Strain identifier

BacDive ID: 132419

Type strain: No

Species: Mongoliibacter ruber

Strain history: <- Y.-X. Wang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM 4-4 <- Y. Liu, YIM

NCBI tax ID(s): 1750599 (species)

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General

@ref: 24208

BacDive-ID: 132419

DSM-Number: 27929

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

description: Mongoliibacter ruber DSM 27929 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface water from haloalkaline lake.

NCBI tax id

  • NCBI tax id: 1750599
  • Matching level: species

strain history

  • @ref: 24208
  • history: <- Y.-X. Wang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM 4-4 <- Y. Liu, YIM

doi: 10.13145/bacdive132419.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Mongoliibacter
  • species: Mongoliibacter ruber
  • full scientific name: Mongoliibacter ruber Wang et al. 2016

@ref: 24208

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Mongoliibacter

species: Mongoliibacter ruber

full scientific name: Mongoliibacter ruber Wang et al. 2016

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43804negative1.3-2 µm0.3-0.4 µmrod-shapedno
69480negative99.984

colony morphology

  • @ref: 43804
  • colony color: Red
  • colony shape: circular
  • incubation period: 4 days
  • medium used: TSA, NA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43804TSA, NAyes
24208NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43804positivegrowth4-40
43804positiveoptimum25-28mesophilic
24208positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43804positivegrowth7.5-11.5alkaliphile
43804positiveoptimum8-11

Physiology and metabolism

oxygen tolerance

  • @ref: 43804
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.78

halophily

@refsaltgrowthtested relationconcentration
43804NaClpositivegrowth0-6 %(w/v)
43804NaClpositiveoptimum0.5-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4380435391aspartate-assimilation
4380417057cellobiose-assimilation
4380416899D-mannitol-assimilation
4380417924D-sorbitol-assimilation
4380465327D-xylose-assimilation
4380425115malate-assimilation
4380428300glutamine-assimilation
4380417266L-sorbose-assimilation
4380417268myo-inositol-assimilation
4380426986threonine-assimilation
4380417234glucose-fermentation
43804casein-hydrolysis
4380462968cellulose-hydrolysis
4380416991dna-hydrolysis
4380428017starch-hydrolysis
4380453423tween 40-hydrolysis
4380453426tween 80-hydrolysis
4380417632nitrate-reduction
4380416449alanine+assimilation
4380436219alpha-lactose+assimilation
4380422653asparagine+assimilation
4380416947citrate+assimilation
4380415824D-fructose+assimilation
4380412936D-galactose+assimilation
4380416024D-mannose+assimilation
4380463150D-rhamnose+assimilation
4380417234glucose+assimilation
4380430849L-arabinose+assimilation
4380417306maltose+assimilation
4380428053melibiose+assimilation
4380416634raffinose+assimilation
4380417992sucrose+assimilation
4380432528turanose+assimilation
438044853esculin+hydrolysis
438045291gelatin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4380428001vancomycinyesyes30 µg (disc)
4380417698chloramphenicolyesyes30 µg (disc)
43804100246norfloxacinyesyes10 µg (disc)
4380448923erythromycinyesyes15 µg (disc)
4380428077rifampicinyesyes5 µg (disc)
43804100241ciprofloxacinyesyes5 µg (disc)
438042637amikacinyesyes30 µg (disc)
4380417334penicillinyesyes10 Unit (disc)
4380428368novobiocinyesyes5 µg (disc)
4380428864tobramycinyesyes10 µg (disc)
4380428971ampicillinyesyes10 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4380415688acetoinno
4380416136hydrogen sulfideno
4380435581indoleno
6836935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
4380415688acetoin-
6836935581indole-

enzymes

@refvalueactivityec
43804arginine dihydrolase+3.5.3.6
43804urease+3.5.1.5
43804alkaline phosphatase+3.1.3.1
43804acid phosphatase+3.1.3.2
43804esterase (C 4)+
43804esterase Lipase (C 8)+
43804leucine arylamidase+3.4.11.1
43804valine arylamidase+
43804cystine arylamidase+3.4.11.3
43804trypsin+3.4.21.4
43804alpha-chymotrypsin+3.4.21.1
43804naphthol-AS-BI-phosphohydrolase+
43804alpha-galactosidase+3.2.1.22
43804alpha-glucosidase+3.2.1.20
43804N-acetyl-beta-glucosaminidase+3.2.1.52
43804lipase (C 14)-
43804beta-galactosidase-3.2.1.23
43804beta-glucosidase-3.2.1.21
43804beta-glucuronidase-3.2.1.31
43804alpha-mannosidase-3.2.1.24
43804alpha-fucosidase-3.2.1.51
43804catalase+1.11.1.6
43804cytochrome oxidase+1.9.3.1
43804tryptophan deaminase+4.1.99.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43804C15:0 anteiso3.3
    43804C15:1ω6c1.8
    43804C16:0 3OH2.5
    43804C16:1ω5c3.8
    43804C16:1ω7c / C16:1ω6c6.8
    43804C17:0 2OH1
    43804C17:1ω6c3.9
    43804C14:0 iso1.5
    43804C15:0 iso22.7
    43804C15:0 iso 3OH1.8
    43804C15:1 iso G3.2
    43804C16:0 iso5.6
    43804C16:0 iso 3OH4.9
    43804iso-C16:1G8.3
    43804C17:0 iso 3OH7.1
    43804C17:1 iso I / C17:1 anteiso B12.9
    43804C17:1 iso ω9c4.5
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA plates
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 5
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Agilent 7890
  • cutoff value:

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24208-----+++------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
24208surface water from haloalkaline lakeInner Mongolia, Hunsandake desert, Lake Dugerno (42° 41' N 115° 51' E)ChinaCHNAsia42.6833115.85
43804Surface water collected from the Dugerno lake (pH 9.5; 4 %, w/v, salinity), a haloalkaline lake located in the Hunsdake desertHunsandake dester, Inner MongoliaChinaCHNAsia42.683115.852011-09

isolation source categories

Cat1Cat2Cat3
#Condition#Saline
#Condition#Alkaline
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Surface water
#Environmental#Terrestrial#Desert

taxonmaps

  • @ref: 69479
  • File name: preview.99_174278.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_23509;97_29399;98_37532;99_174278&stattab=map
  • Last taxonomy: Mongoliibacter ruber subclade
  • 16S sequence: KT253329
  • Sequence Identity:
  • Total samples: 34
  • soil counts: 4
  • aquatic counts: 27
  • animal counts: 3

Safety information

risk assessment

  • @ref: 24208
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24208
  • description: Mongoliibacter ruber strain YIM 4-4 16S ribosomal RNA gene, complete sequence
  • accession: KT253329
  • length: 1511
  • database: ena
  • NCBI tax ID: 1750599

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mongoliibacter ruber DSM 27929GCA_003003005scaffoldncbi1750599
66792Mongoliibacter ruber strain DSM 279291750599.3wgspatric1750599
66792Mongoliibacter ruber DSM 279292731639260draftimg1750599

GC content

@refGC-contentmethod
4380443high performance liquid chromatography (HPLC)
2420843.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.121yes
gram-positiveno97.13no
anaerobicno98.342yes
aerobicyes89.718no
halophileno75.192no
spore-formingno93.287no
glucose-utilyes89.148no
thermophileno96.975yes
motileno92.818yes
glucose-fermentno90.209yes

External links

@ref: 24208

culture collection no.: DSM 27929, CCTCC AB 2012966, YIM 4-4

straininfo link

  • @ref: 90759
  • straininfo: 404964

literature

  • topic: Phylogeny
  • Pubmed-ID: 26652178
  • title: Mongoliibacter ruber gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae isolated from a haloalkaline lake.
  • authors: Wang YX, Liu YP, Huo QQ, Li YP, Feng FY, Xiao W, Ding ZG, Lai YH, Cui XL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000836
  • year: 2015

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24208Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27929Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27929)
43804Yong-Xia Wang, Ya-Peng Liu, Qing-Qing Huo, Ya-Ping Li, Fu-Ying Feng, Wei Xiao, Zhang-Gui Ding, Yong-Hong Lai, Xiao-Long CuiMongoliibacter ruber gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae isolated from a haloalkaline lake10.1099/ijsem.0.000836IJSEM 66: 1088-1094 201626652178
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
68369Automatically annotated from API 20NE
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
90759Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404964.1