Sphingobium fontiphilum (DSM 29348, BCRC 80308, Chen16-4)

Name: Sphingobium fontiphilum (DSM 29348, BCRC 80308, Chen16-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130671

Type strain

Strain Designation Chen16-4

Culture col. no. DSM 29348 BCRC 80308 Chen16-4 KCTC 23559 LMG 26342

NCBI tax ID(s) 944425

Special Collections DSMZ KCTC Literature strains

History DSMZ <- LMG <- W.-M. Chen, Department of Seafood Science, University Kaohsing City; Chen16-4

Links

Sphingobium fontiphilum Chen16-4 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater from spring.

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

Name and taxonomic classification

SI-ID 376912

LMG 26342,BCRC 80308,KCTC 23559,DSM 29348

@ref 20215

Last LPSN update 2026-05-29 08:37:26

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium fontiphilum

Full scientific name Sphingobium fontiphilum Sheu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30869	negative	2 µm	0.5 µm	rod-shaped
125439	negative				98.129
125438	negative				97.9

Pigmentation

30869

Productionyes

Multimedia

@ref:	21783
multimedia content:	DSM_29348.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_29348.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21783	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21783	positive	growth	28
30869	positive	growth	15-40
30869	positive	optimum	37

Culture pH

@ref	Ability	Type	PH	PH range
30869	positive	optimum	7
30869	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30869	aerobe
125439	obligate aerobe	99.349

Spore formation

@ref	Spore formation	Confidence
30869
125438		91.677
125439		98.967

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30869	28644 ChEBI	2-oxopentanoate	+	carbon source
30869	16449 ChEBI	alanine	+	carbon source
30869	23652 ChEBI	dextrin	+	carbon source
30869	4853 ChEBI	esculin	+	hydrolysis
30869	29987 ChEBI	glutamate	+	carbon source
30869	15428 ChEBI	glycine	+	carbon source
30869	28087 ChEBI	glycogen	+	carbon source
30869	24996 ChEBI	lactate	+	carbon source
30869	51850 ChEBI	methyl pyruvate	+	carbon source
30869	26271 ChEBI	proline	+	carbon source
30869	30031 ChEBI	succinate	+	carbon source
30869	53423 ChEBI	tween 40	+	carbon source
30869	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30869	acid phosphatase	+	3.1.3.2
30869	alkaline phosphatase	+	3.1.3.1
30869	alpha-galactosidase	+	3.2.1.22
30869	catalase	+	1.11.1.6
30869	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Spring

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21783	freshwater from spring	Kaohsiung County, Chengcing Lake Park	Taiwan, Province of China	TWN	Asia	22.6533	120.35 22.6533/120.35

Taxonmaps

69479

Global distribution of 16S sequence HQ667767 (>99% sequence identity) for Sphingobium fontiphilum subclade from Microbeatlas

Aquatic Samples	93
Soil Samples	10
Animal Samples	8
Plant Samples	10
Total Samples	121

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21783	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419663v1 assembly for Sphingobium fontiphilum DSM 29348	contig	GCA_014196635	944425.3	2829936462	944425	72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21783	Sphingobium fontiphilum strain Chen 16-4 16S ribosomal RNA gene, partial sequence	HQ667767	1403		944425

GC content

21783

GC-content (mol%)62.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1419663v1 assembly for Sphingobium fontiphilum DSM 29348
NCBI: GCA_014196635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.35	no
125439	gram_stain	BacteriaNetⓘ	negative	98.13	no
125439	spore_formation	BacteriaNetⓘ	no	98.97	no
125439	motility	BacteriaNetⓘ	yes	65.81	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium fontiphilum strain DSM 29348
PATRIC: 944425.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.90	yes
125438	anaerobic	anaerobicⓘ	no	95.46	yes
125438	aerobic	aerobicⓘ	yes	85.53	no
125438	spore-forming	spore-formingⓘ	no	91.68	yes
125438	thermophilic	thermophileⓘ	no	98.54	yes
125438	flagellated	motile2+ⓘ	yes	60.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.	Chaudhary DK, Jeong SW, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002064	2017
Phylogeny	Sphingobium fontiphilum sp. nov., isolated from a freshwater spring.	Sheu SY, Shiau YW, Wei YT, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.046417-0	2012

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 )
#21783	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29348
#27199	IJSEM 1906 2013 ( DOI 10.1099/ijs.0.046417-0 , PubMed 23024141 )
#30869	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 #27199
#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) .
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Sphingobium fontiphilum (DSM 29348, BCRC 80308, Chen16-4)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014196635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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