Name: Tamaricihabitans halophyticus DSM 45765
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131546

Type strain:

Species: Tamaricihabitans halophyticus

Culture col. no.: DSM 45765, NBRC 109361, KLBMP 1356

Strain history: <- S. Qin, Jiangasu Normal University, China; KLBMP 1356

NCBI tax ID(s): 1262583 (species)

SI-ID 400618

DSM 45765

Special Collections

DSMZ

Section

Tamaricihabitans halophyticus DSM 45765 is a spore-forming bacterium that was isolated from surface sterilized root of the halophyte Tamarix chinensis Lour, healthy plant tissue.

spore-forming
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	*Tamaricihabitans*
	Species	**Tamaricihabitans halophyticus**
	Full Scientific Name (LPSN)	Tamaricihabitans halophyticus Qin et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Motility	no Confidence in %91

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22773]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #22773]

Culture medium growth

[Ref.: #22773]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22773]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22773]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

yes Confidence in %98

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	allantoin degradation	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	purine metabolism	87.23	82 of 94
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	histidine metabolism	86.21	25 of 29
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	tryptophan metabolism	78.95	30 of 38
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	carnitine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	oxidative phosphorylation	71.43	65 of 91
[Ref.: #66794]	aclacinomycin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
		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.: #22773]	Sample type/isolated from	surface sterilized root of the halophyte Tamarix chinensis Lour, healthy plant tissue
[Ref.: #22773]	Host species	Tamarix chinensis
[Ref.: #22773]	Geographic location (country and/or sea, region)	Jiangsu province, coastal area
[Ref.: #22773]	Country	China
[Ref.: #22773]	Country ISO 3 Code	CHN
[Ref.: #22773]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JX982738 (>99% sequence identity) for Tamaricihabitans halophyticus subclade from Microbeatlas

Aquatic Samples	170
Soil Samples	458
Animal Samples	241
Plant Samples	68
Total Samples	937

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

[Ref.: #22773]

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.: #22773]	Tamaricihabitans halophyticus 16S ribosomal RNA gene, partial sequence	JX982738	1445	GenBank ENA	1262583 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Tamaricihabitans halophyticus DSM 45765	GCA_004340875	contig	GenBank ENA	1262583 tax ID	*
[Ref.: #66792]	Tamaricihabitans halophyticus strain DSM 45765	1262583.3	wgs	PATRIC	1262583 tax ID	*
[Ref.: #66792]	Tamaricihabitans halophyticus DSM 45765	2795385477	draft	JGI IMG/M	1262583 tax ID	*

[Ref.: #22773]

GC-content

67.2 mol%

high performance liquid chromatography (HPLC)

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: Tamaricihabitans halophyticus strain DSM 45765 PATRIC: 1262583.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	98	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tamaricihabitans halophyticus strain DSM 45765 PATRIC: 1262583.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.387	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.162	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	77.918	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.886	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.984	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	91	no

Availability in culture collections External links

[Ref.: #22773]

Culture collection no.

DSM 45765, NBRC 109361, KLBMP 1356

[Ref.: #89960]

SI-ID 400618

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Tamaricihabitans halophyticus gen. nov., sp. nov., an endophytic actinomycete of the family Pseudonocardiaceae.	Qin S, Bai JL, Wang Y, Feng WW, Yuan B, Sun Y, Cao CL, Ju XY, Huang Y, Jiang JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000628	2015	*

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 )

#22773

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45765

#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 )

#89960

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-ID400618.1 )

* These data were automatically processed and therefore are not curated

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Tamaricihabitans halophyticus strain DSM 45765

Tamaricihabitans halophyticus strain DSM 45765

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