Name: Alkalibacterium iburiense M3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134116

Type strain:

Species: Alkalibacterium iburiense

Strain Designation: M3

Culture col. no.: JCM 12662, NCIMB 14024, BCRC 17791, CIP 108873

Strain history: CIP <- 2005, JCM <- 2004, I. Yumoto, Hokkaido Univ., Sapporo, Japan: strain M3

NCBI tax ID(s): 290589 (species)

SI-ID 237162

NCIMB 14024, JCM 12662, CIP 108873, BCRC 17791

Section

Alkalibacterium iburiense M3 is a facultative anaerobe, Gram-positive, motile bacterium that was isolated from Contaminated culture in alkali broth.

Gram-positive
motile
rod-shaped
facultative anaerobe
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Carnobacteriaceae*
	Genus	*Alkalibacterium*
	Species	**Alkalibacterium iburiense**
	Full Scientific Name (LPSN)	Alkalibacterium iburiense Nakajima et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31409]	Gram stain	positive
[Ref.: #120037]	Gram stain	positive

[Ref.: #31409]	Cell length	1.3-2.7 µm

[Ref.: #31409]	Cell width	0.5-0.7 µm

[Ref.: #31409]	Cell shape	rod-shaped
[Ref.: #120037]	Cell shape	rod-shaped

[Ref.: #31409]	Motility	yes
[Ref.: #120037]	Motility	yes

[Ref.: #120037]

Hemolysis ability

Information on culture and growth conditions Culture and growth conditions

[Ref.: #38351]

Culture medium

MEDIUM 7 - for Actinomyces

[Ref.: #38351]

Culture medium growth

[Ref.: #38351]

Culture medium composition

expand / minimize

[Ref.: #120037]

Culture medium

CIP Medium 7

[Ref.: #120037]

Culture medium growth

[Ref.: #120037]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120037]

Culture medium

CIP Medium 72

[Ref.: #120037]

Culture medium growth

[Ref.: #120037]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #31409]	growth	5.0-45.0 °C
[Ref.: #31409]	optimum	33.5 °C
[Ref.: #38351]	growth	37 °C
[Ref.: #67770]	growth	27 °C

[Ref.: #31409]	Temperature range	mesophilic
[Ref.: #38351]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31409]			optimum	10.5
[Ref.: #31409]			growth	09-12

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31409]	Oxygen tolerance	facultative anaerobe
[Ref.: #120037]	Oxygen tolerance	facultative anaerobe

[Ref.: #31409]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31409]		NaCl		growth	0-14	%
[Ref.: #31409]		NaCl		optimum	8	%

[Ref.: #31409]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31409]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol 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-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31409]	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.: #31409]	glucosamine ChEBI	+	carbon source
[Ref.: #31409]	glucose ChEBI	+	carbon source
[Ref.: #31409]	glycogen 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.: #31409]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31409]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside 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.: #120037]	nitrate ChEBI	+	reduction
[Ref.: #120037]	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.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31409]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31409]	sucrose ChEBI	+	carbon source
[Ref.: #31409]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31409]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120037]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120037]	alcohol dehydrogenase	+	1.1.1.1
[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.: #120037]	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.: #120037]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120037]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120037]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120037]	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.: #120037]	11410	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.: #120037]	11524	-	+	+	+	-	+	-	-	-	-	+	+	-	+	-	+	+	-	-	-

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

[Ref.: #67770]	Sample type/isolated from	Contaminated culture in alkali broth
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #120037]	Sample type/isolated from	Contaminated culture in alkali broth
[Ref.: #120037]	Country	Japan
[Ref.: #120037]	Country ISO 3 Code	JPN
[Ref.: #120037]	Continent	Asia
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AB188091 (>99% sequence identity) for Alkalibacterium iburiense subclade from Microbeatlas

Aquatic Samples	86
Soil Samples	125
Animal Samples	406
Plant Samples	23
Total Samples	640

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

[Ref.: #120037]

Biosafety level

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.: #31409]	Alkalibacterium iburiense gene for 16S rRNA, partial sequence, strain:M3	AB188091	1485	GenBank	290589 tax ID

[Ref.: #31409]	GC-content	42.9 mol%
[Ref.: #67770]	GC-content	42.6-43.2 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #31409]

Culture collection no.

JCM 12662, NCIMB 14024, BCRC 17791, CIP 108873

[Ref.: #91718]

SI-ID 237162

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Alkalibacterium iburiense sp. nov., an obligate alkaliphile that reduces an indigo dye.	Nakajima K, Hirota K, Nodasaka Y, Yumoto I	Int J Syst Evol Microbiol	10.1099/ijs.0.63487-0	2005	*

References

#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 )

#31409

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 #27718 (see below)

#38351 ; Curators of the CIP;
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#69479

João 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 beta .

#91718

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-ID237162.1 )

#120037 Collection of Institut Pasteur ; Curators of the CIP; CIP 108873

#27718

IJSEM 1525 2005 ( DOI 10.1099/ijs.0.63487-0 , PubMed 16014476 )

* These data were automatically processed and therefore are not curated

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