Desulfobaculum xiamenense (DSM 24233, CGMCC 1.5166, P1)

Name: Desulfobaculum xiamenense (DSM 24233, CGMCC 1.5166, P1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4178

Type strain

Strain Designation P1

Culture col. no. DSM 24233 CGMCC 1.5166 P1

NCBI tax ID(s) 995050

Special Collections DSMZ Literature strains

History <- X. Xu, Third Inst. Oceanography, China; P1 <- Z. Gao {2010}

Links

Desulfobaculum xiamenense P1 is an anaerobe, Gram-negative, motile bacterium that was isolated from marine mangrove sediment.

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

Name and taxonomic classification

SI-ID 396903

DSM 24233

@ref 20215

Last LPSN update 2026-02-09 11:18:40

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfovibrionia

Order Desulfovibrionales

Family Desulfovibrionaceae

Genus Desulfobaculum

Species Desulfobaculum xiamenense

Full scientific name Desulfobaculum xiamenense corrig. Zhao et al. 2012

Synonyms (1)

Desulfobaculum xiamenensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30462	negative	1.9 µm	0.6 µm	rod-shaped
125439	negative				97.6
125438	negative				96.477

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17568	DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)		Medium recipe at MediaDive	Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17568	positive	growth	35
30462	positive	growth	22-44
30462	positive	optimum	37.5

Culture pH

@ref	Ability	Type	PH	PH range
30462	positive	optimum	7
30462	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
17568	anaerobe
30462	anaerobe
125439	anaerobe	90.3

Spore formation

@ref	Spore formation	Confidence
30462
125439		97.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30462	NaCl	positive	growth	0.2-3.5 %
30462	NaCl	positive	optimum	0.50 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30462	17057 ChEBI	cellobiose	+	carbon source
30462	28260 ChEBI	galactose	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Mangrove
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17568	marine mangrove sediment	Hainan Island, Dongzhaigang, Qinglan Port	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence HQ697913 (>99% sequence identity) for Desulfobaculum xiamenense subclade from Microbeatlas

Aquatic Samples	28
Soil Samples	7
Animal Samples	83
Plant Samples
Total Samples	118

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17568	1	Risk group (German 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	ASM1192766v1 assembly for Desulfobaculum xiamenense DSM 24233	scaffold	GCA_011927665	995050.3	2829737207	995050	76.17

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17568	Desulfobaculum xiamenense strain P1 16S ribosomal RNA gene, partial sequence	HQ697913	1471		995050

GC content

@ref	GC-content (mol%)	Method
17568	64.5	high performance liquid chromatography (HPLC)
30462	64.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfobaculum xiamenense DSM 24233
NCBI: GCA_011927665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.30	no
125439	motility	BacteriaNetⓘ	yes	76.40	no
125439	gram_stain	BacteriaNetⓘ	negative	97.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	90.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfobaculum xiamenense DSM 24233
NCBI: GCA_011927665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.48	no
125438	anaerobic	anaerobicⓘ	yes	79.65	yes
125438	aerobic	aerobicⓘ	no	85.23	yes
125438	spore-forming	spore-formingⓘ	no	89.46	yes
125438	thermophilic	thermophileⓘ	no	86.30	yes
125438	flagellated	motile2+ⓘ	yes	77.89	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov.	Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK.	Front Microbiol	10.3389/fmicb.2022.738205	2022
Transcriptome	Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria.	Jawaharraj K, Peta V, Dhiman SS, Gnimpieba EZ, Gadhamshetty V.	Sci Rep	10.1038/s41598-023-43089-8	2023
Phylogeny	Desulfobaculum xiamenensis gen. nov., sp. nov., a member of the family Desulfovibrionaceae isolated from marine mangrove sediment.	Zhao C, Gao Z, Qin Q, Li F, Ruan L	Int J Syst Evol Microbiol	10.1099/ijs.0.036632-0	2011

References

#17568	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24233
#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 )
#26797	IJSEM 1570 2012 ( DOI 10.1099/ijs.0.036632-0 , PubMed 21873514 )
#30462	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 #26797
#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 .
#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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Desulfobaculum xiamenense (DSM 24233, CGMCC 1.5166, P1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011927665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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