Flavihumibacter sediminis (CJ663, KACC 18874, JCM 31431)

Name: Flavihumibacter sediminis (CJ663, KACC 18874, JCM 31431)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133189

Type strain

Strain Designation CJ663

Culture col. no. CJ663 KACC 18874 JCM 31431

NCBI tax ID(s) 1571481

Special Collections JCM Literature strains

Links

Flavihumibacter sediminis CJ663 is an aerobe, Gram-positive, rod-shaped prokaryote that forms circular colonies and was isolated from tidal flat sedimen.

Gram-positive rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 133287

JCM 31431

@ref 20215

Last LPSN update 2025-12-16 10:01:42

Domain Pseudomonadati

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Flavihumibacter

Species Flavihumibacter sediminis

Full scientific name Flavihumibacter sediminis Lee and Cha 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
24983	positive	2.2 µm	0.5 µm	rod-shaped
125439	negative					96.5

Colony morphology

@ref	Colony color	Colony shape	Medium used
24983	light yellow	circular	R2A agar (Reasoner's 2A agar)

Culture and growth conditions

Culture medium

@ref	Name	Growth
24983	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24983	positive	growth	20.0-37.0
24983	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
24983	positive	optimum	7
24983	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24983	aerobe
125439	obligate aerobe	94.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24983	NaCl	positive	growth	0.0-1.0 %
24983	NaCl		optimum	0 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24983	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
24983	17256 ChEBI	2-deoxyadenosine	-	builds acid from
24983	30916 ChEBI	2-oxoglutarate	+	carbon source
24983	37054 ChEBI	3-hydroxybutyrate	-	builds acid from
24983	16724 ChEBI	4-hydroxybutyrate	-	builds acid from
24983	18101 ChEBI	4-hydroxyphenylacetic acid	-	builds acid from
24983	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
24983	30089 ChEBI	acetate	+	carbon source
24983	16335 ChEBI	adenosine	-	builds acid from
24983	16335 ChEBI	adenosine	+	carbon source
24983	40585 ChEBI	alpha-cyclodextrin	+	carbon source
24983	17925 ChEBI	alpha-D-glucose	+	carbon source
24983	27613 ChEBI	amygdalin	+	builds acid from
24983	27613 ChEBI	amygdalin	+	carbon source
24983	18305 ChEBI	arbutin	+	builds acid from
24983	18305 ChEBI	arbutin	+	carbon source
24983	495055 ChEBI	beta-cyclodextrin	+	carbon source
24983		casein	+	hydrolysis
24983	17057 ChEBI	cellobiose	+	builds acid from
24983	17057 ChEBI	cellobiose	+	carbon source
24983	62968 ChEBI	cellulose	+	hydrolysis
24983	17108 ChEBI	D-arabinose	+	builds acid from
24983	18333 ChEBI	D-arabitol	-	builds acid from
24983	15824 ChEBI	D-fructose	+	builds acid from
24983	15824 ChEBI	D-fructose	+	carbon source
24983	28847 ChEBI	D-fucose	-	builds acid from
24983	12936 ChEBI	D-galactose	+	builds acid from
24983	12936 ChEBI	D-galactose	+	carbon source
24983	8391 ChEBI	D-gluconate	-	builds acid from
24983	17634 ChEBI	D-glucose	+	assimilation
24983	17634 ChEBI	D-glucose	+	builds acid from
24983	14314 ChEBI	D-glucose 6-phosphate	+	carbon source
24983	62318 ChEBI	D-lyxose	-	builds acid from
24983	16899 ChEBI	D-mannitol	-	assimilation
24983	16899 ChEBI	D-mannitol	-	builds acid from
24983	16024 ChEBI	D-mannose	+	assimilation
24983	16024 ChEBI	D-mannose	+	builds acid from
24983	16988 ChEBI	D-ribose	-	builds acid from
24983	17924 ChEBI	D-sorbitol	-	builds acid from
24983	16443 ChEBI	D-tagatose	-	builds acid from
24983	65327 ChEBI	D-xylose	-	builds acid from
24983	65327 ChEBI	D-xylose	+	builds acid from
24983	27689 ChEBI	decanoate	-	assimilation
24983	23652 ChEBI	dextrin	+	carbon source
24983	16991 ChEBI	dna	-	hydrolysis
24983	17113 ChEBI	erythritol	-	builds acid from
24983	4853 ChEBI	esculin	+	hydrolysis
24983		esculin ferric citrate	+	builds acid from
24983	16813 ChEBI	galactitol	-	builds acid from
24983	5291 ChEBI	gelatin	+	hydrolysis
24983	28066 ChEBI	gentiobiose	+	builds acid from
24983	28066 ChEBI	gentiobiose	+	carbon source
24983	29042 ChEBI	glucose 1-phosphate	+	carbon source
24983	17754 ChEBI	glycerol	-	builds acid from
24983	28087 ChEBI	glycogen	+	builds acid from
24983	28087 ChEBI	glycogen	+	carbon source
24983	15443 ChEBI	inulin	+	builds acid from
24983	15443 ChEBI	inulin	+	carbon source
24983	21217 ChEBI	L-alaninamide	+	carbon source
24983	30849 ChEBI	L-arabinose	+	assimilation
24983	30849 ChEBI	L-arabinose	+	builds acid from
24983	18403 ChEBI	L-arabitol	-	builds acid from
24983	17196 ChEBI	L-asparagine	-	builds acid from
24983	18287 ChEBI	L-fucose	+	builds acid from
24983	62345 ChEBI	L-rhamnose	-	builds acid from
24983	17266 ChEBI	L-sorbose	-	builds acid from
24983	65328 ChEBI	L-xylose	-	builds acid from
24983	17716 ChEBI	lactose	+	builds acid from
24983	17306 ChEBI	maltose	+	assimilation
24983	17306 ChEBI	maltose	+	builds acid from
24983	61993 ChEBI	maltotriose	+	carbon source
24983	6731 ChEBI	melezitose	+	builds acid from
24983	28053 ChEBI	melibiose	+	builds acid from
24983	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
24983	43943 ChEBI	methyl alpha-D-mannoside	+	builds acid from
24983	43943 ChEBI	methyl alpha-D-mannoside	+	carbon source
24983	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from
24983	37657 ChEBI	methyl D-glucoside	+	carbon source
24983	51850 ChEBI	methyl pyruvate	+	carbon source
24983	75146 ChEBI	monomethyl succinate	+	carbon source
24983	17268 ChEBI	myo-inositol	-	builds acid from
24983	63154 ChEBI	N-acetyl-beta-D-mannosamine	+	carbon source
24983	44337 ChEBI	N-acetyl-L-glutamate	+	carbon source
24983	506227 ChEBI	N-acetylglucosamine	+	assimilation
24983	506227 ChEBI	N-acetylglucosamine	+	builds acid from
24983	506227 ChEBI	N-acetylglucosamine	+	carbon source
24983	17632 ChEBI	nitrate	-	reduction
24983	16301 ChEBI	nitrite	-	reduction
24983	18394 ChEBI	palatinose	+	carbon source
24983	18401 ChEBI	phenylacetate	-	assimilation
24983	32032 ChEBI	potassium gluconate	-	builds acid from
24983	15361 ChEBI	pyruvate	+	carbon source
24983	16634 ChEBI	raffinose	+	builds acid from
24983	16634 ChEBI	raffinose	+	carbon source
24983	15963 ChEBI	ribitol	-	builds acid from
24983	17814 ChEBI	salicin	+	builds acid from
24983	17814 ChEBI	salicin	+	carbon source
24983	53258 ChEBI	sodium citrate	-	assimilation
24983	17164 ChEBI	stachyose	+	carbon source
24983	28017 ChEBI	starch	-	hydrolysis
24983	28017 ChEBI	starch	+	builds acid from
24983	30031 ChEBI	succinate	-	builds acid from
24983	17992 ChEBI	sucrose	+	builds acid from
24983	17992 ChEBI	sucrose	+	carbon source
24983	17748 ChEBI	thymidine	-	builds acid from
24983	27082 ChEBI	trehalose	+	builds acid from
24983	27082 ChEBI	trehalose	+	carbon source
24983	32528 ChEBI	turanose	+	builds acid from
24983	32528 ChEBI	turanose	+	carbon source
24983	53426 ChEBI	tween 80	-	hydrolysis
24983	16704 ChEBI	uridine	-	builds acid from
24983	16695 ChEBI	uridine 5'-monophosphate	+	carbon source
24983	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
24983	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
24983	acid phosphatase	+	3.1.3.2
24983	alkaline phosphatase	+	3.1.3.1
24983	alpha-chymotrypsin	+	3.4.21.1
24983	alpha-fucosidase	-	3.2.1.51
24983	alpha-galactosidase	+	3.2.1.22
24983	alpha-glucosidase	+	3.2.1.20
24983	alpha-mannosidase	+	3.2.1.24
24983	arginine dihydrolase	+	3.5.3.6
24983	beta-galactosidase	+	3.2.1.23
24983	beta-glucosidase	+	3.2.1.21
24983	beta-glucuronidase	-	3.2.1.31
24983	catalase	+	1.11.1.6
24983	cystine arylamidase	+	3.4.11.3
24983	esterase (C 4)	+
24983	esterase Lipase (C 8)	+
24983	leucine arylamidase	+	3.4.11.1
24983	lipase (C 14)	-
24983	N-acetyl-beta-glucosaminidase	+	3.2.1.52
24983	naphthol-AS-BI-phosphohydrolase	+
24983	trypsin	+	3.4.21.4
24983	urease	+	3.5.1.5
24983	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture
24983	tidal flat sedimen	Ganghwa-do	Republic of Korea	KOR	Asia	37.5922	126.457 37.5922/126.457	R2A agar (Reasoner's 2A agar;BD)
67770	Tidal flat sediment in Ganghwa-do		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KP126826 (>99% sequence identity) for Flavihumibacter sediminis subclade from Microbeatlas

Aquatic Samples	39
Soil Samples	76
Animal Samples	61
Plant Samples	1
Total Samples	177

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID
66792	ASM2235228v1 assembly for Flavihumibacter sediminis CJ663	contig	GCA_022352285	1571481.3	1571481

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24983	Flavihumibacter sediminis strain CJ663 16S ribosomal RNA gene, partial sequence	KP126826	1420		1571481

GC content

@ref	GC-content (mol%)	Method
67770	47.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavihumibacter sediminis CJ663
NCBI: GCA_022352285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	86.50	no
125439	motility	BacteriaNetⓘ	no	66.50	no
125439	gram_stain	BacteriaNetⓘ	negative	96.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavihumibacter sediminis CJ663
NCBI: GCA_022352285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	69.08	yes
125438	anaerobic	anaerobicⓘ	no	96.78	yes
125438	aerobic	aerobicⓘ	yes	88.51	yes
125438	spore-forming	spore-formingⓘ	no	88.88	no
125438	thermophilic	thermophileⓘ	no	98.47	yes
125438	flagellated	motile2+ⓘ	no	87.13	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pinibacter aurantiacus gen. nov., sp. nov., isolated from rhizospheric soil of a pine tree.	Huq MA, Siddiqi MZ, Balusamy SR, Rahman MM, Ashrafudoulla M, Apu MAI, Maitra P, Naserkheil M, Park JH, Akter S	Int J Syst Evol Microbiol	10.1099/ijsem.0.005132	2021
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 sediminis sp. nov., isolated from tidal flat sediment.	Lee DH, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001349	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 )
#24983	D.-H. C. Lee, Chang-Jun: Flavihumibacter sediminis sp. nov., isolated from tidal flat sediment. IJSEM 66: 4310 - 4314 2016 ( DOI 10.1099/ijsem.0.001349 , PubMed 27472918 )
#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;
#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 .
#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 )

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Flavihumibacter sediminis (CJ663, KACC 18874, JCM 31431)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_022352285

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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