11.3
68224acid phosphatase+3.1.3.2
68224naphthol-AS-BI-phosphohydrolase+
68224beta-galactosidase+3.2.1.23
68224N-acetyl-beta-glucosaminidase+3.2.1.52
68224esterase (C 4)-
68224esterase Lipase (C 8)-
68224alpha-chymotrypsin-3.4.21.1
68224trypsin-3.4.21.4
68224alpha-galactosidase-3.2.1.22
68224beta-glucuronidase-3.2.1.31
68224alpha-glucosidase-3.2.1.20
68224beta-glucosidase-3.2.1.21
68224alpha-mannosidase-3.2.1.24
68224alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68224C16:04.2
    68224C15:0 iso31.6
    68224C15:0 anteiso10.5
    68224C15:1 iso G4.1
    68224C16:0 iso1.1
    68224C17:0 anteiso1.2
    68224C15:0 iso 3OH9.3
    68224C15:0 3OH2.6
    68224C15:0 2OH1.8
    68224C16:0 iso 3OH5.7
    68224C16:0 3OH1.1
    68224C17:0 iso 3OH13.8
    68224C17:0 2OH2
    68224C 15:1 w6c1.2
    68224C16:1 w6c/C16:1 w7c3.7
  • type of FA analysis: whole cell analysis
  • incubation medium: MB
  • incubation temperature: 35
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 68224
  • sample type: tidal flat sediment
  • sampling date: 2018-02-28
  • geographic location: East China Sea
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 30.885
  • longitude: 121.971
  • enrichment culture: marine agar 2216
  • enrichment culture duration: 2 days
  • enrichment culture temperature: 28

Sequence information

16S sequences

  • @ref: 68224
  • description: Confluentibacter sp. strain DSL-48 16S ribosomal RNA gene, partial sequence
  • accession: MK583532
  • length: 1394
  • database: ena
  • NCBI tax ID: 2219045

Genome sequences

  • @ref: 68224
  • description: Confluentibacter sediminis DSL-48
  • accession: GCA_003258355
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2219045

GC content

  • @ref: 68224
  • GC-content: 33.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.063no
gram-positiveno97.754no
anaerobicno99.328yes
aerobicyes85.271yes
halophileno79.909no
spore-formingno97.898no
glucose-utilyes89.08no
motileno90.231yes
glucose-fermentno80.986yes
thermophileno99.505yes

External links

@ref: 68224

culture collection no.: KCTC 62648, MCCC 1K03537

literature

  • topic: Phylogeny
  • Pubmed-ID: 31429814
  • title: Con fl uentibacter sediminis sp. nov., isolated from the junction between the ocean and a freshwater lake and emended description of the genus Confluentibacter.
  • authors: Wei Y, Wang K, Pei J, Zhang Y, Fang J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003665
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Geologic Sediments/*microbiology, Lakes/microbiology, Lipids/chemistry, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saline Waters, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
68224Yuli Wei, Ke Wang, Jiahao Pei, Yan Zhang and Jiasong FangCon?uentibacter sediminis sp. nov., isolated from the junction between the ocean and a freshwater lake and emended description of the genus Confluentibacter10.1099/ijsem.0.003665IJSEM 69: 3581-3585 2019