Name: Edaphobaculum flavum 1-116
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158741

Type strain:

Species: Edaphobaculum flavum

Strain Designation: 1-116

Culture col. no.: CCTCC AB 2017054, KCTC 52843

Strain history: <- Min Cao, Huzhong Agricultural Univ.

NCBI tax ID(s): 1983306 (species)

Special Collections

Section

Edaphobaculum flavum 1-116 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from From soil of Erdos grassland of Inner Mongolia.

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

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	*Edaphobaculum*
	Species	**Edaphobaculum flavum**
	Full Scientific Name (LPSN)	Edaphobaculum flavum Cao et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65492]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #65492]	Cell length	0.8-1.0 µm

[Ref.: #65492]	Cell width	0.5-0.7 µm

[Ref.: #65492]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #65492]	Motility	yes
[Ref.: #67771]	Motility	no

[Ref.: #65492]	Colony color	yellow
[Ref.: #65492]	Colony shape	circular
[Ref.: #65492]	Cultivation medium used	1/10 TSA

[Ref.: #65492]	Pigment production	yes
[Ref.: #65492]	Pigment name	flexirubin

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

1/10 TSA

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Culture medium growth

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Culture medium

MacConkey

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #65492]			growth	16-33 °C
[Ref.: #67771]			growth	28 °C

	pH	Kind of pH		pH
[Ref.: #65492]			optimum	7.0-8.0
[Ref.: #65492]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65492]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

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Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65492]		NaCl		growth	0.5	%
[Ref.: #65492]		NaCl		optimum	0	%

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Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65492]	adipate ChEBI	+	assimilation
[Ref.: #65492]	arginine ChEBI	+	assimilation
[Ref.: #65492]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #65492]	casein	-	hydrolysis
[Ref.: #65492]	cellobiose ChEBI	-	builds acid from
[Ref.: #65492]	cellobiose ChEBI	+	assimilation
[Ref.: #65492]	chitin ChEBI	-	hydrolysis
[Ref.: #65492]	D-fructose ChEBI	-	builds acid from
[Ref.: #65492]	D-fructose ChEBI	+	assimilation
[Ref.: #65492]	D-galactose ChEBI	-	builds acid from
[Ref.: #65492]	D-galactose ChEBI	+	assimilation
[Ref.: #65492]	D-glucose ChEBI	+	assimilation
[Ref.: #65492]	D-mannitol ChEBI	+	assimilation
[Ref.: #65492]	D-mannose ChEBI	-	builds acid from
[Ref.: #65492]	D-mannose ChEBI	+	assimilation
[Ref.: #65492]	D-ribose ChEBI	-	builds acid from
[Ref.: #65492]	D-ribose ChEBI	+	assimilation
[Ref.: #65492]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #65492]	D-sorbitol ChEBI	+	assimilation
[Ref.: #65492]	D-xylose ChEBI	+	assimilation
[Ref.: #65492]	D-xylose ChEBI	-	builds acid from
[Ref.: #65492]	decanoate ChEBI	+	assimilation
[Ref.: #65492]	disodium malate ChEBI	+	assimilation
[Ref.: #65492]	dna ChEBI	-	hydrolysis
[Ref.: #65492]	esculin ChEBI	-	hydrolysis
[Ref.: #65492]	gelatin ChEBI	-	hydrolysis
[Ref.: #65492]	glucose ChEBI	-	builds acid from
[Ref.: #65492]	glucose ChEBI	-	fermentation
[Ref.: #65492]	L-arabinose ChEBI	-	builds acid from
[Ref.: #65492]	L-arabinose ChEBI	+	assimilation
[Ref.: #65492]	L-proline ChEBI	+	assimilation
[Ref.: #65492]	L-sorbose ChEBI	+	assimilation
[Ref.: #65492]	L-tyrosine ChEBI	+	hydrolysis
[Ref.: #65492]	lactose ChEBI	-	builds acid from
[Ref.: #65492]	lactose ChEBI	+	assimilation
[Ref.: #65492]	malate ChEBI	+	assimilation
[Ref.: #65492]	maltose ChEBI	-	builds acid from
[Ref.: #65492]	maltose ChEBI	+	assimilation
[Ref.: #65492]	mannitol ChEBI	-	builds acid from
[Ref.: #65492]	myo-inositol ChEBI	-	builds acid from
[Ref.: #65492]	myo-inositol ChEBI	+	assimilation
[Ref.: #65492]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #65492]	nitrate ChEBI	-	reduction
[Ref.: #65492]	phenylacetate ChEBI	+	assimilation
[Ref.: #65492]	potassium gluconate ChEBI	+	assimilation
[Ref.: #65492]	raffinose ChEBI	-	builds acid from
[Ref.: #65492]	raffinose ChEBI	+	assimilation
[Ref.: #65492]	rhamnose ChEBI	+	assimilation
[Ref.: #65492]	rhamnose ChEBI	+	builds acid from
[Ref.: #65492]	sarcosine ChEBI	+	assimilation
[Ref.: #65492]	sodium citrate ChEBI	+	assimilation
[Ref.: #65492]	starch ChEBI	-	hydrolysis
[Ref.: #65492]	sucrose ChEBI	-	builds acid from
[Ref.: #65492]	sucrose ChEBI	+	assimilation
[Ref.: #65492]	tartrate ChEBI	+	assimilation
[Ref.: #65492]	trehalose ChEBI	-	builds acid from
[Ref.: #65492]	trehalose ChEBI	+	assimilation
[Ref.: #65492]	tween 20 ChEBI	+	hydrolysis
[Ref.: #65492]	tween 40 ChEBI	-	hydrolysis
[Ref.: #65492]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65492]	ampicillin ChEBI				yes	10	Unit (disc)
[Ref.: #65492]	carbenicillin ChEBI				yes	100	µg (disc)
[Ref.: #65492]	cefazolin ChEBI	yes	30	µg (disc)
[Ref.: #65492]	cefoperazone ChEBI	yes	75	µg (disc)
[Ref.: #65492]	ceftazidime ChEBI				yes	30	µg (disc)
[Ref.: #65492]	ceftriaxone ChEBI				yes	30	µg (disc)
[Ref.: #65492]	cefuroxime ChEBI				yes	30	µg (disc)
[Ref.: #65492]	cephalexin ChEBI				yes	30	µg (disc)
[Ref.: #65492]	cephradine ChEBI				yes	30	µg (disc)
[Ref.: #65492]	ciprofloxacin ChEBI				yes	5	µg (disc)
[Ref.: #65492]	furazolidone ChEBI				yes	300	µg (disc)
[Ref.: #65492]	midecamycin ChEBI				yes	30	µg (disc)
[Ref.: #65492]	norfloxacin ChEBI				yes	10	µg (disc)
[Ref.: #65492]	ofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #65492]	oxacillin ChEBI				yes	1	µg (disc)
[Ref.: #65492]	penicillin ChEBI				yes	10	Unit (disc)
[Ref.: #65492]	piperacillin ChEBI	yes	100	µg (disc)
[Ref.: #65492]	polymyxin b ChEBI				yes	300	Unit (disc)
[Ref.: #65492]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65492]		hydrogen sulfide ChEBI	yes
[Ref.: #65492]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65492]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65492]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65492]	beta-galactosidase	-	3.2.1.23
[Ref.: #65492]	catalase	+	1.11.1.6
[Ref.: #65492]	cytochrome oxidase	-	1.9.3.1
[Ref.: #65492]	lipase (C 14)	-
[Ref.: #65492]	phenylalanine deaminase	-	4.3.1.5
[Ref.: #65492]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65492]

Fatty acid	Percentage
C15:1 iso G	25.1
C15:0 iso	20.8
anteiso-C17:1 B / iso-C17:1 I	13.8
C17:0 iso 3OH	13.2
C17:0 iso	4.4
C15:0 iso 3OH	3.7
C13:0 iso	3.3
unkown 13.565	2.3
C17:1 iso ω10c	2.1
iso-C15:1 AT 5	1.7
C16:0 iso	1.2
unkown 16.582	1.1

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

[Ref.: #67771]	Sample type/isolated from	From soil of Erdos grassland of Inner Mongolia
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #65492]	Sample type/isolated from	grassland soil
[Ref.: #65492]	Geographic location (country and/or sea, region)	Erdos grassland, Inner Mongolia
[Ref.: #65492]	Country	China
[Ref.: #65492]	Country ISO 3 Code	CHN
[Ref.: #65492]	Continent	Asia
[Ref.: #65492]	Geographic location	39.8300°/108.7200°
[Ref.: #65492]	Enrichment culture	1/10 TSA
[Ref.: #65492]	Enrichment culture duration	7 days
[Ref.: #65492]	Enrichment culture temperature	28 ̊C
[Ref.: #65492]	Isolation/enrichment procedure	One gram of soil was suspended in 100 ml 0.85 % NaCl and shaken at 28 °C for 2 h. The mixture was serially diluted.
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Grassland
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KY828215 (>99% sequence identity) for Edaphobaculum flavum subclade from Microbeatlas

Aquatic Samples	33
Soil Samples	406
Animal Samples	33
Plant Samples	110
Total Samples	582

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.: #65492]	Edaphobaculum flavum strain 1-116 16S ribosomal RNA gene, partial sequence	KY828215		GenBank ENA

[Ref.: #65492]	GC-content	43.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	43.2 mol%

Availability in culture collections External links

[Ref.: #65492]

Culture collection no.

CCTCC AB 2017054, KCTC 52843

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Edaphobaculum flavum gen. nov., sp. nov., a member of family Chitinophagaceae, isolated from grassland soil.	Cao M, Huang J, Li J, Qiao Z, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.002316	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 )

#65492

Min Cao, Jing Huang, Jingxin Li, Zixu Qiao and Gejiao Wang: Edaphobaculum flavum gen. nov., sp. nov., a member of family Chitinophagaceae, isolated from grassland soil. IJSEM 67: 4475 - 4481 2017 ( DOI 10.1099/ijsem.0.002316 , PubMed 28920838 )

#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 .

* These data were automatically processed and therefore are not curated

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