Name: Sphingomonas carotinifaciens L9-754
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 141164

Type strain:

Species: Sphingomonas carotinifaciens

Strain Designation: L9-754

Culture col. no.: DSM 27347, KACC 17595

Strain history: <- M. Madhaiyan, Temasek Life Sciences Laboratory, Univ. Singapore; L9-754

NCBI tax ID(s): 1166323 (species)

SI-ID 396844

DSM 27347

Special Collections

Section

When using BacDive for research please cite our paper

Sphingomonas carotinifaciens L9-754 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from endophytes of surface-sterilized stem tissue of Jatropha curcas.

colony-forming
Gram-negative
rod-shaped
obligate aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas carotinifaciens**
	Full Scientific Name (LPSN)	Sphingomonas carotinifaciens Madhaiyan et al. 2017

Synonym

Sphingomonas aeria

Information on morphological and physiological properties Morphology

[Ref.: #44084]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %97.802

[Ref.: #44084]	Cell length	1.8-2.1 µm

[Ref.: #44084]	Cell width	0.5-0.8 µm

[Ref.: #44084]	Cell shape	rod-shaped

[Ref.: #44084]	Colony size	1.1-1.4 mm
[Ref.: #44084]	Colony color	yellow
[Ref.: #44084]	Colony shape	circular
[Ref.: #44084]	Incubation period	2 days
[Ref.: #44084]	Cultivation medium used	2xYT

Multimedia content

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

2xYT

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Culture medium growth

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Culture medium

R2A/Nfb

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Culture medium growth

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #44084]	growth	15-37 °C
[Ref.: #44084]	optimum	28-30 °C
[Ref.: #64986]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #44084]			optimum	6.0-7.0
[Ref.: #44084]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #44084]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.8

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44084]		NaCl		growth	0-6	%(w/v)

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Observation

sphingolipid-producing

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44084]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #44084]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #44084]	4-hydroxybenzoate ChEBI	+	assimilation
[Ref.: #44084]	adipate ChEBI	-	assimilation
[Ref.: #44084]	amygdalin ChEBI	+	builds acid from
[Ref.: #44084]	arbutin ChEBI	+	builds acid from
[Ref.: #44084]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #44084]	casein	+	hydrolysis
[Ref.: #44084]	cellobiose ChEBI	+	builds acid from
[Ref.: #44084]	D-arabinose ChEBI	+	builds acid from
[Ref.: #44084]	D-arabitol ChEBI	-	builds acid from
[Ref.: #44084]	D-fructose ChEBI	+	builds acid from
[Ref.: #44084]	D-fucose ChEBI	+	builds acid from
[Ref.: #44084]	D-galactose ChEBI	+	builds acid from
[Ref.: #44084]	D-glucose ChEBI	+	assimilation
[Ref.: #44084]	D-glucose ChEBI	+	builds acid from
[Ref.: #44084]	D-lyxose ChEBI	+	builds acid from
[Ref.: #44084]	D-mannitol ChEBI	-	assimilation
[Ref.: #44084]	D-mannitol ChEBI	-	builds acid from
[Ref.: #44084]	D-mannose ChEBI	+	assimilation
[Ref.: #44084]	D-mannose ChEBI	+	builds acid from
[Ref.: #44084]	D-ribose ChEBI	-	assimilation
[Ref.: #44084]	D-ribose ChEBI	-	builds acid from
[Ref.: #44084]	D-sorbitol ChEBI	-	assimilation
[Ref.: #44084]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #44084]	D-tagatose ChEBI	-	builds acid from
[Ref.: #44084]	D-xylose ChEBI	+	builds acid from
[Ref.: #44084]	decanoate ChEBI	-	assimilation
[Ref.: #44084]	erythritol ChEBI	-	builds acid from
[Ref.: #44084]	esculin ferric citrate	+	builds acid from
[Ref.: #44084]	galactitol ChEBI	-	builds acid from
[Ref.: #44084]	gelatin ChEBI	-	hydrolysis
[Ref.: #44084]	gentiobiose ChEBI	+	builds acid from
[Ref.: #44084]	glucose ChEBI	-	fermentation
[Ref.: #44084]	glycerol ChEBI	-	builds acid from
[Ref.: #44084]	glycogen ChEBI	-	assimilation
[Ref.: #44084]	glycogen ChEBI	-	builds acid from
[Ref.: #44084]	inulin ChEBI	-	builds acid from
[Ref.: #44084]	itaconate ChEBI	-	assimilation
[Ref.: #44084]	L-alanine ChEBI	+	assimilation
[Ref.: #44084]	L-arabinose ChEBI	+	assimilation
[Ref.: #44084]	L-arabinose ChEBI	+	builds acid from
[Ref.: #44084]	L-arabitol ChEBI	-	builds acid from
[Ref.: #44084]	L-fucose ChEBI	+	assimilation
[Ref.: #44084]	L-fucose ChEBI	+	builds acid from
[Ref.: #44084]	L-histidine ChEBI	+	assimilation
[Ref.: #44084]	L-proline ChEBI	+	assimilation
[Ref.: #44084]	L-rhamnose ChEBI	+	assimilation
[Ref.: #44084]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #44084]	L-serine ChEBI	-	assimilation
[Ref.: #44084]	L-sorbose ChEBI	-	builds acid from
[Ref.: #44084]	L-xylose ChEBI	-	builds acid from
[Ref.: #44084]	lactate ChEBI	+	assimilation
[Ref.: #44084]	lactose ChEBI	+	builds acid from
[Ref.: #44084]	malate ChEBI	+	assimilation
[Ref.: #44084]	maltose ChEBI	+	assimilation
[Ref.: #44084]	maltose ChEBI	+	builds acid from
[Ref.: #44084]	melezitose ChEBI	+	builds acid from
[Ref.: #44084]	melibiose ChEBI	+	assimilation
[Ref.: #44084]	melibiose ChEBI	+	builds acid from
[Ref.: #44084]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #44084]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #44084]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #44084]	myo-inositol ChEBI	-	assimilation
[Ref.: #44084]	myo-inositol ChEBI	-	builds acid from
[Ref.: #44084]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #44084]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #44084]	nitrate ChEBI	-	reduction
[Ref.: #44084]	nitrite ChEBI	-	reduction
[Ref.: #44084]	phenylacetate ChEBI	-	assimilation
[Ref.: #44084]	potassium 2-dehydro-D-gluconate	-	assimilation
[Ref.: #44084]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #44084]	potassium 5-dehydro-D-gluconate	-	assimilation
[Ref.: #44084]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #44084]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #44084]	potassium gluconate ChEBI	+	assimilation
[Ref.: #44084]	propionate ChEBI	-	assimilation
[Ref.: #44084]	raffinose ChEBI	+	builds acid from
[Ref.: #44084]	ribitol ChEBI	-	builds acid from
[Ref.: #44084]	salicin ChEBI	+	assimilation
[Ref.: #44084]	salicin ChEBI	+	builds acid from
[Ref.: #44084]	sodium acetate ChEBI	-	assimilation
[Ref.: #44084]	sodium citrate ChEBI	-	assimilation
[Ref.: #44084]	sodium citrate ChEBI	+	assimilation
[Ref.: #44084]	sodium malonate ChEBI	-	assimilation
[Ref.: #44084]	starch ChEBI	-	hydrolysis
[Ref.: #44084]	starch ChEBI	+	builds acid from
[Ref.: #44084]	suberic acid ChEBI	-	assimilation
[Ref.: #44084]	sucrose ChEBI	+	assimilation
[Ref.: #44084]	sucrose ChEBI	+	builds acid from
[Ref.: #44084]	trehalose ChEBI	+	builds acid from
[Ref.: #44084]	turanose ChEBI	+	builds acid from
[Ref.: #44084]	tyrosine ChEBI	-	hydrolysis
[Ref.: #44084]	valerate ChEBI	-	assimilation
[Ref.: #44084]	xylan ChEBI	-	hydrolysis
[Ref.: #44084]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #44084]	ampicillin ChEBI	yes	25	µg/mL
[Ref.: #44084]	carbenicillin ChEBI				yes	50	µg/mL
[Ref.: #44084]	chloramphenicol ChEBI	yes	25	µg/mL
[Ref.: #44084]	hygromycin ChEBI				yes	100	µg/mL
[Ref.: #44084]	kanamycin ChEBI	yes	25	µg/mL
[Ref.: #44084]	nalidixic acid ChEBI	yes	25	µg/mL
[Ref.: #44084]	rifampicin ChEBI	yes	25	µg/mL
[Ref.: #44084]	spectinomycin ChEBI				yes	250	µg/mL
[Ref.: #44084]	tetracycline ChEBI	yes	25	µg/mL

	Metabolite production	Metabolite	Production
[Ref.: #44084]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #44084]	acid phosphatase	+	3.1.3.2
[Ref.: #44084]	alkaline phosphatase	+	3.1.3.1
[Ref.: #44084]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #44084]	alpha-fucosidase	-	3.2.1.51
[Ref.: #44084]	alpha-galactosidase	+	3.2.1.22
[Ref.: #44084]	alpha-glucosidase	+	3.2.1.20
[Ref.: #44084]	alpha-mannosidase	-	3.2.1.24
[Ref.: #44084]	arginine dihydrolase		3.5.3.6
[Ref.: #44084]	beta-galactosidase	+	3.2.1.23
[Ref.: #44084]	beta-glucosidase	+	3.2.1.21
[Ref.: #44084]	beta-glucuronidase	-	3.2.1.31
[Ref.: #44084]	catalase	+	1.11.1.6
[Ref.: #44084]	cystine arylamidase	+	3.4.11.3
[Ref.: #44084]	cytochrome oxidase	+	1.9.3.1
[Ref.: #44084]	esterase (C 4)	+
[Ref.: #44084]	esterase Lipase (C 8)	+
[Ref.: #44084]	leucine arylamidase	+	3.4.11.1
[Ref.: #44084]	lipase (C 14)	-
[Ref.: #44084]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #44084]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #44084]	trypsin	+	3.4.21.4
[Ref.: #44084]	urease	-	3.5.1.5
[Ref.: #44084]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #44084]

Fatty acid	Percentage
C18:1ω7c / C18:1ω9t / C18:1ω12t	72.4
C16:1	9.3
C14:0 2OH	6.1
C16:1ω7t / iso-C15:0 2-OH / C16:1ω7c	5.5
C17:1ω6c	1.6
C16:1ω5c	1.5
C18:1ω6c	1.3
C18:0	1.2
C14:0	0.8

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #44084]	Sample type/isolated from	endophytes of surface-sterilized stem tissue of Jatropha curcas
[Ref.: #44084]	Sampling date	2009-09
[Ref.: #44084]	Geographic location (country and/or sea, region)	Agrotechnology Experimental Station
[Ref.: #44084]	Country	Singapore
[Ref.: #44084]	Country ISO 3 Code	SGP
[Ref.: #44084]	Continent	Asia
[Ref.: #44084]	Geographic location	1.4367°/103.7090°
[Ref.: #44084]	Enrichment culture	R2A/Nfb medium
[Ref.: #44084]	Enrichment culture composition	N-free semi-solid medium
[Ref.: #44084]	Enrichment culture duration	3 days
[Ref.: #44084]	Enrichment culture temperature	30 ̊C

[Ref.: #64986]	Sample type/isolated from	surface-sterilized leaf-tissue of a Jatropha curcas L. cultivar (‘KB-27')
[Ref.: #64986]	Geographic location (country and/or sea, region)	Agrotechnology Experimental Station (1° 26' 12'' N 103° 42' 34'' E)
[Ref.: #64986]	Country	Singapore
[Ref.: #64986]	Country ISO 3 Code	SGP
[Ref.: #64986]	Continent	Asia
[Ref.: #64986]	Geographic location	1.4367°/103.7090°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #64986]

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.: #64986]	Sphingomonas carotinifaciens strain L9-754 16S ribosomal RNA gene, partial sequence	JQ659512	1417	GenBank ENA	1166323 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas carotinifaciens DSM 27347	GCA_009789535	contig	GenBank ENA	1166323 tax ID	*
[Ref.: #66792]	Sphingomonas carotinifaciens DSM 27347	GCA_014197095	scaffold	GenBank ENA	1166323 tax ID	*
[Ref.: #66792]	Sphingomonas carotinifaciens strain DSM 27347	1166323.3	wgs	PATRIC	1166323 tax ID	*
[Ref.: #66792]	Sphingomonas carotinifaciens strain DSM 27347	1166323.4	wgs	PATRIC	1166323 tax ID	*
[Ref.: #66792]	Sphingomonas carotinifaciens L9-754	2651870108	draft	JGI IMG/M	1166323 tax ID	*
[Ref.: #66792]	Sphingomonas carotinifaciens DSM 27347	2830088248	draft	JGI IMG/M	1166323 tax ID	*

[Ref.: #44084]	GC-content	66.9 mol%	genome sequence analysis
[Ref.: #64986]	GC-content	68.5 mol%	sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas carotinifaciens DSM 27347 NCBI: GCA_014197095.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.802	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	90.558	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.661	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.229	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.206	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	71.712	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas carotinifaciens DSM 27347 NCBI: GCA_014197095
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	88.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	57.9
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	65.4

Availability in culture collections External links

[Ref.: #64986]

Culture collection no.

DSM 27347, KACC 17595

[Ref.: #96874]

SI-ID 396844

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.	Madhaiyan M, Alex THH, Cho H, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L	Int J Syst Evol Microbiol	10.1099/ijsem.0.002434	2017	*
Phylogeny	Genome Resource of Sphingomonas carotinifaciens L9-754(T), an Endophyte Isolated From Leaf Tissues of Jatropha curcas.	Li G, Qin J, Zhang T, Yang L, Yang Q, Cao Y, Tang B, Li Z, Luo J, You S, Wan X, Liu Y, Guo L, Jiang K, Zheng J	Plant Dis	10.1094/PDIS-05-20-1052-A	2020	*
Phylogeny	Reclassification of Sphingomonas aeria as a later heterotypic synonym of Sphingomonas carotinifaciens based on whole-genome sequence analysis.	Madhaiyan M, Saravanan VS, Wirth JS, Whitman WB	Int J Syst Evol Microbiol	10.1099/ijsem.0.004045	2020	*

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 )

#44084

Munusamy Madhaiyan, Tan Hian Hwee Alex, Hayoung Cho, Soo-Jin Kim, Hang-Yeon Weon, Soon-Wo Kwon, William B. Whitman and Lianghui Ji: Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.. IJSEM 67: 5150 - 5158 2017 ( DOI 10.1099/ijsem.0.002434 , PubMed 29087271 )

#64986

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27347

#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) .

#96874

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-ID396844.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Sphingomonas carotinifaciens DSM 27347

Sphingomonas carotinifaciens DSM 27347

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