Sphingobacterium humi (KACC 18595, JCM 31225, D1)

Name: Sphingobacterium humi (KACC 18595, JCM 31225, D1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158555

Type strain

Strain Designation D1

Culture col. no. KACC 18595 JCM 31225 D1

NCBI tax ID(s) 1796905

Special Collections JCM Literature strains

History C. O. Jeon; Chung-Ang Univ., South Korea; D1.

Links

Sphingobacterium humi D1 is a facultative aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil sample .

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

Name and taxonomic classification

SI-ID 133500

JCM 31225

@ref 20215

Last LPSN update 2026-02-09 11:38:21

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium humi

Full scientific name Sphingobacterium humi Lee et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
65249	negative	rod-shaped
125438	negative		98.5
125439	negative		99.6

Colony morphology

@ref	Colony shape	Medium used
65249	circular	tryptic soy agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
65249	tryptic soy agar

Culture temp

@ref	Growth	Type	Temperature (°C)
65249	positive	growth	15-40
65249	positive	growth	30-37
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
65249	positive	optimum	7-8
65249	positive	growth	5.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

65249

Oxygen tolerancefacultative aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65249	NaCl	positive	growth	0-5 %(w/v)
65249	NaCl	positive	optimum	0-1 %(w/v)

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65249	27613 ChEBI	amygdalin	-	builds acid from
65249		casein	-	hydrolysis
65249	17634 ChEBI	D-glucose	-	builds acid from
65249	16899 ChEBI	D-mannitol	+	builds acid from
65249	17924 ChEBI	D-sorbitol	-	builds acid from
65249	4853 ChEBI	esculin	+	hydrolysis
65249	5291 ChEBI	gelatin	-	hydrolysis
65249	16136 ChEBI	hydrogen sulfide	-	hydrolysis
65249	30849 ChEBI	L-arabinose	-	builds acid from
65249	62345 ChEBI	L-rhamnose	-	builds acid from
65249	28053 ChEBI	melibiose	-	builds acid from
65249	17268 ChEBI	myo-inositol	-	builds acid from
65249	17632 ChEBI	nitrate	-	reduction
65249	53258 ChEBI	sodium citrate	+	builds acid from
65249	28017 ChEBI	starch	-	hydrolysis
65249	17992 ChEBI	sucrose	+	builds acid from
65249	53424 ChEBI	tween 20	+	hydrolysis
65249	53426 ChEBI	tween 80	-	hydrolysis
65249	18186 ChEBI	tyrosine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65249	16136 ChEBI	hydrogen sulfide
65249	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65249	acid phosphatase	+	3.1.3.2
65249	alkaline phosphatase	+	3.1.3.1
65249	alpha-chymotrypsin	+	3.4.21.1
65249	alpha-fucosidase	-	3.2.1.51
65249	alpha-galactosidase	+	3.2.1.22
65249	alpha-glucosidase	+	3.2.1.20
65249	alpha-mannosidase	+	3.2.1.24
65249	arginine dihydrolase	-	3.5.3.6
65249	beta-galactosidase	+	3.2.1.23
65249	beta-glucosidase	+	3.2.1.21
65249	beta-glucuronidase	+	3.2.1.31
65249	catalase	+	1.11.1.6
65249	cystine arylamidase	+	3.4.11.3
65249	cytochrome oxidase	+	1.9.3.1
65249	esterase (C 4)	+
65249	esterase Lipase (C 8)	+
65249	leucine arylamidase	+	3.4.11.1
65249	lipase (C 14)	-
65249	lysine decarboxylase	-	4.1.1.18
65249	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65249	naphthol-AS-BI-phosphohydrolase	+
65249	ornithine decarboxylase	-	4.1.1.17
65249	trypsin	-	3.4.21.4
65249	tryptophan deaminase	-	4.1.99.1
65249	urease	-	3.5.1.5
65249	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

65249

Fatty acid	Percentage
C15:0 iso	35.3
C16:1ω7c and/or C16:1ω6c	29.9
C17:0 iso 3OH	14
iso-C17:1ω9c and/or C16:0 10-methy	5.3
C15:0 anteiso	2.9
C15:0 iso 3OH	2
C17:1 iso I and/or C17:1 anteiso B	1.7
C16:0	1.6
C16:0 3OH	1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
65249	soil sample (less than 5 cm depth)	soil in Pyeongtaek	Republic of Korea	KOR	Asia	36.9414	126.993 36.9414/126.993	R2A agar	5 days	30	the soil sample (less than 5 cm depth) was serially diluted with 0.85 % (w/v) saline, and aliquots of each serial dilution were spread on R2A agar (BD).
67770	Soil		Republic of Korea	KOR	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM976888v1 assembly for Sphingobacterium humi JCM 31225	contig	GCA_009768885	1796905.3	2896301657	1796905	67.93

16S sequences

@ref	Description	Accession	Database
65249	Sphingobacterium humi strain D1 16S ribosomal RNA gene, partial sequence	KU668559

GC content

@ref	GC-content (mol%)	Method
65249	43.6	Thermal denaturation, fluorometry
67770	43.6	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobacterium humi JCM 31225
NCBI: GCA_009768885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	no	55.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	69.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobacterium humi strain JCM 31225
PATRIC: 1796905.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	95.84	yes
125438	spore-forming	spore-formingⓘ	no	88.68	no
125438	aerobic	aerobicⓘ	yes	81.76	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	no	85.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium humi sp. nov., isolated from soil.	Lee Y, Jin HM, Jung HS, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002345	2017

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 )
#65249	Yunhee Lee, Hyun Mi Jin, Hye Su Jung, Che Ok Jeon: Sphingobacterium humi sp. nov., isolated from soil. IJSEM 67: 4632 - 4638 2017 ( DOI 10.1099/ijsem.0.002345 , PubMed 28945541 )
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Sphingobacterium humi (KACC 18595, JCM 31225, D1)

Name and taxonomic classification