Sphingomonas rhizophila (KACC 19189, CCTCC AB 2016245, THG-T61)

Name: Sphingomonas rhizophila (KACC 19189, CCTCC AB 2016245, THG-T61)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158693

Type strain

Strain Designation THG-T61

Culture col. no. KACC 19189 CCTCC AB 2016245 THG-T61

NCBI tax ID(s) 2071607

Special Collections Literature strains

Sphingomonas rhizophila THG-T61 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from rhizosphere of Hibiscus syriacus collected from Kyung Hee University.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

Culture Collection Numbers

KACC 19189 CCTCC AB 2016245 THG-T61

@ref 20215

Last LPSN update 2026-05-29 08:44:01

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas rhizophila

Full scientific name Sphingomonas rhizophila Yan et al. 2018

Synonyms (1)

Pseudosphingomonas rhizophila

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
65433	negative	0.8-1.2 µm	0.4-0.6 µm	rod-shaped
125438	negative				97.712
125439	negative				93.481

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
65433	positive	growth	10-37
65433	positive	optimum	25-30

Culture pH

@ref	Ability	Type	PH	PH range
65433	positive	optimum	7
65433	positive	growth	5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65433	aerobe
125439	obligate aerobe	97.583

Spore formation

@ref	Spore formation	Confidence
125438		91.204
125439		98.945

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65433	NaCl	positive	growth	0-2 %
65433	NaCl	positive	optimum	0 %

Observation

@ref	Observation
65433	the polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, one unidentified lipid, one unidentified phospholipid, one unidentified glycolipid and one unidentified phosphoglycol
65433	the isoprenoid quinone is Q-10
65433	the polyamine is homospermidine

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65433	16808 ChEBI	2-dehydro-D-gluconate	+	assimilation
65433	37054 ChEBI	3-hydroxybutyrate	-	assimilation
65433	17879 ChEBI	4-hydroxybenzoate	-	assimilation
65433	58143 ChEBI	5-dehydro-D-gluconate	+	assimilation
65433	17128 ChEBI	adipate	+	assimilation
65433		casein	+	hydrolysis
65433	62968 ChEBI	cellulose	+	hydrolysis
65433	17029 ChEBI	chitin	-	hydrolysis
65433	17634 ChEBI	D-glucose	+	assimilation
65433	16899 ChEBI	D-mannitol	+	assimilation
65433	16024 ChEBI	D-mannose	+	assimilation
65433	16988 ChEBI	D-ribose	-	assimilation
65433	17924 ChEBI	D-sorbitol	+	assimilation
65433	27689 ChEBI	decanoate	-	assimilation
65433	16991 ChEBI	dna	+	hydrolysis
65433	24265 ChEBI	gluconate	-	assimilation
65433	17234 ChEBI	glucose	-	builds acid from
65433	28087 ChEBI	glycogen	+	assimilation
65433	16087 ChEBI	isocitrate	+	assimilation
65433	17240 ChEBI	itaconate	-	assimilation
65433		L-alanine 4-nitroanilide	+	assimilation
65433	30849 ChEBI	L-arabinose	+	assimilation
65433	18287 ChEBI	L-fucose	-	assimilation
65433	15971 ChEBI	L-histidine	-	assimilation
65433	17203 ChEBI	L-proline	+	assimilation
65433	62345 ChEBI	L-rhamnose	-	assimilation
65433	17115 ChEBI	L-serine	-	assimilation
65433	17895 ChEBI	L-tyrosine	-	hydrolysis
65433	24996 ChEBI	lactate	-	assimilation
65433	25115 ChEBI	malate	+	assimilation
65433	17306 ChEBI	maltose	+	assimilation
65433	28053 ChEBI	melibiose	+	assimilation
65433	17268 ChEBI	myo-inositol	+	assimilation
65433	44337 ChEBI	N-acetyl-L-glutamate	+	assimilation
65433	17632 ChEBI	nitrate	-	reduction
65433	18401 ChEBI	phenylacetate	+	assimilation
65433	17272 ChEBI	propionate	+	assimilation
65433	17814 ChEBI	salicin	+	assimilation
65433	30762 ChEBI	salicylate	-	assimilation
65433	32954 ChEBI	sodium acetate	-	assimilation
65433	53258 ChEBI	sodium citrate	-	assimilation
65433	62983 ChEBI	sodium malonate	-	assimilation
65433	28017 ChEBI	starch	-	hydrolysis
65433	9300 ChEBI	suberic acid	+	assimilation
65433	17992 ChEBI	sucrose	+	assimilation
65433	53426 ChEBI	tween 80	-	hydrolysis
65433	31011 ChEBI	valerate	+	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65433	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65433	acid phosphatase	+	3.1.3.2
65433	alpha-chymotrypsin	+	3.4.21.1
65433	alpha-fucosidase	-	3.2.1.51
65433	alpha-galactosidase	-	3.2.1.22
65433	alpha-glucosidase	+	3.2.1.20
65433	alpha-mannosidase	-	3.2.1.24
65433	arginine dihydrolase	+	3.5.3.6
65433	beta-galactosidase	+	3.2.1.23
65433	beta-glucosidase	+	3.2.1.21
65433	beta-glucuronidase	-	3.2.1.31
65433	catalase	+	1.11.1.6
65433	cystine arylamidase	+	3.4.11.3
65433	cytochrome oxidase	+	1.9.3.1
65433	esterase	-
65433	esterase Lipase (C 8)	+
65433	leucine arylamidase	+	3.4.11.1
65433	lipase (C 14)	-
65433	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65433	naphthol-AS-BI-phosphohydrolase	+
65433	phosphatase	+
65433	protease	+
65433	trypsin	+	3.4.21.4
65433	urease	+	3.5.1.5
65433	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

65433

Fatty acid	Percentage
C18:1ω7c, C18:1ω9t and/or C18:1ω	42.5
C17:1ω6c	20.6
C15:0 iso 2OH and/or C16:1ω7c	16.2
C16:0	9.1
C15:0	3.6
C17:1ω8c	1.9
C17:0	1.6
C16:1ω5c	1.4
C18:1ω5c	1.2
C14:0 2OH	1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Plant	#Rhizosphere
#Host	#Plants	#Shrub (Scrub)
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
65433	rhizosphere of Hibiscus syriacus collected from Kyung Hee University	Yongin	Republic of Korea	KOR	Asia	nutrient agar (NA, Oxoid)	1 week	30

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1439658v1 assembly for Sphingomonas rhizophila KACC 19189	complete	GCA_014396585	2071607.3	2896429255	2071607	89.23

16S sequences

@ref	Description	Accession	Database
65433	Sphingomonas rhizophila strain THG-T61 16S ribosomal RNA gene, partial sequence	KY287249

GC content

@ref	GC-content (mol%)	Method
65433	65.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1439658v1 assembly for Sphingomonas rhizophila KACC 19189
BV-BRC: 2071607.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.58	no
125439	motility	BacteriaNetⓘ	yes	40.40	no
125439	gram_stain	BacteriaNetⓘ	negative	93.48	no
125439	spore_formation	BacteriaNetⓘ	no	98.95	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas rhizophila KACC 19189
NCBI: GCA_014396585.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.71	yes
125438	anaerobic	anaerobicⓘ	no	96.63	no
125438	aerobic	aerobicⓘ	yes	86.86	no
125438	spore-forming	spore-formingⓘ	no	91.20	no
125438	thermophilic	thermophileⓘ	no	92.28	no
125438	flagellated	motile2+ⓘ	no	57.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea.	Kim H, Chhetri G, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.003780	2020
Phylogeny	Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus.	Yan ZF, Lin P, Won KH, Li CT, Park G, Chin B, Kook M, Wang QJ, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002566	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 )
#65433	Zheng-Fei Yan, Pei Lin, Kyung-Hwa Won, Chang-Tian Li, GyungSoo Park, ByungSun Chin, MooChang Kook, Qi-Jun Wang and Tae-Hoo Yi: Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus. IJSEM 68: 681 - 686 2018 ( DOI 10.1099/ijsem.0.002566 , PubMed 29388549 )
#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) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

Content

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Sphingomonas rhizophila (KACC 19189, CCTCC AB 2016245, THG-T61)

Name and taxonomic classification

Culture Collection Numbers

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014396585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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