Empedobacter brevis (CIP 103104, ATCC 43319, CCM 3299)

Name: Empedobacter brevis (CIP 103104, ATCC 43319, CCM 3299)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 138772

Type strain

Strain Designation CL 88-76

Culture col. no. CIP 103104 ATCC 43319 CCM 3299 NCTC 11099 CCUG 7320 12 more

NCBI tax ID(s) 1218108 247

Special Collections CCUG JCM KCTC CIP

History NCTC 11099 <-- J. Würst CL 88/76. CIP <- 1988, NCTC, Flavobacterium breve <- J. Wust, Zürich, Switzerland: strain CL 88-76

Links

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

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

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2026-02-09 11:33:11

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Weeksellaceae

Genus Empedobacter

Species Empedobacter brevis

Full scientific name Empedobacter brevis (Holmes and Owen 1982 ex Lustig 1890) Vandamme et al. 1994

Synonyms (2)

"Flavobacterium brevis"
Flavobacterium breve

BacDive ID	Other strains from **Empedobacter brevis** (30)	Type strain
134412	E. brevis CIP 103060
135104	E. brevis B68189, 14-74, CIP 78.46
135183	E. brevis CIP 103067
135866	E. brevis CIP 103061
135982	E. brevis CIP 102965
136020	E. brevis 539-85, CIP 101742
136166	E. brevis CIP 103077
136167	E. brevis CIP 103083
137225	E. brevis CIP 103046
137227	E. brevis CIP 103081
137588	E. brevis 24-74, 90 809, CIP 79.25, NCTC 11307
137597	E. brevis 25-79, CIP 79.41, NCTC 11380
137979	E. brevis CIP 102377
138770	E. brevis CIP 103076
139061	E. brevis 68-78, 8 A, CIP 78.68, NCTC 11308
139489	E. brevis CIP 111032
139517	E. brevis CIP 111072, CIP 200682
142681	E. brevis CCUG 13901, NCTC 11163
142743	E. brevis CCUG 14337 A
142744	E. brevis CCUG 14338
142789	E. brevis CCUG 14815
143498	E. brevis CCUG 19540 B
143857	E. brevis CCUG 21606
143971	E. brevis CCUG 22174
144647	E. brevis CCUG 26050
145353	E. brevis CCUG 28266
165416	E. brevis JCM 6810
165417	E. brevis JCM 6811
171316	E. brevis R528, CIP 109971
171317	E. brevis R563, Legall, CIP 109974

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438			90
125438	negative		97.464
125439	negative		98.9
40523	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Composition	Medium link
40523	MEDIUM 3 - Columbia agar	Columbia agar (39.000 g);distilled water (1000.000 ml)
40523	CIP Medium 3		Medium recipe at CIP
40523	CIP Medium 72		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
40523	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
40523	obligate aerobe
125439	obligate aerobe	95.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
40523	17632 ChEBI	nitrate	-	reduction
40523	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
40523	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
40523	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
40523	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
40523	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
40523	-	+	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Infection	#Patient	-
#Host Body-Site	#Oral cavity and airways	#Lung
#Host Body Product	#Fluids	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
44972	Human bronchial secretion		Switzerland	CHE	Europe
67770	Bronchial secretion of a 70-year-old female patient with chronic bronchitis	Zurich	Switzerland	CHE	Europe
40523	Human, Bronchial secretion

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
40523	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM38242v1 assembly for Empedobacter brevis NBRC 14943 = ATCC 43319	scaffold	GCA_000382425	1218108.3	2521172654	1218108	72.67
67770	ASM799079v1 assembly for Empedobacter brevis NBRC 14943 = ATCC 43319	contig	GCA_007990795	1218108.8		1218108	60.39

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67770	Empedobacter brevis partial 16S rRNA gene type strain LMG 4011T	AM177497	1485	247
67770	Flavobacterium breve 16S ribosomal RNA	D14022	1262	247
67770	Empedobacter brevis gene for 16S ribosomal RNA, partial cds, strain: JCM 1276	LC050176	1441	247
124043	Empedobacter brevis gene for 16S ribosomal RNA, partial sequence, strain: NBRC 14943.	AB517707	1444	247
124043	Empedobacter brevis culture BCCM/LMG:4011 16S ribosomal RNA gene, partial sequence.	PP095703	1380	247

GC content

@ref	GC-content (mol%)	Method
67770	32.4	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: Empedobacter brevis NBRC 14943 = ATCC 43319
NCBI: GCA_000382425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.50	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	motility	BacteriaNetⓘ	no	69.50	no
125439	spore_formation	BacteriaNetⓘ	no	89.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Empedobacter brevis NBRC 14943 = ATCC 43319
PATRIC: 1218108.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.46	no
125438	anaerobic	anaerobicⓘ	no	94.57	yes
125438	spore-forming	spore-formingⓘ	no	88.30	no
125438	aerobic	aerobicⓘ	yes	84.68	no
125438	thermophilic	thermophileⓘ	no	99.48	yes
125438	flagellated	motile2+ⓘ	no	90.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Concurrence of Inactivation Enzyme-Encoding Genes tet(X), bla_EBR, and estT in Empedobacter Species from Chickens and Surrounding Environments.	Chen C, Lv Y, Wu T, Liu J, Guo Y, Huang J.	Foods	10.3390/foods13193201	2024
Phylogeny	Recognition of individual genes in diverse microorganisms by cycling primed in situ amplification.	Kenzaka T, Tamaki S, Yamaguchi N, Tani K, Nasu M.	Appl Environ Microbiol	10.1128/aem.71.11.7236-7244.2005	2005
Phylogeny	Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria.	Mellmann A, Cloud J, Maier T, Keckevoet U, Ramminger I, Iwen P, Dunn J, Hall G, Wilson D, Lasala P, Kostrzewa M, Harmsen D.	J Clin Microbiol	10.1128/jcm.00157-08	2008
	alpha-Lipoic acid increases phagocytosis of some lactic acid bacteria via modulation of CD36 expression.	Nomura N, Miyadai N, Kawase I.	Biosci Microbiota Food Health	10.12938/bmfh.2024-019	2025
	Combination of fluorescent reagents with 2-(4-aminophenyl) benzothiazole and safranin O was useful for analysis of spore structure, indicating the diversity of Bacillales species spores.	Kuwana R, Ito K, Takamatsu H.	Front Microbiol	10.3389/fmicb.2025.1603957	2025
Genetics	Complete genome sequence of astaxanthin-producing bacterium Altererythrobacter ishigakiensis NBRC 107699.	Shi XL, Wu YH, Cheng H, Zhang XQ, Wang CS, Xu XW.	Mar Genomics	10.1016/j.margen.2016.08.001	2016
	Genetic Characterization of the Tetracycline-Resistance Gene tet(X) Carried by Two Epilithonimonas Strains Isolated from Farmed Diseased Rainbow Trout, Oncorhynchus mykiss in Chile.	Concha C, Miranda CD, Santander J, Roberts MC.	Antibiotics (Basel)	10.3390/antibiotics10091051	2021
Metabolism	Rapid discrimination of strain-dependent fermentation characteristics among Lactobacillus strains by NMR-based metabolomics of fermented vegetable juice.	Tomita S, Saito K, Nakamura T, Sekiyama Y, Kikuchi J.	PLoS One	10.1371/journal.pone.0182229	2017
Metabolism	Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales.	Siddaramappa S, Viswanathan V, Thiyagarajan S, Narjala A.	Microb Genom	10.1099/mgen.0.000172	2018
Genetics	Taxonogenomics and description of Vaginella massiliensis gen. nov., sp. nov., strain Marseille P2517^T, a new bacterial genus isolated from the human vagina.	Diop K, Bretelle F, Michelle C, Richez M, Rathored J, Raoult D, Fournier PE, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2016.11.006	2017
	Description and genome-wide analysis of Profundicola chukchiensis gen. nov., sp. nov., marine bacteria isolated from bottom sediments of the Chukchi Sea.	Romanenko L, Otstavnykh N, Kurilenko V, Velansky P, Eremeev V, Mikhailov V, Isaeva MP.	PLoS One	10.1371/journal.pone.0287346	2023
Genetics	Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov.	Sankar SA, Lo CI, Fall B, Sambe-Ba B, Mediannikov O, Diallo I, Labas N, Faye N, Wade B, Raoult D, Fournier PE, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2015.09.013	2015
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
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Rate our new design

Content

About us

Empedobacter brevis (CIP 103104, ATCC 43319, CCM 3299)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000382425

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media