Name: Herbihabitans rhizosphaerae DSM 101727
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132633

Type strain:

Species: Herbihabitans rhizosphaerae

Culture col. no.: DSM 101727, NBRC 111774, CPCC 204279

Strain history: <- Zhang Y. Q., Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, CPCC 204279 <- Zhang Ch.F

NCBI tax ID(s): 1872711 (species)

SI-ID 405701

DSM 101727

Section

Herbihabitans rhizosphaerae DSM 101727 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from rhizosphere soil of the herb Limonium sinense .

Gram-positive
rod-shaped
spore-forming
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	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Herbihabitans*
	Species	**Herbihabitans rhizosphaerae**
	Full Scientific Name (LPSN)	Herbihabitans rhizosphaerae Zhang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24899]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #24899]	Cell shape	rod-shaped

[Ref.: #24899]	Motility	no

[Ref.: #24899]	Pigment production	no
[Ref.: #24899]	Pigment name	no pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24422]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #24422]

Culture medium growth

[Ref.: #24422]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24422]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24422]	growth	28 °C
[Ref.: #24899]	growth	20-40 °C
[Ref.: #24899]	optimum	28 °C

[Ref.: #24422]	Temperature range	mesophilic
[Ref.: #24899]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #24899]			optimum	7
[Ref.: #24899]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24899]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.447

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24899]		NaCl		growth	0-3	%(w/v)
[Ref.: #24899]		NaCl		optimum	1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24899]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #24899]	cellobiose ChEBI	+	carbon source
[Ref.: #24899]	cellobiose ChEBI	+	builds acid from
[Ref.: #24899]	D-arabinose ChEBI	+	carbon source
[Ref.: #24899]	D-arabinose ChEBI	+	builds acid from
[Ref.: #24899]	D-fucose ChEBI	+	carbon source
[Ref.: #24899]	D-galactose ChEBI	+	carbon source
[Ref.: #24899]	D-gluconate ChEBI	+	carbon source
[Ref.: #24899]	D-glucuronate ChEBI	+	carbon source
[Ref.: #24899]	D-mannitol ChEBI	+	carbon source
[Ref.: #24899]	D-mannose ChEBI	+	carbon source
[Ref.: #24899]	dextrin ChEBI	+	carbon source
[Ref.: #24899]	gelatin ChEBI	+	hydrolysis
[Ref.: #24899]	glucuronamide ChEBI	+	carbon source
[Ref.: #24899]	glycerol ChEBI	+	carbon source
[Ref.: #24899]	glycerol ChEBI	+	builds acid from
[Ref.: #24899]	L-fucose ChEBI	+	carbon source
[Ref.: #24899]	nitrate ChEBI	+	reduction
[Ref.: #24899]	salicin ChEBI	+	carbon source
[Ref.: #24899]	starch ChEBI	-	hydrolysis
[Ref.: #24899]	tryptophan ChEBI	+	energy source
[Ref.: #24899]	turanose ChEBI	+	carbon source
[Ref.: #24899]	tween 40 ChEBI	+	hydrolysis
[Ref.: #24899]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #24899]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #24899]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #24899]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24899]	beta-glucosidase	+	3.2.1.21
[Ref.: #24899]	catalase	+	1.11.1.6
[Ref.: #24899]	chymotrypsin	+	3.4.4.5
[Ref.: #24899]	cystine arylamidase	+	3.4.11.3
[Ref.: #24899]	cytochrome oxidase	+	1.9.3.1
[Ref.: #24899]	esterase (C 4)	+
[Ref.: #24899]	esterase lipase (C 8)	+
[Ref.: #24899]	lipase (C 14)	+
[Ref.: #24899]	tryptophan deaminase	+	4.1.99.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	purine metabolism	85.11	80 of 94
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	lysine metabolism	78.57	33 of 42
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	polyamine pathway	73.91	17 of 23
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	aclacinomycin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	50	4 of 8
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	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]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol 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]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #24422]	Sample type/isolated from	rhizosphere soil of the herb Limonium sinense (Girard)
[Ref.: #24422]	Host species	Limonium sinense
[Ref.: #24422]	Geographic location (country and/or sea, region)	Xinjiang Province, Yili Valley (42° 34' 16.11'' N 81° 13' 14.07'' E, 1323 m H)
[Ref.: #24422]	Country	China
[Ref.: #24422]	Country ISO 3 Code	CHN
[Ref.: #24422]	Continent	Asia
[Ref.: #24422]	Geographic location	42.5711°/81.2206°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX128908 (>99% sequence identity) for Herbihabitans rhizosphaerae subclade from Microbeatlas

Aquatic Samples	34
Soil Samples	714
Animal Samples	74
Plant Samples	275
Total Samples	1097

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

[Ref.: #24422]

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.: #24422]	Herbihabitans rhizosphaerae strain CPCC 204279 16S ribosomal RNA gene, partial sequence	KX128908	1496	ENA	1872711 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Herbihabitans rhizosphaerae DSM 101727	GCA_004216555	scaffold	GenBank	1872711 tax ID	*
[Ref.: #66792]	Herbihabitans rhizosphaerae strain DSM 101727	1872711.3	wgs	PATRIC	1872711 tax ID	*
[Ref.: #66792]	Herbihabitans rhizosphaerae DSM 101727	2795385472	draft	JGI IMG/M	1872711 tax ID	*

[Ref.: #24899]	GC-content	73.2 mol%	Thermal denaturation, fluorometry
[Ref.: #24422]	GC-content	73.2 mol%	thermal denaturation, midpoint method (Tm)

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: Herbihabitans rhizosphaerae DSM 101727 NCBI: GCA_004216555.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Herbihabitans rhizosphaerae DSM 101727 NCBI: GCA_004216555.1
[Ref.: #69480]	motile	no	95.327	yes
[Ref.: #69480]	flagellated	no	96.903	yes
[Ref.: #69480]	gram-positive	yes	88.15	yes
[Ref.: #69480]	anaerobic	no	98.94	no
[Ref.: #69480]	aerobic	yes	93.604	yes
[Ref.: #69480]	halophile	no	85.851	no
[Ref.: #69480]	spore-forming	yes	88.743	no
[Ref.: #69480]	glucose-util	yes	89.613	yes
[Ref.: #69480]	thermophile	no	91.888	yes
[Ref.: #69480]	glucose-ferment	no	91.953	no

Availability in culture collections External links

[Ref.: #24422]

Culture collection no.

DSM 101727, NBRC 111774, CPCC 204279

[Ref.: #90947]

SI-ID 405701

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard).	Zhang CF, Ai MJ, Wang JX, Liu SW, Zhao LL, Su J, Sun CH, Yu LY, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001325	2016	*

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 )

#24422

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101727

#24899

C.-F. A. Zhang, Meng-Jie,Wang, Ju-Xian,Liu, Shao-Wei,Zhao, Li-Li,Su, Jing,Sun, Cheng-Hang,Yu, Li-Yan,Zhang, Yu-Qin: Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard). IJSEM 66: 4156 - 4161 2016 ( DOI 10.1099/ijsem.0.001325 , PubMed 27470940 )

#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 )

#90947

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-ID405701.1 )

* These data were automatically processed and therefore are not curated

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