Strain identifier

BacDive ID: 140994

Type strain: Yes

Species: Roseibium sediminis

Strain Designation: BSS09

Strain history: <- Xiao-Hua Zhang, Ocean Univ. of China

NCBI tax ID(s): 1775174 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 8.1 (current version)

General

@ref: 43880

BacDive-ID: 140994

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

description: Roseibium sediminis BSS09 is a facultative aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from surface sediment of Bohai Sea, PR China.

NCBI tax id

  • NCBI tax id: 1775174
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Xiao-Hua Zhang, Ocean Univ. of China

doi: 10.13145/bacdive140994.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Stappiaceae
  • genus: Roseibium
  • species: Roseibium sediminis
  • full scientific name: Roseibium sediminis Liu et al. 2017

@ref: 43880

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhodobacteraceae

genus: Roseibium

species: Roseibium sediminis

strain designation: BSS09

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43880negative2.0-4.0 µm0.5-0.8 µmrod-shapedyesmonotrichous
69480yes92.159
69480negative99.995

colony morphology

  • @ref: 43880
  • colony color: pale yellow
  • colony shape: circular
  • medium used: Marine agar 2216

Culture and growth conditions

culture medium

  • @ref: 43880
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43880positivegrowth10-45
43880positiveoptimum32mesophilic
67771positivegrowth35mesophilic

culture pH

@refabilitytypepH
43880positivegrowth5.0-8.0
43880positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43880facultative aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.946

halophily

@refsaltgrowthtested relationconcentration
43880NaClpositivegrowth1-7 %(w/v)
43880NaClpositiveoptimum4 %(w/v)

observation

  • @ref: 43880
  • observation: quinone Q-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43880casein-hydrolysis
43880dna-hydrolysis16991
43880starch-hydrolysis28017
438805-dehydro-D-gluconate+builds acid from58143
43880amygdalin+builds acid from27613
43880cellobiose+builds acid from17057
43880D-mannitol+builds acid from16899
43880D-sorbitol+builds acid from17924
43880turanose+builds acid from32528
43880gentiobiose+builds acid from28066
43880glycogen+builds acid from28087
43880lactose+builds acid from17716
43880melezitose+builds acid from6731
43880methyl alpha-D-glucopyranoside+builds acid from320061
43880methyl alpha-D-mannoside+builds acid from43943
43880N-acetylglucosamine+builds acid from506227
43880raffinose+builds acid from16634
43880salicin+builds acid from17814
43880starch+builds acid from28017
43880xylitol+builds acid from17151
438802-oxoglutarate+carbon source30916
438802,3-butanediol+carbon source62064
438804-hydroxy-L-proline+carbon source18240
43880acetate+carbon source30089
43880alpha-cyclodextrin+carbon source40585
43880alpha-D-glucose+carbon source17925
43880alpha-lactose+carbon source36219
438802-hydroxybutyrate+carbon source64552
43880beta-hydroxybutyrate+carbon source8295
43880cellobiose+carbon source17057
43880cis-aconitate+carbon source16383
43880citrate+carbon source16947
43880D-alanine+carbon source15570
43880D-arabitol+carbon source18333
43880D-fructose+carbon source15824
43880D-galacturonic acid+carbon source18024
43880D-gluconate+carbon source8391
43880D-glucosaminic acid+carbon source17784
43880D-glucose 6-phosphate+carbon source14314
43880D-glucuronate+carbon source15748
43880D-mannitol+carbon source16899
43880D-mannose+carbon source16024
43880D-saccharate+carbon source33801
43880D-serine+carbon source16523
43880D-sorbitol+carbon source17924
43880DL-carnitine+carbon source17126
43880lactate+carbon source24996
43880gamma-aminobutyric acid+carbon source16865
438804-hydroxybutyrate+carbon source16724
43880gentiobiose+carbon source28066
43880glycerol 1-phosphate+carbon source14336
43880glycogen+carbon source28087
43880glycyl L-aspartic acid+carbon source73804
43880inosine+carbon source17596
43880itaconate+carbon source17240
43880L-alanine 4-nitroanilide+carbon source
43880L-alanylglycine+carbon source73786
43880L-asparagine+carbon source17196
43880L-aspartate+carbon source29991
43880L-ornithine+carbon source15729
43880L-phenylalanine+carbon source17295
43880L-proline+carbon source17203
43880L-pyroglutamic acid+carbon source18183
43880L-rhamnose+carbon source62345
43880L-serine+carbon source17115
43880lactulose+carbon source6359
43880malonate+carbon source15792
43880maltose+carbon source17306
43880melibiose+carbon source28053
43880methyl pyruvate+carbon source51850
43880myo-inositol+carbon source17268
43880N-acetyl-L-glutamate+carbon source44337
43880N-acetylgalactosamine+carbon source28037
43880N-acetylglucosamine+carbon source506227
43880glycyl-l-glutamate+carbon source73784
43880propionate+carbon source17272
43880putrescine+carbon source17148
43880quinate+carbon source26490
43880raffinose+carbon source16634
43880succinamate+carbon source143136
43880succinate+carbon source30031
43880sucrose+carbon source17992
43880thymidine+carbon source17748
43880trehalose+carbon source27082
43880turanose+carbon source32528
43880uridine+carbon source16704
43880xylitol+carbon source17151
43880D-mannitol+fermentation16899
43880L-arabinose+fermentation30849
43880alginate+hydrolysis58187
43880tween 20+hydrolysis53424
43880tween 40+hydrolysis53423
43880tween 80+hydrolysis53426
43880amygdalin+oxidation27613
43880D-glucose+oxidation17634
43880D-sorbitol+oxidation17924
43880L-arabinose+oxidation30849
43880L-rhamnose+oxidation62345
43880melibiose+oxidation28053
43880myo-inositol+oxidation17268
43880sucrose+oxidation17992
43880nitrate+reduction17632
43880gelatin+/-hydrolysis5291

enzymes

@refvalueactivityec
43880cytochrome oxidase+1.9.3.1
43880catalase-1.11.1.6
43880alkaline phosphatase+3.1.3.1
43880esterase (C 4)+
43880esterase Lipase (C 8)+
43880leucine arylamidase+3.4.11.1
43880trypsin+3.4.21.4
43880alpha-galactosidase+3.2.1.22
43880alpha-glucosidase+3.2.1.20
43880alpha-mannosidase+3.2.1.24
43880lipase (C 14)-
43880valine arylamidase-
43880naphthol-AS-BI-phosphohydrolase-
43880acid phosphatase-3.1.3.2
43880N-acetyl-beta-glucosaminidase-3.2.1.52
43880cystine arylamidase-3.4.11.3
43880alpha-chymotrypsin-3.4.21.1
438806-phospho-beta-galactosidase-3.2.1.85
43880beta-glucosidase-3.2.1.21
43880beta-glucuronidase-3.2.1.31
43880alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    43880C15:0 anteiso3.1
    43880C16:01.4
    43880C18:02.7
    43880C18:1ω7c72.7
    43880C18:1ω9c1.3
    43880C20:1ω7c2.1
    43880C20:1ω9c1.5
    43880unknown 10.928 / C12:0 aldehyde9.3
    43880unknown 18.8141.518814
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 0.5
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture temperature
43880surface sediment of Bohai Sea, PR China2015-09Bohai SeaChinaCHNAsia38.3203118.996Marine agar 221628
67771From surface mud of the Bohai SeaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Sequence information

16S sequences

  • @ref: 43880
  • description: 16S rRNA gene sequence
  • accession: KU321206
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseibium sediminis KCTC 52373GCA_008711325contigncbi1775174
66792Roseibium sediminis strain KCTC 523731775174.3wgspatric1775174
66792Roseibium sediminis KCTC 523732889952345draftimg1775174

GC content

  • @ref: 43880
  • GC-content: 57.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.178yes
gram-positiveno98.936yes
anaerobicno97.938no
aerobicyes90.901no
halophileno58.071no
spore-formingno94.369no
thermophileno95.309yes
glucose-utilyes91.201yes
flagellatedyes80.928yes
glucose-fermentno90.656no

External links

@ref: 43880

culture collection no.: KCTC 52373, MCCC 1K03201

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28857737Roseibium sediminis sp. nov., isolated from sea surface sediment.Liu J, Wang Y, Yang X, Sun Z, Ren Q, Zhang Y, Liu J, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0020342017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny34846293Roseibium limicola sp. nov., isolated from tidal mudflat.Weerawongwiwat V, Kim JH, Yoon JH, Suh MK, Kim HS, Lee JS, Sukhoom A, Kim WInt J Syst Evol Microbiol10.1099/ijsem.0.0050972021Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43880Jiwen Liu, Yanan Wang, Xiaoting Yang, Zhongcheng Sun, Qiaomeng Ren, Yan Zhang, Ji Liu, Xiao-Hua ZhangRoseibium sediminis sp. nov., isolated from sea surface sediment10.1099/ijsem.0.002034IJSEM 67: 2862-2867 201728857737
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1