Name: Serratia nematodiphila DZ0503SBS1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5168

Type strain:

Species: Serratia nematodiphila

Strain Designation: DZ0503SBS1

Culture col. no.: DSM 21420, CGMCC 1.6853, DSM 22964, KCTC 22130, JCM 14855, LMG 26067, CCM 7985, CIP 111051

Strain history: CIP <- 2016, KCTC

NCBI tax ID(s): 1449981 (strain), 458197 (species)

SI-ID 363429

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

Special Collections

Other strains from Serratia nematodiphila

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Yersiniaceae*
	Genus	*Serratia*
	Species	**Serratia nematodiphila**
	Full Scientific Name (LPSN)	Serratia nematodiphila Zhang et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29013]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #121260]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #29013]	Cell length	1.05 µm

[Ref.: #29013]	Cell width	0.65 µm

[Ref.: #29013]	Cell shape	rod-shaped
[Ref.: #121260]	Cell shape	rod-shaped

[Ref.: #29013]	Motility	yes
[Ref.: #121260]	Motility	yes

[Ref.: #29013]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15696]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #15696]

Culture medium growth

[Ref.: #15696]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15696]

Culture medium composition

expand / minimize

[Ref.: #121260]

Culture medium

CIP Medium 72

[Ref.: #121260]

Culture medium growth

[Ref.: #121260]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15696]	growth	28 °C
[Ref.: #29013]	growth	04-42 °C
[Ref.: #29013]	optimum	33.5 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29013]			optimum	8
[Ref.: #29013]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29013]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29013]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29013]		NaCl		growth	02-07	%
[Ref.: #29013]		NaCl		optimum	4.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29013]	4-hydroxy-L-proline ChEBI	+	carbon source
[Ref.: #29013]	alanine ChEBI	+	carbon source
[Ref.: #29013]	arabinose ChEBI	+	carbon source
[Ref.: #29013]	arginine ChEBI	+	carbon source
[Ref.: #29013]	citrate ChEBI	+	carbon source
[Ref.: #29013]	D-tryptophan ChEBI	+	carbon source
[Ref.: #29013]	dextrin ChEBI	+	carbon source
[Ref.: #29013]	esculin ChEBI	+	hydrolysis
[Ref.: #29013]	fructose ChEBI	+	carbon source
[Ref.: #29013]	fucose ChEBI	+	carbon source
[Ref.: #29013]	galactose ChEBI	+	carbon source
[Ref.: #29013]	gelatin ChEBI	+	carbon source
[Ref.: #29013]	glucose ChEBI	+	carbon source
[Ref.: #29013]	histidine ChEBI	+	carbon source
[Ref.: #29013]	L-arabitol ChEBI	+	carbon source
[Ref.: #29013]	lactate ChEBI	+	carbon source
[Ref.: #29013]	lactose ChEBI	+	carbon source
[Ref.: #29013]	maltose ChEBI	+	carbon source
[Ref.: #29013]	mannitol ChEBI	+	carbon source
[Ref.: #29013]	mannose ChEBI	+	carbon source
[Ref.: #29013]	melibiose ChEBI	+	carbon source
[Ref.: #29013]	myo-inositol ChEBI	+	carbon source
[Ref.: #29013]	ornithine ChEBI	+	carbon source
[Ref.: #29013]	proline ChEBI	+	carbon source
[Ref.: #29013]	raffinose ChEBI	+	carbon source
[Ref.: #29013]	ribitol ChEBI	+	carbon source
[Ref.: #29013]	ribose ChEBI	+	carbon source
[Ref.: #29013]	salicin ChEBI	+	carbon source
[Ref.: #29013]	serine ChEBI	+	carbon source
[Ref.: #29013]	sorbitol ChEBI	+	carbon source
[Ref.: #29013]	succinate ChEBI	+	carbon source
[Ref.: #29013]	sucrose ChEBI	+	carbon source
[Ref.: #29013]	tween 20 ChEBI	+	carbon source
[Ref.: #29013]	tween 80 ChEBI	+	carbon source
[Ref.: #29013]	xylitol ChEBI	+	carbon source
[Ref.: #29013]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29013]		catalase	+	1.11.1.6
[Ref.: #29013]		gelatinase	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #15696]	Sample type/isolated from	intestine of nematode
[Ref.: #15696]	Geographic location (country and/or sea, region)	Shanghai
[Ref.: #15696]	Country	China
[Ref.: #15696]	Country ISO 3 Code	CHN
[Ref.: #15696]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Intestine of the nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae)
[Ref.: #67770]	Host species	Heterorhabditidoides chongmingensis

[Ref.: #67771]	Sample type/isolated from	From intestine of nematode
[Ref.: #67771]	Geographic location (country and/or sea, region)	Shanghai province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #121260]	Sample type/isolated from	Animal, Intestine of the nematode, Heterorhabditidoides chongmingensis
[Ref.: #121260]	Geographic location (country and/or sea, region)	Shangai, China
[Ref.: #121260]	Country	China
[Ref.: #121260]	Country ISO 3 Code	CHN
[Ref.: #121260]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15696]	Pathogenicity (animal)	yes
[Ref.: #15696]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121260]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15696]	Serratia nematodiphila strain DZ0503SBS1 16S ribosomal RNA gene, partial sequence	EU036987	1500	GenBank ENA	1449981 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Serratia nematodiphila CGMCC 1.6853	GCA_900101535	scaffold	GenBank ENA	458197 tax ID
[Ref.: #67770]	Serratia nematodiphila DZ0503SBS1	GCA_002082525	contig	GenBank ENA	1449981 tax ID
[Ref.: #67770]	Serratia nematodiphila DZ0503SBS1 DSM 21420	GCA_000738675	contig	GenBank ENA	1449981 tax ID
[Ref.: #66792]	Serratia nematodiphila strain CGMCC 1.6853	458197.16	wgs	PATRIC	458197 tax ID	*
[Ref.: #66792]	Serratia nematodiphila strain DSM 21420	458197.4	wgs	PATRIC	458197 tax ID	*
[Ref.: #66792]	Serratia nematodiphila CGMCC 1.6853	2596583578	draft	JGI IMG/M	458197 tax ID	*

[Ref.: #29013]

GC-content

59.52 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Serratia nematodiphila strain CGMCC 1.6853 PATRIC: 458197.16
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.132	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.12	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	52.935	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.992	no

Availability in culture collections External links

[Ref.: #15696]

Culture collection no.

DSM 21420, CGMCC 1.6853, DSM 22964, KCTC 22130, JCM 14855, LMG 26067, CCM 7985, CIP 111051

[Ref.: #74660]

SI-ID 363429

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	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 )

#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 (see below)

#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;
#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#74660

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID363429.1 )

#121260 Collection of Institut Pasteur ; Curators of the CIP; CIP 111051

#25444

IJSEM 1603 2009 ( DOI 10.1099/ijs.0.003871-0 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Serratia nematodiphila in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Serratia nematodiphila strain CGMCC 1.6853

Change proposal

Change proposal