Flavobacterium caeni (CGMCC 1.7031, NBRC 104239, LM5)

Name: Flavobacterium caeni (CGMCC 1.7031, NBRC 104239, LM5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133522

Type strain

Strain Designation LM5

Culture col. no. CGMCC 1.7031 NBRC 104239 LM5 CIP 110388

NCBI tax ID(s) 490189

Special Collections Literature strains CIP

History CIP <- 2012, NBRC <- Z.P. Liu, Chinese Acad. Sci., China: strain LM5

Links

Flavobacterium caeni LM5 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Sludge.

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

Name and taxonomic classification

SI-ID 363753

NBRC 104239,CGMCC 1.7031,CIP 110388

@ref 20215

Last LPSN update 2026-05-29 08:38:06

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium caeni

Full scientific name Flavobacterium caeni Liu et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29307	negative	1 µm	0.5 µm	rod-shaped
125439	negative				98.715
125438	negative				97.227
125438					90.5
117092	negative			rod-shaped

Pigmentation

29307

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link
117092	CIP Medium 566		Medium recipe at CIP
117092	CIP Medium 72		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
29307	positive	growth	10-35
29307	positive	optimum	22.5

Culture pH

@ref	Ability	Type	PH	PH range
29307	positive	optimum	7
29307	positive	growth	5.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29307	aerobe
117092	facultative anaerobe
125439	obligate aerobe	91.595

Spore formation

@ref	Spore formation	Confidence
29307
125438		92.303
125439		99.912

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29307	NaCl	positive	growth	0-2 %
29307	NaCl	positive	optimum	0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29307	28644 ChEBI	2-oxopentanoate	+	carbon source
29307	40585 ChEBI	alpha-cyclodextrin	+	carbon source
29307	23652 ChEBI	dextrin	+	carbon source
29307	15740 ChEBI	formate	+	carbon source
29307	28260 ChEBI	galactose	+	carbon source
29307	17234 ChEBI	glucose	+	carbon source
29307	28087 ChEBI	glycogen	+	carbon source
29307	17716 ChEBI	lactose	+	carbon source
29307	17306 ChEBI	maltose	+	carbon source
29307	37684 ChEBI	mannose	+	carbon source
117092	17632 ChEBI	nitrate	-	reduction
117092	16301 ChEBI	nitrite	-	reduction
29307	26271 ChEBI	proline	+	carbon source
29307	17272 ChEBI	propionate	+	carbon source
29307	26986 ChEBI	threonine	+	carbon source
29307	16704 ChEBI	uridine	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
117092	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
29307	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
29307	alkaline phosphatase	+	3.1.3.1
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
29307	catalase	+	1.11.1.6
117092	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
29307	cytochrome oxidase	+	1.9.3.1
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
117092	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
117092	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	sulfopterin metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	NAD metabolism	83.33	15 of 18
66794	starch degradation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	propionate fermentation	70	7 of 10
66794	purine metabolism	68.09	64 of 94
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	glycogen metabolism	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	alanine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	methionine metabolism	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	glutathione metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	heme metabolism	57.14	8 of 14
66794	tryptophan metabolism	52.63	20 of 38
66794	isoleucine metabolism	50	4 of 8
66794	Entner Doudoroff pathway	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	degradation of pentoses	46.43	13 of 28
66794	leucine metabolism	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	vitamin B6 metabolism	45.45	5 of 11
66794	pentose phosphate pathway	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	mevalonate metabolism	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	degradation of sugar acids	40	10 of 25
66794	coenzyme M biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	degradation of hexoses	38.89	7 of 18
66794	vitamin B1 metabolism	38.46	5 of 13
66794	oxidative phosphorylation	38.46	35 of 91
66794	histidine metabolism	37.93	11 of 29
66794	ketogluconate metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	pantothenate biosynthesis	33.33	2 of 6
66794	formaldehyde oxidation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	octane oxidation	33.33	1 of 3
66794	phenol degradation	30	6 of 20
66794	arginine metabolism	29.17	7 of 24
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	sulfate reduction	23.08	3 of 13
66794	urea cycle	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	valine metabolism	22.22	2 of 9

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
117092	-	-	+	+	-	+	+	-	-	+	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
29307	Sludge
117092	Dye-treating bioreactor	Beijing	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU313814 (>99% sequence identity) for Flavobacterium caeni subclade from Microbeatlas

Aquatic Samples	480
Soil Samples	397
Animal Samples	106
Plant Samples	132
Total Samples	1115

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
117092	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2596583574 annotated assembly for Flavobacterium caeni CGMCC 1.7031	scaffold	GCA_900101895	490189.4	2596583574	490189	58.87

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
29307	Flavobacterium caeni strain LM5 16S ribosomal RNA gene, partial sequence	EU313814	1387	490189
124043	Flavobacterium caeni gene for 16S rRNA, partial sequence, strain: NBRC 104239.	AB682162	1443	490189
124043	Flavobacterium caeni NBRC 104239 gene for 16S rRNA, partial sequence.	LC752400	579	490189

GC content

29307

GC-content (mol%)52

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2596583574 annotated assembly for Flavobacterium caeni CGMCC 1.7031
NCBI: GCA_900101895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	98.72	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.60	no
125439	motility	BacteriaNetⓘ	no	82.66	no
125439	spore_formation	BacteriaNetⓘ	no	99.91	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium caeni CGMCC 1.7031
NCBI: GCA_900101895.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.23	yes
125438	anaerobic	anaerobicⓘ	no	94.36	no
125438	aerobic	aerobicⓘ	yes	80.45	no
125438	spore-forming	spore-formingⓘ	no	92.30	yes
125438	thermophilic	thermophileⓘ	no	96.62	yes
125438	flagellated	motile2+ⓘ	no	90.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents.	Liu Y, Jin JH, Zhou YG, Liu HC, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.010603-0	2009

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 )
#25720	IJSEM 417 2010 ( DOI 10.1099/ijs.0.010603-0 , PubMed 19651715 )
#29307	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25720
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#117092	Collection of Institut Pasteur ; Curators of the CIP; CIP 110388
#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 )

Content

About us

Flavobacterium caeni (CGMCC 1.7031, NBRC 104239, LM5)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900101895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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