Name: Microbacterium indicum BBH6
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7434

Type strain:

Species: Microbacterium indicum

Strain Designation: BBH6

Culture col. no.: DSM 19969, CIP 109607, IAM 15355, JCM 21800, LMG 23459

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

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

SI-ID 290079

LMG 23459, IAM 15355, JCM 21800, DSM 19969, CIP 109607

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium indicum**
	Full Scientific Name (LPSN)	Microbacterium indicum Shivaji et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31998]	Gram stain	positive
[Ref.: #120081]	Gram stain	positive

[Ref.: #31998]	Cell shape	rod-shaped
[Ref.: #120081]	Cell shape	rod-shaped

[Ref.: #120081]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90

[Ref.: #31998]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37787]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37787]

Culture medium growth

[Ref.: #37787]

Culture medium composition

expand / minimize

[Ref.: #120081]

Culture medium

CIP Medium 72

[Ref.: #120081]

Culture medium growth

[Ref.: #120081]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #31998]	growth	08-30 °C
[Ref.: #31998]	optimum	22 °C
[Ref.: #37787]	growth	25 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #31998]			optimum	7
[Ref.: #31998]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120081]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31998]		NaCl		growth	<6	%

[Ref.: #8414]	Murein short key	B06
[Ref.: #8414]	Murein types	B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

[Ref.: #67770]

Observation

quinones: MK-11, MK-12

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31998]	acetate ChEBI	+	carbon source
[Ref.: #31998]	arabinose ChEBI	+	carbon source
[Ref.: #31998]	arginine ChEBI	+	carbon source
[Ref.: #31998]	asparagine ChEBI	+	carbon source
[Ref.: #31998]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	esculin ChEBI	+	hydrolysis
[Ref.: #31998]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	lactose ChEBI	+	carbon source
[Ref.: #31998]	malonate ChEBI	+	carbon source
[Ref.: #31998]	maltose ChEBI	+	carbon source
[Ref.: #31998]	mannitol ChEBI	+	carbon source
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	nitrate ChEBI	+	reduction
[Ref.: #120081]	nitrate ChEBI	-	reduction
[Ref.: #120081]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	raffinose ChEBI	+	carbon source
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	ribose ChEBI	+	carbon source
[Ref.: #31998]	serine ChEBI	+	carbon source
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	sucrose ChEBI	+	carbon source
[Ref.: #31998]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31998]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120081]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120081]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #120081]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120081]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #120081]	11613	not determinedn.d.	+/-	-	-	+/-	-	+/-	-	-	-	+/-	+/-	-	+/-	-	-	-	-	+/-	-	-	+/-	-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	+/-	+/-	-	+/-	-	-	-	-	+/-	+/-	+/-	-	-	-	+/-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120081]	11995	-	-	-	-	-	+	-	-	-	-	+	-	+	+	-	+	+	-	+	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8414]	Sample type/isolated from	deep sea sediment
[Ref.: #8414]	Geographic location (country and/or sea, region)	Indian Ocean, Chagos Trench
[Ref.: #8414]	Country	India
[Ref.: #8414]	Country ISO 3 Code	IND
[Ref.: #8414]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Deep-sea sediment at a water depth of 5,904 m
[Ref.: #67770]	Geographic location (country and/or sea, region)	Chagos Trench
[Ref.: #67770]	Country	Indian Ocean

[Ref.: #120081]	Sample type/isolated from	Environment, Deep sea sediment
[Ref.: #120081]	Geographic location (country and/or sea, region)	Chagos trench, Indian Ocean
[Ref.: #120081]	Country	India
[Ref.: #120081]	Country ISO 3 Code	IND
[Ref.: #120081]	Continent	Asia
[Ref.: #120081]	Isolation date	2005
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8414]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120081]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Microbacterium indicum partial rRNA gene, type strain BBH6T	AM158907	1450	GenBank ENA	358100 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Microbacterium indicum DSM 19969	GCA_000422385	scaffold	GenBank ENA	1122238 tax ID
[Ref.: #66792]	Microbacterium indicum DSM 19969	1122238.3	wgs	PATRIC	1122238 tax ID	*
[Ref.: #66792]	Microbacterium indicum DSM 19969	2523533558	draft	JGI IMG/M	1122238 tax ID	*

[Ref.: #8414]	GC-content	65.5 mol%
[Ref.: #67770]	GC-content	65.5 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	71.4 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Microbacterium indicum DSM 19969 DSM 19969 NCBI: GCA_000422385.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbacterium indicum DSM 19969 PATRIC: 1122238.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.294	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.588	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	76.792	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	79.398	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90	no

Availability in culture collections External links

[Ref.: #8414]

Culture collection no.

DSM 19969, CIP 109607, IAM 15355, JCM 21800, LMG 23459

[Ref.: #76883]

SI-ID 290079

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site.	Anand S, Bala K, Saxena A, Schumann P, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.034439-0	2011	*
Phylogeny	Microbacterium 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 C	Int J Syst Evol Microbiol	10.1099/ijs.0.64782-0	2007	*

References

#8414

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19969

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#31998

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28252 (see below)

#37787 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76883

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID290079.1 )

#120081 Collection of Institut Pasteur ; Curators of the CIP; CIP 109607

#28252

IJSEM 1819 2007 ( DOI 10.1099/ijs.0.64782-0 , PubMed 17684264 )

* These data were automatically processed and therefore are not curated

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Microbacterium indicum DSM 19969 DSM 19969

Microbacterium indicum DSM 19969

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