Thalassospira xiamenensis (DSM 17429, CGMCC 1.3998, CIP 109533)

Name: Thalassospira xiamenensis (DSM 17429, CGMCC 1.3998, CIP 109533)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13966

Type strain

Strain Designation M-5

Culture col. no. DSM 17429 CGMCC 1.3998 CIP 109533 M-5

NCBI tax ID(s) 1123366 220697

Special Collections DSMZ CIP Literature strains

History <- Z. Shao; M-5 <- C. Liu CIP <- 2007, DSMZ <- Z. Shao, Marine Biogen. Res., China: strain M-5

Links

Thalassospira xiamenensis M-5 is an anaerobe, Gram-negative, motile bacterium that was isolated from surface water sample collected in a waste-oil pool at the storage dock.

Gram-negative motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 297361

CGMCC 1.3998,DSM 17429,CIP 109533

@ref 20215

Last LPSN update 2026-02-09 11:21:17

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Thalassospiraceae

Genus Thalassospira

Species Thalassospira xiamenensis

Full scientific name Thalassospira xiamenensis Liu et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31858	negative	5.5 µm	1.55 µm	rod-shaped
123977	negative			rod-shaped
125438	negative				97
125439	negative				97.9

Pigmentation

31858

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6981	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37759	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
123977	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6981	positive	growth	25
31858	positive	growth	04-40
31858	positive	optimum	22
37759	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31858	anaerobe
123977	obligate aerobe
125439	obligate aerobe	96.7

Spore formation

@ref	Spore formation	Confidence
31858
125439		95

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31858	NaCl	positive	growth	0.5-10 %
31858	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31858	18240 ChEBI	4-hydroxy-L-proline	+	carbon source
31858	16449 ChEBI	alanine	+	carbon source
31858	22599 ChEBI	arabinose	+	carbon source
31858	22653 ChEBI	asparagine	+	carbon source
31858	17057 ChEBI	cellobiose	+	carbon source
31858	15740 ChEBI	formate	+	carbon source
31858	28757 ChEBI	fructose	+	carbon source
31858	28260 ChEBI	galactose	+	carbon source
31858	24265 ChEBI	gluconate	+	carbon source
31858	17234 ChEBI	glucose	+	carbon source
31858	29987 ChEBI	glutamate	+	carbon source
31858	17754 ChEBI	glycerol	+	carbon source
31858	27570 ChEBI	histidine	+	carbon source
31858	21217 ChEBI	L-alaninamide	+	carbon source
31858	18403 ChEBI	L-arabitol	+	carbon source
31858	24996 ChEBI	lactate	+	carbon source
31858	15792 ChEBI	malonate	+	carbon source
31858	17306 ChEBI	maltose	+	carbon source
31858	29864 ChEBI	mannitol	+	carbon source
31858	37684 ChEBI	mannose	+	carbon source
31858	51850 ChEBI	methyl pyruvate	+	carbon source
31858	17268 ChEBI	myo-inositol	+	carbon source
31858	506227 ChEBI	N-acetylglucosamine	+	carbon source
31858	17632 ChEBI	nitrate	+	reduction
123977	17632 ChEBI	nitrate	+	reduction
123977	16301 ChEBI	nitrite	+	reduction
31858	18257 ChEBI	ornithine	+	carbon source
31858	26271 ChEBI	proline	+	carbon source
31858	17272 ChEBI	propionate	+	carbon source
31858	26490 ChEBI	quinate	+	carbon source
31858	17822 ChEBI	serine	+	carbon source
31858	30031 ChEBI	succinate	+	carbon source
31858	17992 ChEBI	sucrose	+	carbon source
31858	17748 ChEBI	thymidine	+	carbon source
31858	27082 ChEBI	trehalose	+	carbon source
31858	27248 ChEBI	urocanic acid	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123977	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31858	catalase	+	1.11.1.6
123977	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31858	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123977	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
123977	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123977	-	+	+	-	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	#Water reservoir (Aquarium/pool)
#Engineered	#Industrial	#Oil reservoir
#Engineered	#Waste	-
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6981	surface water sample collected in a waste-oil pool at the storage dock	Xiamen, Fujian	China	CHN	Asia
123977	Environment, Surface water sample, waste-oil pool storage dock		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY189753 (>99% sequence identity) for Thalassospira from Microbeatlas

Aquatic Samples	2971
Soil Samples	250
Animal Samples	192
Plant Samples	77
Total Samples	3490

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6981	1	Risk group (German classification) According to TRBA 466
123977	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	ASM30023v2 assembly for Thalassospira xiamenensis M-5 = DSM 17429	complete	GCA_000300235	1123366.3	2534681947	1123366	98.46
66792	IMG-taxon 2681813519 annotated assembly for Thalassospira xiamenensis M-5 = DSM 17429	contig	GCA_900156715	1123366.5	2681813519	1123366	72.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6981	Thalassospira xiamenensis strain M-5 16S ribosomal RNA gene, partial sequence	AY189753	1439		1123366

GC content

6981

GC-content (mol%)52.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thalassospira xiamenensis M-5 = DSM 17429
NCBI: GCA_000300235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.70	no
125439	gram_stain	BacteriaNetⓘ	negative	97.90	no
125439	motility	BacteriaNetⓘ	yes	73.90	no
125439	spore_formation	BacteriaNetⓘ	no	95.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thalassospira xiamenensis M-5 = DSM 17429 M-5
NCBI: GCA_000300235.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	yes
125438	anaerobic	anaerobicⓘ	no	93.44	no
125438	aerobic	aerobicⓘ	yes	75.30	no
125438	spore-forming	spore-formingⓘ	no	89.60	yes
125438	thermophilic	thermophileⓘ	no	97.37	yes
125438	flagellated	motile2+ⓘ	yes	85.68	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Marinobacter sp. from marine sediments produce highly stable surface-active agents for combatting marine oil spills.	Raddadi N, Giacomucci L, Totaro G, Fava F.	Microb Cell Fact	10.1186/s12934-017-0797-3	2017
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Thalassospira xianhensis sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium.	Zhao B, Wang H, Li R, Mao X	Int J Syst Evol Microbiol	10.1099/ijs.0.013201-0	2009
Phylogeny	Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.	Liu C, Wu Y, Li L, Ma Y, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.64544-0	2007

References

#6981	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17429
#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 )
#28121	IJSEM 316 2007 ( DOI 10.1099/ijs.0.64544-0 , PubMed 17267971 )
#31858	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 #28121
#37759	; Curators of the CIP;
#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) .
#68382	Automatically annotated from API zym .
#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 .
#123977	Collection of Institut Pasteur ; Curators of the CIP; CIP 109533
#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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Thalassospira xiamenensis (DSM 17429, CGMCC 1.3998, CIP 109533)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000300235

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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