Name: Empedobacter brevis CL 88-76
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 138772

Type strain:

Species: Empedobacter brevis

Strain Designation: CL 88-76

Culture col. no.: CIP 103104, ATCC 43319, CCM 3299, NCTC 11099, CCUG 7320, LMG 4011, LMG 12437, IFO 14943, JCM 1276, CFBP 3031, IAM 14197, JCM 21064, KCTC 2489, KCTC 2902, NBRC 14943, VTT E-91455

Strain history: CIP <- 1988, NCTC, Flavobacterium breve <- J. Wust, Zürich, Switzerland: strain CL 88-76

NCBI tax ID(s): 1218108 (strain), 247 (species)

SI-ID 2814

LMG 4011, ATCC 43319, CCM 3299, CCUG 7320, CIP 103104, IFO 14943, LMG 12437, NCTC 11099, JCM 1276, IAM 14197, KCTC 2489, KCTC 2902, CIP 10314, NBRC 14943, JCM 21064, CFBP 3031, VTT E-91455

Other strains from Empedobacter brevis

Section

Empedobacter brevis CL 88-76 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from Human bronchial secretion.

Gram-negative
rod-shaped
mesophilic
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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Weeksellaceae*
	Genus	*Empedobacter*
	Species	**Empedobacter brevis**
	Full Scientific Name (LPSN)	Empedobacter brevis (Holmes and Owen 1982 ex Lustig 1890) Vandamme et al. 1994

	Synonym	"Flavobacterium* brevis"*
	Synonym	Flavobacterium breve

Information on morphological and physiological properties Morphology

[Ref.: #40523]	Gram stain	negative

[Ref.: #40523]	Cell shape	rod-shaped

[Ref.: #40523]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #40523]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #40523]

Culture medium growth

[Ref.: #40523]

Culture medium composition

expand / minimize

[Ref.: #40523]

Culture medium

CIP Medium 3

[Ref.: #40523]

Culture medium growth

[Ref.: #40523]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #40523]

Culture medium

CIP Medium 72

[Ref.: #40523]

Culture medium growth

[Ref.: #40523]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #40523]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #40523]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #40523]

Oxygen tolerance

obligate aerobe

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #40523]		nitrate ChEBI	-	reduction
[Ref.: #40523]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #40523]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #40523]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #40523]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #40523]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #40523]	7369	-	+	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #44972]	Sample type/isolated from	Human bronchial secretion
[Ref.: #44972]	Country	Switzerland
[Ref.: #44972]	Country ISO 3 Code	CHE
[Ref.: #44972]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Bronchial secretion of a 70-year-old female patient with chronic bronchitis
[Ref.: #67770]	Geographic location (country and/or sea, region)	Zurich
[Ref.: #67770]	Country	Switzerland
[Ref.: #67770]	Country ISO 3 Code	CHE
[Ref.: #67770]	Continent	Europe

[Ref.: #40523]	Sample type/isolated from	Human, Bronchial secretion
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Infection	#Patient	-
#Host Body-Site	#Oral cavity and airways	#Lung
#Host Body Product	#Fluids	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM177497 (>99% sequence identity) for Empedobacter brevis subclade from Microbeatlas

Aquatic Samples	588
Soil Samples	324
Animal Samples	1470
Plant Samples	188
Total Samples	2570

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

[Ref.: #40523]

Biosafety level

Risk group (French classification)

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.: #67770]	Flavobacterium breve 16S ribosomal RNA	D14022	1262	ENA	247 tax ID
[Ref.: #67770]	Empedobacter brevis partial 16S rRNA gene type strain LMG 4011T	AM177497	1485	ENA	247 tax ID
[Ref.: #67770]	Empedobacter brevis gene for 16S ribosomal RNA, partial cds, strain: JCM 1276	LC050176	1441	ENA	247 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Empedobacter brevis NBRC 14943 = ATCC 43319	GCA_000382425	scaffold	GenBank	1218108 tax ID
[Ref.: #67770]	Empedobacter brevis NBRC 14943 = ATCC 43319	GCA_007990795	contig	GenBank	1218108 tax ID
[Ref.: #66792]	Empedobacter brevis NBRC 14943 = ATCC 43319	1218108.8	wgs	PATRIC	1218108 tax ID	*
[Ref.: #66792]	Empedobacter brevis NBRC 14943 = ATCC 43319	1218108.3	wgs	PATRIC	1218108 tax ID	*
[Ref.: #66792]	Empedobacter brevis ATCC 43319	2521172654	draft	JGI IMG/M	1218108 tax ID	*

[Ref.: #67770]

GC-content

32.4 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Empedobacter brevis NBRC 14943 = ATCC 43319 PATRIC: 1218108.8
[Ref.: #69480]	motile	no	89.753	no
[Ref.: #69480]	gram-positive	no	97.37	no
[Ref.: #69480]	anaerobic	no	98.762	no
[Ref.: #69480]	aerobic	yes	85.109	no
[Ref.: #69480]	halophile	no	85.157	no
[Ref.: #69480]	spore-forming	no	95.298	no
[Ref.: #69480]	thermophile	no	99.578	yes
[Ref.: #69480]	glucose-util	yes	80.714	no
[Ref.: #69480]	flagellated	no	96.624	no
[Ref.: #69480]	glucose-ferment	no	93.07	no

Availability in culture collections External links

[Ref.: #40523]

Culture collection no.

CIP 103104, ATCC 43319, CCM 3299, NCTC 11099, CCUG 7320, LMG 4011, LMG 12437, IFO 14943, JCM 1276, CFBP 3031, IAM 14197, JCM 21064, KCTC 2489, KCTC 2902, NBRC 14943, VTT E-91455

[Ref.: #95430]

SI-ID 2814

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Algoriella xinjiangensis gen. nov., sp. nov., a new psychrotolerant bacterium of the family Flavobacteriaceae.	Yang N, Zhang L, Sun C	Antonie Van Leeuwenhoek	10.1007/s10482-015-0564-6	2015	*

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 )

#40523 Collection of Institut Pasteur ; Curators of the CIP; CIP 103104
#44972 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 7320

#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;

#68382

Automatically annotated from API zym .

#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) .

#95430

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-ID2814.1 )

* These data were automatically processed and therefore are not curated

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Empedobacter brevis NBRC 14943 = ATCC 43319

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