Chryseobacterium scophthalmum (DSM 16779, ATCC 700039, CCM 4109)

Name: Chryseobacterium scophthalmum (DSM 16779, ATCC 700039, CCM 4109)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5673

Type strain

Strain Designation MM1

Culture col. no. DSM 16779 ATCC 700039 CCM 4109 CCUG 33454 CIP 104199 2 more

NCBI tax ID(s) 59733

Special Collections DSMZ CCUG CIP

History DSMZ <- CIP <- J. F. Bernadet, INRA, Jouy-en-Josas, France; MM1 <- CCM <- B. Austin, Herriot-Watt Univ., Edinburg, UK CIP <- 1994, J.F. Bernardet, INRA, Jouy-en-Josas, France: strain MM1, Flavobacterium scophthalmum <- CCM <- B. Austin, Herriot-Watt Univ., Edinburg, UK

Links

Chryseobacterium scophthalmum MM1 is an animal pathogen that was isolated from turbot, gill.

animal pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 9865

LMG 13028,CCM 4109,CIP 104199,ATCC 700039,CCUG 33454,NCIMB 13463,KCTC 2907,BCRC 17334,CCRC 17334,DSM 16779

@ref 20215

Last LPSN update 2026-05-29 08:26:13

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Weeksellaceae

Genus Chryseobacterium

Species Chryseobacterium scophthalmum

Full scientific name Chryseobacterium scophthalmum (Mudarris et al. 1994) Vandamme et al. 1994

Synonyms (1)

Flavobacterium scophthalmum

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	91
125438	96.955	negative
125439	99.688	negative

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6582	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
37164	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
122526	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6582	positive	growth	30
37164	positive	growth	30
51528	positive	growth	18-24

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.079

Spore formation

@ref	Spore formation	Confidence
125439		99.671

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fishes
#Host Body-Site	#Oral cavity and airways

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6582	turbot, gill	Scotland	United Kingdom	GBR	Europe
51528	Turbot (Scophthalmus maximus),gills		United Kingdom	GBR	Europe
122526	Turbot, gill	Scotland	United Kingdom	GBR	Europe	1987

Taxonmaps

69479

Global distribution of 16S sequence AJ271009 (>99% sequence identity) for Chryseobacterium scophthalmum from Microbeatlas

Aquatic Samples	104
Soil Samples	35
Animal Samples	160
Plant Samples	172
Total Samples	471

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
6582		2	Risk group (German classification) According to TRBA 466
122526		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2690315624 annotated assembly for Chryseobacterium scophthalmum DSM 16779	contig	GCA_900143185	59733.4	2690315624	59733	77.31
124043	ASM4243348v1 assembly for Chryseobacterium scophthalmum CCM 4109	contig	GCA_042433485			59733	73.92

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6582	Chryseobacterium scophthalmum 16S rRNA gene, strain LMG 13028	AJ271009	1458		59733
124043	Chryseobacterium scophthalmum strain CCM 4109 16S ribosomal RNA gene, partial sequence.	MT760105	1329		59733

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2690315624 annotated assembly for Chryseobacterium scophthalmum DSM 16779
NCBI: GCA_900143185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.08	no
125439	gram_stain	BacteriaNetⓘ	negative	99.69	no
125439	motility	BacteriaNetⓘ	no	81.66	no
125439	spore_formation	BacteriaNetⓘ	no	99.67	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chryseobacterium scophthalmum strain DSM 16779
PATRIC: 59733.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.96	no
125438	anaerobic	anaerobicⓘ	no	97.31	no
125438	spore-forming	spore-formingⓘ	no	87.18	no
125438	aerobic	aerobicⓘ	yes	87.09	no
125438	thermophilic	thermophileⓘ	no	97.48	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phylogenetic insights into the diversity of Chryseobacterium species.	Siddaramappa S, Narjala A, Viswanathan V, Maliye C, Lakshminarayanan R.	Access Microbiol	10.1099/acmi.0.000019	2019
Genetics	Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology.	Karimi E, Geslain E, KleinJan H, Tanguy G, Legeay E, Corre E, Dittami SM.	Genome Biol Evol	10.1093/gbe/evz278	2020
	Genome sequence of Chryseobacterium scophthalmum LGBM4, isolated from a red-backed salamander (Plethodon cinereus) in Rugar Woods, NY, USA.	Grossman L, McLaughlin B, Ankrah NYD, Garneau DE.	Microbiol Resour Announc	10.1128/mra.00124-25	2025
Genetics	Characterization and Genomics of Pectinolytic Bacteria Isolated from Soft Rot Symptomatic Produce.	Radke K, Rivers B, Simpkins M, Hardy J, Schachterle JK.	Pathogens	10.3390/pathogens13121096	2024
	Chemical basis of microbiome preference in the nematode C. elegans.	Chai VZ, Farajzadeh T, Meng Y, Lo SB, Asaed TA, Taylor CJ, Glater EE.	Sci Rep	10.1038/s41598-024-51533-6	2024
Pathogenicity	Distinct members of the Caenorhabditis elegans CeMbio reference microbiota exert cryptic virulence that is masked by host defense.	Gonzalez X, Irazoqui JE.	Mol Microbiol	10.1111/mmi.15258	2024
	Characterization and pathogenicity study of Chryseobacterium scophthalmum recovered from gill lesions of diseased golden mahseer, Tor putitora (Hamilton, 1822) in India	Shahi N, Sharma P, Pandey J, Bisht I, Mallik SK.	Aquaculture	10.1016/j.aquaculture.2017.11.018	2018
Phylogeny	Culturomics revealed the bacterial constituents of the microbiota of a 10-year-old laboratory culture of planarian species S. mediterranea.	Kangale LJ, Raoult D, Fournier PE, Ghigo E.	Sci Rep	10.1038/s41598-021-03719-5	2021
Metabolism	[Isolation, identification and characterization of 68 protease-producing bacterial strains from the Arctic].	Chen M, Li H, Chen W, Diao W, Liu C, Yuan M, Li X.	Wei Sheng Wu Xue Bao		2013
Enzymology	Pathogenic Potential and Control of Chryseobacterium Species from Clinical, Fish, Food and Environmental Sources.	Mwanza EP, Hugo A, Charimba G, Hugo CJ.	Microorganisms	10.3390/microorganisms10050895	2022
Genetics	Detection by Whole-Genome Sequencing of a Novel Metallo-beta-Lactamase Produced by Wautersiella falsenii Causing Urinary Tract Infection in Tunisia.	Maaroufi R, Dziri O, Hadjadj L, Diene SM, Rolain JM, Chouchani C.	Pol J Microbiol	10.33073/pjm-2022-010	2022
Pathogenicity	CeMbio - The Caenorhabditis elegans Microbiome Resource.	Dirksen P, Assie A, Zimmermann J, Zhang F, Tietje AM, Marsh SA, Felix MA, Shapira M, Kaleta C, Schulenburg H, Samuel BS.	G3 (Bethesda)	10.1534/g3.120.401309	2020
	Small RNAs couple embryonic developmental programs to gut microbes.	Ohno H, Bao Z.	Sci Adv	10.1126/sciadv.abl7663	2022
Phylogeny	Atypical flavobacteria recovered from diseased fish in the Western United States.	Heckman TI, Yazdi Z, Pomaranski EK, Sebastiao FA, Mukkatira K, Vuglar BM, Cain KD, Loch TP, Soto E.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1149032	2023
	Preliminary differentiation of food strains of Chryseobacterium and Empedobacter using multilocus enzyme electrophoresis	Hugo CJ, Jooste PJ.	Food Microbiol	10.1006/fmic.1996.0069	1997
	Immunization with bacterial antigens: Flavobacterium and Flexibacter infections.	Bernardet JF.	Dev Biol Stand		1997
	Comparison of traditional field retting and Phlebia radiata Cel 26 retting of hemp fibres for fibre-reinforced composites.	Liu M, Ale MT, Kolaczkowski B, Fernando D, Daniel G, Meyer AS, Thygesen A.	AMB Express	10.1186/s13568-017-0355-8	2017
Enzymology	Occurrence and characterisation of biofilms in drinking water systems of broiler houses.	Maes S, Vackier T, Nguyen Huu S, Heyndrickx M, Steenackers H, Sampers I, Raes K, Verplaetse A, De Reu K.	BMC Microbiol	10.1186/s12866-019-1451-5	2019
Phylogeny	Use of a packed-column bioreactor for isolation of diverse protease-producing bacteria from antarctic soil.	Wery N, Gerike U, Sharman A, Chaudhuri JB, Hough DW, Danson MJ.	Appl Environ Microbiol	10.1128/aem.69.3.1457-1464.2003	2003
Phylogeny	Chryseobacterium formosus sp. nov., a bacterium isolated from an ancient tree trunk.	Akter S, NGO HT, Du J, Won K, Singh H, Yin CS, Kook M, Yi TH.	Arch Microbiol	10.1007/s00203-015-1137-9	2015
Phylogeny	Chryseobacterium piscium sp. nov., isolated from fish of the South Atlantic Ocean off South Africa.	de Beer H, Hugo CJ, Jooste PJ, Vancanneyt M, Coenye T, Vandamme P.	Int J Syst Evol Microbiol	10.1099/ijs.0.64014-0	2006
Phylogeny	Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce).	Young CC, Kampfer P, Shen FT, Lai WA, Arun AB.	Int J Syst Evol Microbiol	10.1099/ijs.0.63331-0	2005
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	Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea.	Kangale LJ, Raoult D, Ghigo E, Fournier PE	Sci Rep	10.1038/s41598-021-90562-3	2021
Phylogeny	Chryseobacterium mulctrae sp. nov., isolated from raw cow's milk.	Yoon SH, Lee JE, Han RH, Kwon M, Kim GB	Int J Syst Evol Microbiol	10.1099/ijsem.0.003647	2019
Phylogeny	Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of Chryseobacterium gleum.	Nguyen NL, Kim YJ, Hoang VA, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.045427-0	2013
Phylogeny	Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater.	Joung Y, Song J, Lee K, Oh HM, Joh K, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.017707-0	2009
Phylogeny	Chryseobacterium aquaticum sp. nov., isolated from a water reservoir.	Kim KK, Lee KC, Oh HM, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.65491-0	2008
Phylogeny	Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch.	Kim MK, Im WT, Shin YK, Lim JH, Kim SH, Lee BC, Park MY, Lee KY, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.02998-0	2004
Phylogeny	Flavobacterium scophthalmum sp. nov., a pathogen of turbot (Scophthalmus maximus L.).	Mudarris M, Austin B, Segers P, Vancanneyt M, Hoste B, Bernardet JF	Int J Syst Bacteriol	10.1099/00207713-44-3-447	1994

References

#6582	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16779
#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 )
#37164	; Curators of the CIP;
#51528	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 33454
#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) .
#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 .
#122526	Collection of Institut Pasteur ; Curators of the CIP; CIP 104199
#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

Chryseobacterium scophthalmum (DSM 16779, ATCC 700039, CCM 4109)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900143185

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media