Name: Arthrobacter ruber MDB1-42
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158722

Type strain:

Species: Arthrobacter ruber

Strain Designation: MDB1-42

Culture col. no.: CGMCC 1.9772, NBRC 113088

NCBI tax ID(s): 1258893 (species)

Section

Arthrobacter ruber MDB1-42 is an obligate aerobe, Gram-positive bacterium that forms circular colonies and was isolated from ice collected from the ice tongue surface of Midui glacier.

colony-forming
Gram-positive
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	*Micrococcaceae*
	Genus	*Arthrobacter*
	Species	**Arthrobacter ruber**
	Full Scientific Name (LPSN)	Arthrobacter ruber Liu et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65469]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #65469]	Cell length	1-1.2 µm

[Ref.: #65469]	Motility	no

[Ref.: #65469]	Colony size	1 mm
[Ref.: #65469]	Colony color	red
[Ref.: #65469]	Colony shape	circular
[Ref.: #65469]	Incubation period	4 days
[Ref.: #65469]	Cultivation medium used	Trypticase soy agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65469]

Culture medium

Trypticase soy agar

[Ref.: #65469]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #65469]			growth	0-34 °C
[Ref.: #65469]			optimum	25-28 °C

[Ref.: #65469]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65469]			optimum	7
[Ref.: #65469]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65469]

Oxygen tolerance

obligate aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.931
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65469]		NaCl		growth	0-4	%(w/v)

[Ref.: #65469]	Observation	cells occur singly, in pairs or in clusters
[Ref.: #65469]	Observation	polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, one unidentified glycolipid and one unidentified lipid
[Ref.: #65469]	Observation	peptidoglycan contains lysine, threonine and alanine. Rhamnose and galactose are the main sugar components of the whole-cell sugars
[Ref.: #65469]	Observation	predominant menaquinone is MK-9(H2)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65469]	(S)-lactate ChEBI	+	assimilation
[Ref.: #65469]	2-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #65469]	2-oxobutanoate ChEBI	+	carbon source
[Ref.: #65469]	4-hydroxyphenylacetic acid ChEBI	+	carbon source
[Ref.: #65469]	acetoacetate ChEBI	+	assimilation
[Ref.: #65469]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #65469]	alpha-D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #65469]	bromosuccinate ChEBI	+	carbon source
[Ref.: #65469]	casein	-	hydrolysis
[Ref.: #65469]	cellobiose ChEBI	+	carbon source
[Ref.: #65469]	citrate ChEBI	+	carbon source
[Ref.: #65469]	D-fructose ChEBI	+	carbon source
[Ref.: #65469]	D-fructose 6-phosphate ChEBI	+	assimilation
[Ref.: #65469]	D-galactose ChEBI	+	carbon source
[Ref.: #65469]	D-gluconate ChEBI	+	carbon source
[Ref.: #65469]	D-malate ChEBI	+	carbon source
[Ref.: #65469]	D-mannitol ChEBI	+	carbon source
[Ref.: #65469]	D-mannose ChEBI	+	carbon source
[Ref.: #65469]	D-sorbitol ChEBI	+	carbon source
[Ref.: #65469]	dextrin ChEBI	+	carbon source
[Ref.: #65469]	esculin ChEBI	+	hydrolysis
[Ref.: #65469]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #65469]	gelatin ChEBI	+	carbon source
[Ref.: #65469]	gelatin ChEBI	+	hydrolysis
[Ref.: #65469]	glucuronamide ChEBI	+	assimilation
[Ref.: #65469]	glycerol ChEBI	+	carbon source
[Ref.: #65469]	glycine-proline ChEBI	+	carbon source
[Ref.: #65469]	inosine ChEBI	+	carbon source
[Ref.: #65469]	L-alanine ChEBI	+	carbon source
[Ref.: #65469]	L-arginine ChEBI	+	carbon source
[Ref.: #65469]	L-aspartate ChEBI	+	carbon source
[Ref.: #65469]	L-glutamate ChEBI	+	carbon source
[Ref.: #65469]	L-histidine ChEBI	+	carbon source
[Ref.: #65469]	L-malate ChEBI	+	carbon source
[Ref.: #65469]	L-rhamnose ChEBI	+	carbon source
[Ref.: #65469]	L-serine ChEBI	+	carbon source
[Ref.: #65469]	maltose ChEBI	+	carbon source
[Ref.: #65469]	nitrate ChEBI	-	reduction
[Ref.: #65469]	pectin ChEBI	+	carbon source
[Ref.: #65469]	propionate ChEBI	+	carbon source
[Ref.: #65469]	sodium citrate ChEBI	+	assimilation
[Ref.: #65469]	starch ChEBI	-	hydrolysis
[Ref.: #65469]	sucrose ChEBI	+	carbon source
[Ref.: #65469]	trehalose ChEBI	+	carbon source
[Ref.: #65469]	turanose ChEBI	+	carbon source
[Ref.: #65469]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65469]		sulfide ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #65469]		acetoin ChEBI	+
[Ref.: #65469]		indole ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #65469]	acid phosphatase	-	3.1.3.2
[Ref.: #65469]	alkaline phosphatase	-	3.1.3.1
[Ref.: #65469]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65469]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65469]	alpha-galactosidase	+	3.2.1.22
[Ref.: #65469]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65469]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65469]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65469]	beta-galactosidase	+	3.2.1.23
[Ref.: #65469]	beta-glucosidase	+	3.2.1.21
[Ref.: #65469]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65469]	catalase	+	1.11.1.6
[Ref.: #65469]	cystine arylamidase	-	3.4.11.3
[Ref.: #65469]	cytochrome oxidase	-	1.9.3.1
[Ref.: #65469]	esterase (C 4)	+
[Ref.: #65469]	esterase Lipase (C 8)	+
[Ref.: #65469]	leucine arylamidase	+	3.4.11.1
[Ref.: #65469]	lipase (C 14)	+
[Ref.: #65469]	lysine decarboxylase	-	4.1.1.18
[Ref.: #65469]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65469]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65469]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #65469]	trypsin	-	3.4.21.4
[Ref.: #65469]	tryptophan deaminase	-	4.1.99.1
[Ref.: #65469]	urease	-	3.5.1.5
[Ref.: #65469]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #65469]	Sample type/isolated from	ice collected from the ice tongue surface of Midui glacier
[Ref.: #65469]	Geographic location (country and/or sea, region)	Tibet
[Ref.: #65469]	Country	China
[Ref.: #65469]	Country ISO 3 Code	CHN
[Ref.: #65469]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Glacier
#Environmental	#Aquatic	#Ice

What are isolation sources categories?

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.: #65469]	16S rRNA gene sequence	JX949648		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Arthrobacter ruber MDB1-42	GCA_002954225	contig	GenBank	1258893 tax ID	*
[Ref.: #66792]	Arthrobacter ruber strain MDB1-42	1258893.3	wgs	PATRIC	1258893 tax ID	*
[Ref.: #66792]	Arthrobacter ruber MDB1-42	2859220365	draft	JGI IMG/M	1258893 tax ID	*

[Ref.: #65469]

GC-content

69 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Arthrobacter ruber strain MDB1-42 PATRIC: 1258893.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arthrobacter ruber strain MDB1-42 PATRIC: 1258893.3
[Ref.: #69480]	motile	yes	56.597	no
[Ref.: #69480]	gram-positive	yes	91.7	no
[Ref.: #69480]	anaerobic	no	99.504	yes
[Ref.: #69480]	aerobic	yes	95.174	yes
[Ref.: #69480]	halophile	no	80.576	no
[Ref.: #69480]	spore-forming	no	89.488	no
[Ref.: #69480]	thermophile	no	99.21	yes
[Ref.: #69480]	glucose-util	yes	84.762	yes
[Ref.: #69480]	flagellated	no	90.619	yes
[Ref.: #69480]	glucose-ferment	no	87.373	no

Availability in culture collections External links

[Ref.: #65469]

Culture collection no.

CGMCC 1.9772, NBRC 113088

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arthrobacter crusticola sp. nov., Isolated from Biological Soil Crusts in the Mu Us Sandy Land, China.	Liu L, Liang L, He S, Xu L, Chi M, Shi S, Zhang X, Li L	Curr Microbiol	10.1007/s00284-020-02070-8	2020	*
Phylogeny	Arthrobacter ruber sp. nov., isolated from glacier ice.	Liu Q, Xin YH, Chen XL, Liu HC, Zhou YG, Chen WX	Int J Syst Evol Microbiol	10.1099/ijsem.0.002719	2018	*

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 )

#65469

Qing Liu, Yu-Hua Xin, Xiu-Ling Chen, Hong-Can Liu, Yu-Guang Zhou, Wen-Xin Chen: Arthrobacter ruber sp. nov., isolated from glacier ice. IJSEM 68: 1616 - 1621 2018 ( DOI 10.1099/ijsem.0.002719 , PubMed 29561255 )

#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) .

#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 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Arthrobacter ruber in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Arthrobacter ruber strain MDB1-42

Arthrobacter ruber strain MDB1-42

Change proposal

Change proposal