Name: Flavihumibacter stibioxidans YS-17
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133199

Type strain:

Species: Flavihumibacter stibioxidans

Strain Designation: YS-17

Culture col. no.: CCTCC AB 2016053, KCTC 52205

Strain history: <- Yushan Han, Huzhong Agricultrural Univ.

NCBI tax ID(s): 1834163 (species)

Section

Flavihumibacter stibioxidans YS-17 is an obligate aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from soil of an antimony mine.

colony-forming
Gram-positive
rod-shaped
obligate aerobe
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	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Flavihumibacter*
	Species	**Flavihumibacter stibioxidans**
	Full Scientific Name (LPSN)	Flavihumibacter stibioxidans Han et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24997]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #24997]	Cell length	0.8-1.5 µm

[Ref.: #24997]	Cell width	0.2-0.3 µm

[Ref.: #24997]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #24997]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #24997]	Colony size	2.0-4.0 mm
[Ref.: #24997]	Colony color	yellow
[Ref.: #24997]	Colony shape	circular
[Ref.: #24997]	Incubation period	2 days
[Ref.: #24997]	Cultivation medium used	R2A agar (Reasoner's 2A agar)

[Ref.: #24997]	Pigment production	yes
[Ref.: #24997]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24997]

Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

LB (lysogeny broth) agar

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Culture medium growth

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Culture medium

TSA (Trypticase soy agar)

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Culture medium growth

		Temperature
[Ref.: #24997]	growth	16.0-37.0 °C
[Ref.: #24997]	optimum	28 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #24997]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #24997]			optimum	7
[Ref.: #24997]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24997]	Oxygen tolerance	obligate aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.987

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24997]		NaCl		optimum	0	%
[Ref.: #24997]		NaCl		growth	0.0-1.0	%(w/v)

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24997]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #24997]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #24997]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #24997]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #24997]	adipate ChEBI	-	assimilation
[Ref.: #24997]	butyrate ChEBI	-	assimilation
[Ref.: #24997]	casein	-	hydrolysis
[Ref.: #24997]	D-fucose ChEBI	-	assimilation
[Ref.: #24997]	D-glucose ChEBI	+	assimilation
[Ref.: #24997]	D-mannitol ChEBI	-	assimilation
[Ref.: #24997]	D-mannose ChEBI	+	assimilation
[Ref.: #24997]	D-ribose ChEBI	-	assimilation
[Ref.: #24997]	D-sorbitol ChEBI	-	assimilation
[Ref.: #24997]	esculin ChEBI	+	hydrolysis
[Ref.: #24997]	gelatin ChEBI	-	hydrolysis
[Ref.: #24997]	glucose ChEBI	-	fermentation
[Ref.: #24997]	glycogen ChEBI	+	assimilation
[Ref.: #24997]	L-arabinose ChEBI	+	assimilation
[Ref.: #24997]	L-histidine ChEBI	-	assimilation
[Ref.: #24997]	L-proline ChEBI	+	assimilation
[Ref.: #24997]	L-rhamnose ChEBI	+	assimilation
[Ref.: #24997]	L-serine ChEBI	-	assimilation
[Ref.: #24997]	L-tyrosine ChEBI	-	assimilation
[Ref.: #24997]	lactate ChEBI	-	assimilation
[Ref.: #24997]	malate ChEBI	-	assimilation
[Ref.: #24997]	malonate ChEBI	-	assimilation
[Ref.: #24997]	maltose ChEBI	+	assimilation
[Ref.: #24997]	melibiose ChEBI	+	assimilation
[Ref.: #24997]	myo-inositol ChEBI	-	assimilation
[Ref.: #24997]	myo-inositol ChEBI	+	assimilation
[Ref.: #24997]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #24997]	nitrate ChEBI	-	reduction
[Ref.: #24997]	phenylacetate ChEBI	-	assimilation
[Ref.: #24997]	potassium gluconate ChEBI	-	assimilation
[Ref.: #24997]	propionate ChEBI	-	assimilation
[Ref.: #24997]	rhamnose ChEBI	+	assimilation
[Ref.: #24997]	salicin ChEBI	-	assimilation
[Ref.: #24997]	sodium acetate ChEBI	-	assimilation
[Ref.: #24997]	sodium citrate ChEBI	-	assimilation
[Ref.: #24997]	starch ChEBI	-	hydrolysis
[Ref.: #24997]	suberic acid ChEBI	-	assimilation
[Ref.: #24997]	sucrose ChEBI	+	assimilation
[Ref.: #24997]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #24997]	acetoin ChEBI	no
[Ref.: #24997]	hydrogen sulfide ChEBI	yes
[Ref.: #24997]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #24997]		acetoin ChEBI	-
[Ref.: #24997]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #24997]	acid phosphatase	+/-	3.1.3.2
[Ref.: #24997]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24997]	alpha-chymotrypsin	+/-	3.4.21.1
[Ref.: #24997]	alpha-galactosidase	+/-	3.2.1.22
[Ref.: #24997]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24997]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24997]	beta-D-fucosidase	+/-	3.2.1.38
[Ref.: #24997]	beta-galactosidase	+/-	3.2.1.23
[Ref.: #24997]	beta-glucosidase	+	3.2.1.21
[Ref.: #24997]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24997]	catalase	+	1.11.1.6
[Ref.: #24997]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #24997]	cytochrome oxidase	+	1.9.3.1
[Ref.: #24997]	esterase (C 4)	+/-
[Ref.: #24997]	esterase Lipase (C 8)	+/-
[Ref.: #24997]	leucine arylamidase	+	3.4.11.1
[Ref.: #24997]	lipase (C 14)	-
[Ref.: #24997]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #24997]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24997]	trypsin	+	3.4.21.4
[Ref.: #24997]	valine arylamidase	+
	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.: #24997]	Sample type/isolated from	soil of an antimony mine
[Ref.: #24997]	Geographic location (country and/or sea, region)	Lengshuijiang city, Hunan Province
[Ref.: #24997]	Country	Republic of China
[Ref.: #24997]	Country ISO 3 Code	CHN
[Ref.: #24997]	Continent	Asia
[Ref.: #24997]	Geographic location	28.0000°/111.0000°
[Ref.: #24997]	Enrichment culture	R2A agar (Reasoner's 2A agar)
[Ref.: #24997]	Enrichment culture duration	7 days
[Ref.: #24997]	Enrichment culture temperature	28 ̊C

[Ref.: #67771]	Sample type/isolated from	From soil, antimony mining area
[Ref.: #67771]	Geographic location (country and/or sea, region)	Lengshuijiang city, Hunan province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX014806 (>99% sequence identity) for Flavihumibacter stibioxidans subclade from Microbeatlas

Aquatic Samples	1052
Soil Samples	246
Animal Samples	134
Plant Samples	38
Total Samples	1470

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.: #24997]	Flavihumibacter sp. YS-17 16S ribosomal RNA gene, partial sequence	KX014806	1490	GenBank	1834163 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavihumibacter stibioxidans YS-17	GCA_014332695	scaffold	GenBank	1834163 tax ID	*
[Ref.: #66792]	Flavihumibacter stibioxidans YS-17	2920284866	draft	JGI IMG/M	1834163 tax ID	*

[Ref.: #24997]	GC-content	47.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	47.8 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Flavihumibacter stibioxidans YS-17 NCBI: GCA_014332695.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavihumibacter stibioxidans YS-17 NCBI: GCA_014332695.1
[Ref.: #69480]	flagellated	no	98.318	yes
[Ref.: #69480]	gram-positive	no	97.295	no
[Ref.: #69480]	anaerobic	no	99.115	yes
[Ref.: #69480]	aerobic	yes	89.2	yes
[Ref.: #69480]	halophile	no	96.893	yes
[Ref.: #69480]	spore-forming	no	95.892	no
[Ref.: #69480]	thermophile	no	90.382	no
[Ref.: #69480]	glucose-util	yes	87.512	yes
[Ref.: #69480]	motile	no	95.133	yes
[Ref.: #69480]	glucose-ferment	no	92.251	yes

Availability in culture collections External links

[Ref.: #24997]

Culture collection no.

CCTCC AB 2016053, KCTC 52205

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavihumibacter soli sp. nov., Isolated from Soil.	Seo YL, Jung J, Khan SA, Kim KH, Jeon CO	Curr Microbiol	10.1007/s00284-020-02103-2	2020	*
Phylogeny	Flavihumibacter profundi sp. nov., isolated from eutrophic freshwater sediment.	Ren TT, Jin CZ, Jin FJ, Li T, Kim CJ, Oh HM, Lee HG, Jin L	J Microbiol	10.1007/s12275-018-7567-8	2018	*
Phylogeny	Flavihumibacter stibioxidans sp. nov., an antimony-oxidizing bacterium isolated from antimony mine soil.	Han Y, Zhang F, Wang Q, Zheng S, Guo W, Feng L, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.001409	2016	*

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 )

#24997

Y. Z. Han, Fujun,Wang, Qian,Zheng, Shixue,Guo, Wei,Feng, Liang,Wang, Gejiao: Flavihumibacter stibioxidans sp. nov., an antimony-oxidizing bacterium isolated from antimony mine soil. IJSEM 66: 4676 - 4680 2016 ( DOI 10.1099/ijsem.0.001409 , PubMed 27506768 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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