Name: Endobacter medicaginis M1MS02
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133844

Type strain:

Species: Endobacter medicaginis

Strain Designation: M1MS02, MIMS02

Culture col. no.: LMG 26838, CECT 8088, CIP 110365

Strain history: CIP <- 2012, MH Ramirez-Bahena, IRNASA-CSIC, Salamanca, Spain: strain MIMS02

NCBI tax ID(s): 1181271 (species)

SI-ID 379236

LMG 26838, CECT 8088, CIP 110365

Special Collections

Section

Endobacter medicaginis M1MS02 is an aerobe, Gram-negative, motile bacterium that was isolated from Plant, Root nodules of Medicago sativa.

Gram-negative
motile
rod-shaped
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Endobacter*
	Species	**Endobacter medicaginis**
	Full Scientific Name (LPSN)	Endobacter medicaginis Ramírez-Bahena et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30659]	Gram stain	negative
[Ref.: #120868]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %94.828

[Ref.: #30659]	Cell shape	rod-shaped
[Ref.: #120868]	Cell shape	ovoid-shaped

[Ref.: #30659]	Motility	yes
[Ref.: #120868]	Motility	no

[Ref.: #30659]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #34724]

Culture medium

MEDIUM 600 - for Desovia neptuniae

[Ref.: #34724]

Culture medium growth

[Ref.: #34724]

Culture medium composition

expand / minimize

[Ref.: #120868]

Culture medium

CIP Medium 600

[Ref.: #120868]

Culture medium growth

[Ref.: #120868]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #30659]	growth	20-37 °C
[Ref.: #30659]	optimum	28 °C
[Ref.: #34724]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30659]			optimum	6
[Ref.: #30659]			growth	3.5-7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30659]

Oxygen tolerance

aerobe

[Ref.: #30659]

Ability of spore formation

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30659]	glutamate ChEBI	+	carbon source
[Ref.: #30659]	mannitol ChEBI	+	carbon source
[Ref.: #120868]	nitrate ChEBI	+	reduction
[Ref.: #120868]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120868]		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.: #30659]	catalase	+	1.11.1.6
[Ref.: #120868]	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.: #120868]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120868]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #120868]	12552	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #120868]	Sample type/isolated from	Plant, Root nodules of Medicago sativa
[Ref.: #120868]	Geographic location (country and/or sea, region)	Salamanca
[Ref.: #120868]	Country	Spain
[Ref.: #120868]	Country ISO 3 Code	ESP
[Ref.: #120868]	Continent	Europe
[Ref.: #120868]	Isolation date	2011
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence JQ436923 (>99% sequence identity) for Endobacter medicaginis subclade from Microbeatlas

Aquatic Samples	325
Soil Samples	556
Animal Samples	1194
Plant Samples	226
Total Samples	2301

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

[Ref.: #120868]

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.: #30659]	Endobacter medicaginis strain M1MS02 16S ribosomal RNA gene, partial sequence	JQ436923	1492	GenBank ENA	1181271 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Endobacter medicaginis CECT 8088	GCA_014192375	scaffold	GenBank ENA	1181271 tax ID	*
[Ref.: #66792]	Endobacter medicaginis LMG 26838	GCA_013376135	contig	GenBank ENA	1181271 tax ID	*
[Ref.: #66792]	Endobacter medicaginis strain CECT 8088	1181271.5	wgs	PATRIC	1181271 tax ID	*
[Ref.: #66792]	Endobacter medicaginis strain LMG 26838	1181271.4	wgs	PATRIC	1181271 tax ID	*
[Ref.: #66792]	Endobacter medicaginis CECT 8088	2824439340	draft	JGI IMG/M	1181271 tax ID	*
[Ref.: #66792]	Endobacter medicaginis M1MS02	GCA_026341395	contig	GenBank ENA	1181271 tax ID	*

[Ref.: #30659]

GC-content

60.3 mol%

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: Endobacter medicaginis CECT 8088 NCBI: GCA_014192375.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	68	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Endobacter medicaginis CECT 8088 NCBI: GCA_014192375.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	94.828	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	90.021	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.7	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.569	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.964	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	68.522	no

Availability in culture collections External links

[Ref.: #30659]

Culture collection no.

LMG 26838, CECT 8088, CIP 110365

[Ref.: #91617]

SI-ID 379236

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil.	Ramirez-Bahena MH, Tejedor C, Martin I, Velazquez E, Peix A	Int J Syst Evol Microbiol	10.1099/ijs.0.041368-0	2012	*

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 )

#30659

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 #26990 (see below)

#34724 ; 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) .

#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 .

#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 )

#91617

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-ID379236.1 )

#120868 Collection of Institut Pasteur ; Curators of the CIP; CIP 110365

#26990

IJSEM 1760 2013 ( DOI 10.1099/ijs.0.041368-0 , PubMed 23002052 )

* These data were automatically processed and therefore are not curated

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Endobacter medicaginis CECT 8088

Endobacter medicaginis CECT 8088

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