Serratia nematodiphila (DSM 21420, CGMCC 1.6853, DSM 22964)

Name: Serratia nematodiphila (DSM 21420, CGMCC 1.6853, DSM 22964)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5168

Type strain

Strain Designation DZ0503SBS1

Culture col. no. DSM 21420 CGMCC 1.6853 DSM 22964 KCTC 22130 DZ0503SBS1 4 more

NCBI tax ID(s) 1449981 458197

Special Collections DSMZ JCM KCTC CIP Literature strains

History <- H. Liu, Nanjing Agric. Univ., P.R. China; KCTC 22130 {2008} C. Zhang DZ0503SBS1. <- H Liu, Nanjing Agri. Univ., China CIP <- 2016, KCTC

Links

Serratia nematodiphila DZ0503SBS1 is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from intestine of the nematode Heterorhabditidoides chongmingensis.

Gram-negative motile rod-shaped aerobe mesophilic animal pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 363429

CGMCC 1.6853,KCTC 22130,LMG 26067,DSM 21420,DSM 22964,CIP 111051

@ref 20215

Last LPSN update 2026-02-09 11:18:54

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Yersiniaceae

Genus Serratia

Species Serratia nematodiphila

Full scientific name Serratia nematodiphila Zhang et al. 2009

BacDive ID	Other strains from **Serratia nematodiphila** (7)	Type strain
137064	S. nematodiphila CIP 53.98, ATCC 4002, IFO 3759, NCTC 2847, ...
138184	S. nematodiphila S3255, CIP 105187
139233	S. nematodiphila LRA 004 03 73, CIP 103551, ATCC 43862
139244	S. nematodiphila CU37, CIP 53.89, ATCC 4003, CDC 2437-57, ...
139245	S. nematodiphila PI-3, CIP 53.91, ATCC 275
173314	S. nematodiphila CIP 107873, ATCC 49779
173315	S. nematodiphila joue, CIP 53.101

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29013	negative	1.05 µm	0.65 µm	rod-shaped
67771	negative
121260	negative			rod-shaped
125438	negative				99
125439	negative				99.9
125439					90.6

Pigmentation

29013

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15696	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
121260	CIP Medium 72		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15696	positive	growth	28	mesophilic
29013	positive	growth	04-42
29013	positive	optimum	33.5	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29013	positive	optimum	8
29013	positive	growth	05-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29013	aerobe
67771	aerobe
125439	aerobe	96.4

Spore formation

@ref	Spore formation	Confidence
29013
125439		97.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29013	NaCl	positive	growth	02-07 %
29013	NaCl	positive	optimum	4.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29013	18240 ChEBI	4-hydroxy-L-proline	+	carbon source
29013	16449 ChEBI	alanine	+	carbon source
29013	22599 ChEBI	arabinose	+	carbon source
29013	29016 ChEBI	arginine	+	carbon source
29013	16947 ChEBI	citrate	+	carbon source
29013	16296 ChEBI	D-tryptophan	+	carbon source
29013	23652 ChEBI	dextrin	+	carbon source
29013	4853 ChEBI	esculin	+	hydrolysis
29013	28757 ChEBI	fructose	+	carbon source
29013	33984 ChEBI	fucose	+	carbon source
29013	28260 ChEBI	galactose	+	carbon source
29013	5291 ChEBI	gelatin	+	carbon source
29013	17234 ChEBI	glucose	+	carbon source
29013	27570 ChEBI	histidine	+	carbon source
29013	18403 ChEBI	L-arabitol	+	carbon source
29013	24996 ChEBI	lactate	+	carbon source
29013	17716 ChEBI	lactose	+	carbon source
29013	17306 ChEBI	maltose	+	carbon source
29013	29864 ChEBI	mannitol	+	carbon source
29013	37684 ChEBI	mannose	+	carbon source
29013	28053 ChEBI	melibiose	+	carbon source
29013	17268 ChEBI	myo-inositol	+	carbon source
29013	18257 ChEBI	ornithine	+	carbon source
29013	26271 ChEBI	proline	+	carbon source
29013	16634 ChEBI	raffinose	+	carbon source
29013	15963 ChEBI	ribitol	+	carbon source
29013	33942 ChEBI	ribose	+	carbon source
29013	17814 ChEBI	salicin	+	carbon source
29013	17822 ChEBI	serine	+	carbon source
29013	30911 ChEBI	sorbitol	+	carbon source
29013	30031 ChEBI	succinate	+	carbon source
29013	17992 ChEBI	sucrose	+	carbon source
29013	53424 ChEBI	tween 20	+	carbon source
29013	53426 ChEBI	tween 80	+	carbon source
29013	17151 ChEBI	xylitol	+	carbon source
29013	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29013	catalase	+	1.11.1.6
29013	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Nematoda
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Host species
15696	intestine of the nematode Heterorhabditidoides chongmingensis	Shanghai city, Chongming Islands	China	CHN	Asia
67770	Intestine of the nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae)					Heterorhabditidoides chongmingensis
67771	From intestine of nematode	Shanghai province	China	CHN	Asia
121260	Animal, Intestine of the nematode, Heterorhabditidoides chongmingensis	Shangai, China	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU036987 (>99% sequence identity) for Serratia marcescens from Microbeatlas

Aquatic Samples	2336
Soil Samples	1270
Animal Samples	18103
Plant Samples	995
Total Samples	22704

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
15696		1	Risk group (German classification) According to TRBA 466
121260		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
67770	ASM73867v1 assembly for Serratia nematodiphila DZ0503SBS1 DSM 21420	contig	GCA_000738675	458197.4	2983796802	1449981	78.99
67770	IMG-taxon 2596583578 annotated assembly for Serratia nematodiphila CGMCC 1.6853	scaffold	GCA_900101535	458197.16	2596583578	458197	73.22
67770	SeNem1.0 assembly for Serratia nematodiphila DZ0503SBS1	contig	GCA_002082525	1449981.6		1449981

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15696	Serratia nematodiphila strain DZ0503SBS1 16S ribosomal RNA gene, partial sequence	EU036987	1500		1449981
124043	Serratia nematodiphila strain DSM 21420(T) 16S ribosomal RNA gene, partial sequence.	PP068848	1464		458197

GC content

29013

GC-content (mol%)59.52

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Serratia nematodiphila CGMCC 1.6853
NCBI: GCA_900101535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.20	no
125439	motility	BacteriaNetⓘ	yes	90.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Serratia nematodiphila strain CGMCC 1.6853
PATRIC: 458197.16

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	97.13	yes
125438	spore-forming	spore-formingⓘ	no	88.12	yes
125438	aerobic	aerobicⓘ	no	52.94	yes
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	77.99	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Pesticide degradation capacity of a novel strain belonging to Serratia sarumanii with its genomic profile.	Alatassi G, Baysal O, Silme RS, Ornek GP, Ornek H, Can A.	Biodegradation	10.1007/s10532-025-10144-2	2025
Genetics	Genome Sequences of Serratia Strains Revealed Common Genes in Both Serratomolides Gene Clusters.	Marques-Pereira C, Proenca DN, Morais PV.	Biology (Basel)	10.3390/biology9120482	2020
	Optimization of physicochemical parameters influencing the production of prodigiosin from Serratia nematodiphila RL2 and exploring its antibacterial activity.	Gondil VS, Asif M, Bhalla TC.	3 Biotech	10.1007/s13205-017-0979-z	2017
Genetics	Genome sequence of Serratia nematodiphila DSM 21420T, a symbiotic bacterium from entomopathogenic nematode.	Kwak Y, Khan AR, Shin JH	J Biotechnol	10.1016/j.jbiotec.2014.11.002	2014
Phylogeny	Enterobacillus tribolii gen. nov., sp. nov., a novel member of the family Enterobacteriaceae, isolated from the gut of a red flour beetle, Tribolium castaneum.	Patil VS, Salunkhe RC, Patil RH, Husseneder C, Shouche YS, Venkata Ramana V	Antonie Van Leeuwenhoek	10.1007/s10482-015-0412-8	2015
Phylogeny	Serratia nematodiphila sp. nov., associated symbiotically with the entomopathogenic nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae).	Zhang CX, Yang SY, Xu MX, Sun J, Liu H, Liu JR, Liu H, Kan F, Sun J, Lai R, Zhang KY	Int J Syst Evol Microbiol	10.1099/ijs.0.65718-0	2009

References

#15696	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21420
#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 )
#25444	IJSEM 1603 2009 ( DOI 10.1099/ijs.0.003871-0 )
#29013	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 #25444
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#121260	Collection of Institut Pasteur ; Curators of the CIP; CIP 111051
#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 )

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Serratia nematodiphila (DSM 21420, CGMCC 1.6853, DSM 22964)

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

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000738675

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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