Name: Shewanella gelidii RZB5-4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 141062

Type strain:

Species: Shewanella gelidii

Strain Designation: RZB5-4

Culture col. no.: JCM 30804, KCTC 42663, MCCC 1K00697

Strain history: Y. Wang; Sch. of Life Sci. & Technol., Xin Xiang Med. Univ., China; RZB5-4.

NCBI tax ID(s): 1642821 (species)

Special Collections

Section

Shewanella gelidii RZB5-4 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from red algae Gelidium amansii collected from the coastal region of Rizhao, Yellow Sea, PR China.

colony-forming
Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Alteromonadales*
	Family	*Shewanellaceae*
	Genus	*Shewanella*
	Species	**Shewanella gelidii**
	Full Scientific Name (LPSN)	Shewanella gelidii Wang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43941]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #43941]	Cell length	1.5-2.5 µm

[Ref.: #43941]	Cell width	0.5-1.0 µm

[Ref.: #43941]	Cell shape	rod-shaped

[Ref.: #43941]	Motility	yes

[Ref.: #43941]	Flagellum arrangement	polar

[Ref.: #43941]	Colony size	1.0-2.0 mm
[Ref.: #43941]	Colony color	white
[Ref.: #43941]	Colony shape	circular
[Ref.: #43941]	Incubation period	1 day
[Ref.: #43941]	Cultivation medium used	Marine ahar 2216

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43941]

Culture medium

Marine ahar 2216

[Ref.: #43941]

Culture medium growth

		Temperature
[Ref.: #43941]	growth	4-32 °C
[Ref.: #43941]	optimum	24-28 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #43941]			optimum	7
[Ref.: #43941]			growth	6.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43941]

Oxygen tolerance

facultative anaerobe

[Ref.: #43941]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %92.436
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43941]		NaCl		growth	1-5	%(w/v)
[Ref.: #43941]		NaCl		optimum	2-3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43941]	acetate ChEBI	-	carbon source
[Ref.: #43941]	benzoate ChEBI	-	carbon source
[Ref.: #43941]	casein	+	hydrolysis
[Ref.: #43941]	cellobiose ChEBI	-	carbon source
[Ref.: #43941]	chitin ChEBI	-	hydrolysis
[Ref.: #43941]	citrate ChEBI	-	carbon source
[Ref.: #43941]	D-galactose ChEBI	-	carbon source
[Ref.: #43941]	D-glucose ChEBI	-	builds acid from
[Ref.: #43941]	D-glucose ChEBI	-	carbon source
[Ref.: #43941]	D-mannose ChEBI	-	carbon source
[Ref.: #43941]	D-xylose ChEBI	-	carbon source
[Ref.: #43941]	dl-alanine ChEBI	-	carbon source
[Ref.: #43941]	dna ChEBI	+	hydrolysis
[Ref.: #43941]	esculin ChEBI	+	hydrolysis
[Ref.: #43941]	fructose ChEBI	-	carbon source
[Ref.: #43941]	gelatin ChEBI	+	hydrolysis
[Ref.: #43941]	glycerol ChEBI	-	carbon source
[Ref.: #43941]	glycerol 3-phosphate ChEBI	-	carbon source
[Ref.: #43941]	L-histidine ChEBI	-	carbon source
[Ref.: #43941]	L-leucine ChEBI	+	carbon source
[Ref.: #43941]	L-ornithine ChEBI	+	carbon source
[Ref.: #43941]	L-phenylalanine ChEBI	-	carbon source
[Ref.: #43941]	L-proline ChEBI	-	carbon source
[Ref.: #43941]	lactate ChEBI	+	carbon source
[Ref.: #43941]	lactose ChEBI	-	carbon source
[Ref.: #43941]	lysine ChEBI	+	carbon source
[Ref.: #43941]	maltose ChEBI	-	carbon source
[Ref.: #43941]	myo-inositol ChEBI	-	carbon source
[Ref.: #43941]	N-acetyl-L-glutamate ChEBI	-	carbon source
[Ref.: #43941]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #43941]	nitrate ChEBI	+	reduction
[Ref.: #43941]	starch ChEBI	-	hydrolysis
[Ref.: #43941]	sucrose ChEBI	-	builds acid from
[Ref.: #43941]	sucrose ChEBI	-	carbon source
[Ref.: #43941]	tween 20 ChEBI	+	carbon source
[Ref.: #43941]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43941]	tween 20 ChEBI	+/-	hydrolysis
[Ref.: #43941]	tween 40 ChEBI	+	carbon source
[Ref.: #43941]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43941]	tween 60 ChEBI	+	carbon source
[Ref.: #43941]	tween 60 ChEBI	+	hydrolysis
[Ref.: #43941]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43941]	tween 80 ChEBI	+	carbon source
[Ref.: #43941]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43941]	amikacin ChEBI				yes	30	µg (disc)
[Ref.: #43941]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #43941]	carbenicillin ChEBI	yes	100	µg (disc)
[Ref.: #43941]	cefoperazone ChEBI	yes	75	µg (disc)
[Ref.: #43941]	ceftazidime ChEBI	yes	30	µg (disc)
[Ref.: #43941]	cephalexin ChEBI	yes	30	µg (disc)
[Ref.: #43941]	cephradine ChEBI				yes	30	µg (disc)
[Ref.: #43941]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #43941]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #43941]	clindamycin ChEBI				yes	2	µg (disc)
[Ref.: #43941]	co-trimoxazole ChEBI	yes	25	µg (disc)
[Ref.: #43941]	doxycycline ChEBI				yes	30	µg (disc)
[Ref.: #43941]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #43941]	gentamicin ChEBI				yes	10	µg (disc)
[Ref.: #43941]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #43941]	midecamycin ChEBI	yes	30	µg (disc)
[Ref.: #43941]	minocycline ChEBI				yes	30	µg (disc)
[Ref.: #43941]	neomycin ChEBI				yes	30	µg (disc)
[Ref.: #43941]	norfloxacin ChEBI	yes	10	µg (disc)
[Ref.: #43941]	ofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #43941]	oxacillin ChEBI				yes	1	µg (disc)
[Ref.: #43941]	penicillin ChEBI				yes	10	µg (disc)
[Ref.: #43941]	piperacillin ChEBI				yes	100	µg (disc)
[Ref.: #43941]	polymyxin b ChEBI				yes	300	µg (disc)
[Ref.: #43941]	tetracycline ChEBI				yes	30	µg (disc)
[Ref.: #43941]	vancomycin ChEBI				yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43941]		hydrogen sulfide ChEBI	yes
[Ref.: #43941]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43941]	acid phosphatase	+	3.1.3.2
[Ref.: #43941]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43941]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43941]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43941]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43941]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43941]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43941]	beta-galactosidase	-	3.2.1.23
[Ref.: #43941]	beta-glucosidase	-	3.2.1.21
[Ref.: #43941]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43941]	catalase	+	1.11.1.6
[Ref.: #43941]	cystine arylamidase	-	3.4.11.3
[Ref.: #43941]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43941]	esterase (C 4)	+
[Ref.: #43941]	esterase Lipase (C 8)	+
[Ref.: #43941]	leucine arylamidase	+	3.4.11.1
[Ref.: #43941]	lipase (C 14)	-
[Ref.: #43941]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43941]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43941]	trypsin	-	3.4.21.4
[Ref.: #43941]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43941]

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	23.3
C16:0	20.2
C15:0 iso	18.9
C17:1ω8c	7.4
C17:1 iso I /C17:1 anteiso B	3.7
C11:0 iso 3OH	3.3
C17:0	2.9
C14:0	2.6
C18:1ω7c / C18:1ω6c	2
C16:0 iso	1.8
C10:0	1.8
C17:0 iso	1.7
C12:0 3OH	1.7
C11:0 3OH	1.5
C13:0 iso	1.2
C18:0	1.2
C13:0 iso 3OH	1
C15:0 anteiso	1
C14:0 iso	0.9
C18:1ω9c	0.9
C15:1ω8c	0.8

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

[Ref.: #43941]	Sample type/isolated from	red algae Gelidium amansii collected from the coastal region of Rizhao, Yellow Sea, PR China
[Ref.: #43941]	Sampling date	2014-11
[Ref.: #43941]	Geographic location (country and/or sea, region)	Rizhao, Yellow Sea
[Ref.: #43941]	Country	China
[Ref.: #43941]	Country ISO 3 Code	CHN
[Ref.: #43941]	Continent	Asia
[Ref.: #43941]	Geographic location	35.5170°/119.6250°
[Ref.: #43941]	Enrichment culture	Marine agar 2216
[Ref.: #43941]	Enrichment culture temperature	25 ̊C

[Ref.: #67770]	Sample type/isolated from	Red algae Gelidium amansii from the coastal region of Rizhao
[Ref.: #67770]	Host species	Gelidium amansii
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Coast
#Environmental	#Aquatic	#Marine
#Host	#Algae	#Red algae

What are isolation sources categories?

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.: #43941]	Shewanella gelidii strain RZB5-4 16S ribosomal RNA gene, partial sequence	KR080702		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shewanella gelidii JCM 30804	GCA_014647855	scaffold	GenBank ENA	1642821 tax ID	*
[Ref.: #66792]	Shewanella gelidii strain JCM 30804	1642821.3	wgs	PATRIC	1642821 tax ID	*
[Ref.: #66792]	Shewanella gelidii KCTC 42663	GCA_023283645	contig	GenBank ENA	1642821 tax ID	*

[Ref.: #67770]

GC-content

47 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Shewanella gelidii JCM 30804 NCBI: GCA_014647855.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shewanella gelidii JCM 30804 NCBI: GCA_014647855.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	89.001	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	57.781	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.436	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	89.052	no

Availability in culture collections External links

[Ref.: #43941]

Culture collection no.

JCM 30804, KCTC 42663, MCCC 1K00697

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shewanella maritima sp. nov., a facultative anaerobic marine bacterium isolated from seawater, and emended description of Shewanella intestini.	Bae SS, Jung YH, Baek K	Int J Syst Evol Microbiol	10.1099/ijsem.0.003916	2020	*
Phylogeny	Shewanella gelidii sp. nov., isolated from the red algae Gelidium amansii, and emended description of Shewanella waksmanii.	Wang Y, Chen H, Liu Z, Ming H, Zhou C, Zhu X, Zhang P, Jing C, Feng H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001075	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 )

#43941

Yan Wang, Hongli Chen, Zhenhua Liu, Hong Ming, Chenyan Zhou, Xinshu Zhu, Peng Zhang, Changqin Jing, Huigen Feng: Shewanella gelidii sp. nov., isolated from the red algae Gelidium amansii, and emended description of Shewanella waksmanii. IJSEM 66: 2899 - 2905 2016 ( DOI 10.1099/ijsem.0.001075 , PubMed 27064664 )

#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;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Shewanella gelidii JCM 30804

Shewanella gelidii JCM 30804

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