Strain identifier

BacDive ID: 7434

Type strain: Yes

Species: Microbacterium indicum

Strain Designation: BBH6

Strain history: CIP <- 2007, S. Shivaji, CCMB, Hyderabad, India: strain BBH6

NCBI tax ID(s): 1122238 (strain), 358100 (species)

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General

@ref: 8414

BacDive-ID: 7434

DSM-Number: 19969

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-positive, rod-shaped

description: Microbacterium indicum BBH6 is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from deep sea sediment.

NCBI tax id

NCBI tax idMatching level
358100species
1122238strain

strain history

@refhistory
8414<- CIP <- S. Shivaji, MTCC; BBH6
377872007, S. Shivaji; CCMB, Hyderabad, India: strain BBH6
67770IAM 15355 <-- S. Shivaji BBH6.
120081CIP <- 2007, S. Shivaji, CCMB, Hyderabad, India: strain BBH6

doi: 10.13145/bacdive7434.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium indicum
  • full scientific name: Microbacterium indicum Shivaji et al. 2007

@ref: 8414

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium indicum

full scientific name: Microbacterium indicum Shivaji et al. 2007

strain designation: BBH6

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31998positiverod-shaped
120081positiverod-shapedno
69480no90

pigmentation

  • @ref: 31998
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37787MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120081CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
31998positivegrowth08-30
31998positiveoptimum22
37787positivegrowth25
67770positivegrowth28

culture pH

@refabilitytypepHPH range
31998positivegrowth05-09alkaliphile
31998positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 120081
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

  • @ref: 31998
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <6 %

murein

  • @ref: 8414
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3199830089acetate+carbon source
3199822599arabinose+carbon source
3199829016arginine+carbon source
3199822653asparagine+carbon source
3199817057cellobiose+carbon source
3199828757fructose+carbon source
3199817234glucose+carbon source
3199817716lactose+carbon source
3199815792malonate+carbon source
3199817306maltose+carbon source
3199829864mannitol+carbon source
3199816634raffinose+carbon source
3199833942ribose+carbon source
3199817822serine+carbon source
3199817992sucrose+carbon source
3199827082trehalose+carbon source
3199818222xylose+carbon source
319984853esculin+hydrolysis
3199817632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12008117632nitrate-reduction
12008116301nitrite-reduction

metabolite production

  • @ref: 120081
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
120081oxidase+
120081catalase+1.11.1.6
120081urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120081-----+----+-++-++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120081+/---+/--+/----+/-+/--+/-----+/---+/--+/-+/-+/-+/-+/-+/-+/--+/-+/--+/-----+/-+/-+/----+/-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
8414deep sea sedimentIndian Ocean, Chagos TrenchIndiaINDAsia
67770Deep-sea sediment at a water depth of 5,904 mChagos TrenchIndian Ocean
120081Environment, Deep sea sedimentChagos trench, Indian OceanIndiaINDAsia2005

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
84141Risk group (German classification)
1200811Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Microbacterium indicum partial rRNA gene, type strain BBH6T
  • accession: AM158907
  • length: 1450
  • database: nuccore
  • NCBI tax ID: 358100

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium indicum DSM 199691122238.3wgspatric1122238
66792Microbacterium indicum DSM 199692523533558draftimg1122238
67770Microbacterium indicum DSM 19969GCA_000422385scaffoldncbi1122238

GC content

@refGC-contentmethod
841465.5
6777065.5thermal denaturation, midpoint method (Tm)
6777071.4genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.294no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.588no
69480spore-formingspore-formingAbility to form endo- or exosporesno76.792no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.398no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97yes
69480flagellatedmotile2+Ability to perform flagellated movementno90no

External links

@ref: 8414

culture collection no.: DSM 19969, CIP 109607, IAM 15355, JCM 21800, LMG 23459

straininfo link

  • @ref: 76883
  • straininfo: 290079

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684264Microbacterium indicum sp. nov., isolated from a deep-sea sediment sample from the Chagos Trench, Indian Ocean.Shivaji S, Bhadra B, Rao RS, Chaturvedi P, Pindi PK, Raghukumar CInt J Syst Evol Microbiol10.1099/ijs.0.64782-02007Actinomycetales/classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny22039005Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site.Anand S, Bala K, Saxena A, Schumann P, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.034439-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, India, *Industrial Waste, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8414Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19969)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19969
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31998Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2825228776041
37787Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7369
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76883Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290079.1StrainInfo: A central database for resolving microbial strain identifiers
120081Curators of the CIPCollection of Institut Pasteur (CIP 109607)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109607