Name: Jatrophihabitans endophyticus S9-650
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23030

Type strain:

Species: Jatrophihabitans endophyticus

Strain Designation: S9-650

Culture col. no.: DSM 45627, KACC 16232

Strain history: <- M. Munusamy, National University of Singapore, Temasek Life Scs. Lab.; S9-650

NCBI tax ID(s): 1206085 (species)

SI-ID 402501

DSM 45627

Section

Jatrophihabitans endophyticus S9-650 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface sterilized stem tissue of Jatropha curcas L..

Gram-positive
rod-shaped
aerobe
mesophilic
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	*Jatrophihabitantales*
	Family	*Jatrophihabitantaceae*
	Genus	*Jatrophihabitans*
	Species	**Jatrophihabitans endophyticus**
	Full Scientific Name (LPSN)	Jatrophihabitans endophyticus Madhaiyan et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30600]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30600]	Cell length	1.2 µm

[Ref.: #30600]	Cell width	0.5 µm

[Ref.: #30600]	Cell shape	rod-shaped

[Ref.: #30600]	Motility	no

[Ref.: #30600]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19294]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #19294]

Culture medium growth

[Ref.: #19294]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19294]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #19294]

Culture medium growth

[Ref.: #19294]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19294]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #19294]

Culture medium growth

[Ref.: #19294]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19294]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #19294]

Culture medium growth

[Ref.: #19294]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19294]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19294]	growth	28 °C
[Ref.: #30600]	growth	10-32 °C
[Ref.: #30600]	optimum	25 °C

[Ref.: #19294]	Temperature range	mesophilic
[Ref.: #30600]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30600]			optimum	7
[Ref.: #30600]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30600]

Oxygen tolerance

aerobe

[Ref.: #30600]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %90
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.805

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30600]		NaCl		growth	0-2	%

[Ref.: #30600]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30600]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #30600]	arabinose ChEBI	+	carbon source
[Ref.: #30600]	esculin ChEBI	+	hydrolysis
[Ref.: #30600]	histidine ChEBI	+	carbon source
[Ref.: #30600]	mannitol ChEBI	+	carbon source
[Ref.: #30600]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30600]	propionate ChEBI	+	carbon source
[Ref.: #30600]	serine ChEBI	+	carbon source
[Ref.: #30600]	valerate ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30600]	acid phosphatase	+	3.1.3.2
[Ref.: #30600]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30600]	catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
		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.: #19294]	Sample type/isolated from	surface sterilized stem tissue of Jatropha curcas L.
[Ref.: #19294]	Host species	Jatropha curcas
[Ref.: #19294]	Geographic location (country and/or sea, region)	Agrotechnology Experimental Station at Lim Chu Kang, Jatropha farm
[Ref.: #19294]	Country	Singapore
[Ref.: #19294]	Country ISO 3 Code	SGP
[Ref.: #19294]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Stem (Branch)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ346802 (>99% sequence identity) for Jatrophihabitans endophyticus from Microbeatlas

Aquatic Samples	109
Soil Samples	1160
Animal Samples	190
Plant Samples	93
Total Samples	1552

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

[Ref.: #19294]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #19294]	Jatrophihabitans endophyticus strain S9-650 16S ribosomal RNA gene, partial sequence	JQ346802	1484	ENA	1206085 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Jatrophihabitans endophyticus DSM 45627	GCA_900129455	contig	GenBank	1206085 tax ID	*
[Ref.: #66792]	Jatrophihabitans endophyticus strain DSM 45627	1206085.4	wgs	PATRIC	1206085 tax ID	*
[Ref.: #66792]	Jatrophihabitans endophyticus DSM 45627	2695420949	draft	JGI IMG/M	1206085 tax ID	*

[Ref.: #19294]	GC-content	71.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30600]	GC-content	71.2 mol%

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: Jatrophihabitans endophyticus strain DSM 45627 PATRIC: 1206085.4
[Ref.: #69481]	spore-forming	no	90	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Jatrophihabitans endophyticus strain DSM 45627 PATRIC: 1206085.4
[Ref.: #69480]	motile	no	70.354	yes
[Ref.: #69480]	gram-positive	yes	91.696	yes
[Ref.: #69480]	anaerobic	no	98.989	no
[Ref.: #69480]	aerobic	yes	90.791	yes
[Ref.: #69480]	halophile	no	95.688	no
[Ref.: #69480]	spore-forming	no	56.409	no
[Ref.: #69480]	thermophile	no	97.563	no
[Ref.: #69480]	glucose-util	yes	83.316	no
[Ref.: #69480]	flagellated	no	95.251	no
[Ref.: #69480]	glucose-ferment	no	90.622	no

Availability in culture collections External links

[Ref.: #19294]

Culture collection no.

DSM 45627, KACC 16232

[Ref.: #87270]

SI-ID 402501

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Jatrophihabitans huperziae sp. nov., an endophytic actinobacterium isolated from surface-sterilized tissue of the medicinal plant Huperzia serrata (Thunb.).	Gong ZL, Ai MJ, Sun HM, Liu HY, Yu LY, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001296	2016	*
Phylogeny	Jatrophihabitans fulvus sp. nov., an actinobacterium isolated from grass soil.	Jin L, Lee HG, Ko SR, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijsem.0.000443	2015	*
Phylogeny	Jatrophihabitans soli sp. nov., isolated from soil.	Kim SJ, Moon JY, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.000173	2015	*
Phylogeny	Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L.	Madhaiyan M, Hu CJ, Kim SJ, Weon HY, Kwon SW, Ji L	Int J Syst Evol Microbiol	10.1099/ijs.0.039685-0	2012	*

References

#19294

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45627

#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 )

#30600

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 #26931 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#87270

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-ID402501.1 )

#26931

IJSEM 1241 2013 ( DOI 10.1099/ijs.0.039685-0 , PubMed 22798659 )

* These data were automatically processed and therefore are not curated

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Jatrophihabitans endophyticus strain DSM 45627

Jatrophihabitans endophyticus strain DSM 45627

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