Halodesulfovibrio marinisediminis (DSM 17456, JCM 14577, NBRC 101113)

Name: Halodesulfovibrio marinisediminis (DSM 17456, JCM 14577, NBRC 101113)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4153

Type strain

Strain Designation NMRC 101113, C/L 2

Culture col. no. DSM 17456 JCM 14577 NBRC 101113 NMRC 101113 C/L 2

NCBI tax ID(s) 1121457 458711

Special Collections DSMZ JCM Literature strains

History <- Y. Uchino <- S. Takii; C/L2 S. Takii C/L2.

Links

Halodesulfovibrio marinisediminis NMRC 101113 is an anaerobe, vibrio-shaped bacterium that was isolated from anoxic coastal sediment, highly eutrophic area.

vibrio-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401170

JCM 14577,NBRC 101113,DSM 17456

@ref 20215

Last LPSN update 2026-02-09 11:18:39

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfovibrionia

Order Desulfovibrionales

Family Desulfovibrionaceae

Genus Halodesulfovibrio

Species Halodesulfovibrio marinisediminis

Full scientific name Halodesulfovibrio marinisediminis (Takii et al. 2008) Shivani et al. 2017

Synonyms (1)

Desulfovibrio marinisediminis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25150		1.0-3.5 µm		vibrio-shaped
32597	negative	1-3.5 µm	0.7-1 µm	coccus-shaped
125438	negative				94.983
125439	negative				99.9

Pigmentation

32597

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6996	DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)		Medium recipe at MediaDive	Name: DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c; with strain-specific modifications) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-L-lactate 2.49252 g/l Na2CO3 1.49551 g/l Yeast extract 0.997009 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6996	positive	growth	37
25150	positive	optimum	37
25150	positive	growth	15.0-40.0
32597	positive	growth	15-40
32597	positive	optimum	37
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
25150	positive	optimum	7.5
32597	positive	optimum	7.5
25150	positive	growth	6.3-8.6	alkaliphile
32597	positive	growth	6.3-8.6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6996	anaerobe
25150	obligate anaerobe
32597	anaerobe
125439	obligate aerobe	97.6

Spore formation

@ref	Spore formation	Confidence
32597
125439		99.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25150	NaCl	positive	optimum	1.5-3.5 %(w/v)
25150	NaCl	positive	growth	0.05-3.5 %(w/v)

Observation

@ref	Observation
32597	aggregates in chains
67770	quinones: MK-6(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25150	30089 ChEBI	acetate	+	electron donor
25150	35391 ChEBI	aspartate	+	electron donor
32597	35391 ChEBI	aspartate	+	carbon source
25150	16150 ChEBI	benzoate	-	electron donor
25150	15356 ChEBI	cysteine	-	electron donor
25150	5291 ChEBI	gelatin	-	hydrolysis
25150	17754 ChEBI	glycerol	+	electron donor
32597	17754 ChEBI	glycerol	+	carbon source
25150	17822 ChEBI	serine	+	electron donor
32597	30031 ChEBI	succinate	+	carbon source
25150	17359 ChEBI	sulfite	+	electron acceptor
25150	27897 ChEBI	tryptophan	-	energy source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25150	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25150	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
25150	catalase	+	1.11.1.6
32597	catalase	+	1.11.1.6
25150	tryptophan deaminase	-	4.1.99.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6996	anoxic coastal sediment, highly eutrophic area	Tokyo Bay	Japan	JPN	Asia
67770	Coastal marine sediment from the eutrophic Tokyo Bay		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB353727 (>99% sequence identity) for Halodesulfovibrio from Microbeatlas

Aquatic Samples	424
Soil Samples	30
Animal Samples	382
Plant Samples	43
Total Samples	879

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6996	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
67770	IMG-taxon 2585428071 annotated assembly for Halodesulfovibrio marinisediminis DSM 17456	scaffold	GCA_900129975	1121457.4	2585428071	1121457	76.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6996	Desulfovibrio marinisediminis gene for 16S rRNA, partial sequence	AB353727	1533		1121457

GC content

@ref	GC-content (mol%)	Method
6996	46.2	high performance liquid chromatography (HPLC)
25150	45	genome sequence analysis
32597	46.2
6996	45	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halodesulfovibrio marinisediminis DSM 17456
NCBI: GCA_900129975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	motility	BacteriaNetⓘ	yes	86.10	no
125439	spore_formation	BacteriaNetⓘ	no	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halodesulfovibrio marinisediminis DSM 17456
PATRIC: 1121457.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.98	yes
125438	anaerobic	anaerobicⓘ	yes	83.60	no
125438	spore-forming	spore-formingⓘ	no	89.18	yes
125438	aerobic	aerobicⓘ	no	85.18	yes
125438	thermophilic	thermophileⓘ	no	91.90	yes
125438	flagellated	motile2+ⓘ	yes	75.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome-Guided Identification of Organohalide-Respiring Deltaproteobacteria from the Marine Environment.	Liu J, Haggblom MM.	mBio	10.1128/mbio.02471-18	2018
Genetics	Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae.	Isokpehi RD, McInnis DS, Destefano AM, Johnson GS, Walker AD, Hall YA, Mapp BW, Johnson MO, Simmons SS.	Microorganisms	10.3390/microorganisms9081780	2021
	Production of extracellular lipase from psychrotrophic bacterium Oceanisphaera sp. RSAP17 isolated from arctic soil.	Uddin MR, Roy P, Mandal S.	Antonie Van Leeuwenhoek	10.1007/s10482-021-01671-y	2021
Pathogenicity	Sanguinarine impedes metastasis and causes inversion of epithelial to mesenchymal transition in breast cancer.	Ghauri MA, Su Q, Ullah A, Wang J, Sarwar A, Wu Q, Zhang D, Zhang Y.	Phytomedicine	10.1016/j.phymed.2021.153500	2021
	Immunogenicity of mannan derived from Mycobacterium bovis as a promising adjuvant in vaccine BCG.	Mardani R, Alavi A, Mousavi Nasab SD, Ahmadi N, Hossein Tehrani MJ, Shahali M, Doroud D.	Iran J Microbiol	10.18502/ijm.v16i3.15767	2024
	The Efficacy of Hellebrigenin Against Nasopharyngeal Carcinoma Cells: The Molecular and Bioinformatic Analysis.	Ho HY, Chen MK, Tsai YJ, Lin CC, Lo YS, Chuang YC, Hsieh MJ.	J Cell Mol Med	10.1111/jcmm.70624	2025
	Regulating the expression of matrix metalloproteinases to inhibit ovarian carcinoma using isoquinoline alkaloid from Allium ascalonicum.	Ravindranath KJ, Srinivasan H.	Sci Rep	10.1038/s41598-025-94111-0	2025
	Systemic and Mucosal Antibody Responses to SARS-CoV-2 Variant-Specific Prime-and-Boost and Prime-and-Spike Vaccination: A Comparison of Intramuscular and Intranasal Bivalent Vaccine Administration in a Murine Model.	Maltseva M, Galipeau Y, McCluskie P, Castonguay N, Cooper CL, Langlois MA.	Vaccines (Basel)	10.3390/vaccines13040351	2025
	STING agonist, SMA-2, inhibits clear cell renal cell carcinoma through improving tumor microenvironment.	Wang W, Zhang F, Hu Y, Liu G.	Mol Cell Biochem	10.1007/s11010-024-04970-w	2024
	Promising anticancer activity of cromolyn in colon cancer: in vitro and in vivo analysis.	Aliabadi A, Haghshenas MR, Kiani R, Panjehshahin MR, Erfani N.	J Cancer Res Clin Oncol	10.1007/s00432-024-05741-2	2024
	Biotin/Folate-decorated Human Serum Albumin Nanoparticles of Docetaxel: Comparison of Chemically Conjugated Nanostructures and Physically Loaded Nanoparticles for Targeting of Breast Cancer.	Nateghian N, Goodarzi N, Amini M, Atyabi F, Khorramizadeh MR, Dinarvand R.	Chem Biol Drug Des	10.1111/cbdd.12624	2016
	GliSODin® prevents airway inflammation by inhibiting T-cell differentiation and activation in a mouse model of asthma.	Klein M, Dijoux E, Cheminant MA, Intes L, Bouchaud G.	Front Allergy	10.3389/falgy.2023.1199355	2023
	Single cell RNA-seq reveals cellular and transcriptional heterogeneity in the splenic CD11b⁺Ly6C^high monocyte population expanded in sepsis-surviving mice.	Watanabe H, Rana M, Son M, Chiu PY, Fei-Bloom Y, Choi K, Diamond B, Sherry B.	Mol Med	10.1186/s10020-024-00970-0	2024
	Chemical conjugation mitigates immunotoxicity of chemotherapy via reducing receptor-mediated drug leakage from lipid nanoparticles	Zheng C, Zhang W, Gong X, Xiong F, Jiang L, Zhou L, Zhang Y, Zhu H, Wang H, Li Y, Zhang P.	Sci Adv		2024
	The efficacy of hydro alcoholic extract of Seidlitzia rosmarinus on experimental zoonotic cutaneous leishmaniasis lesions in murine model.	Ahmadi M, Fata A, Khamesipour A, Rakhshandeh H, Miramin Mohammadi A, Salehi G, Monavari H.	Avicenna J Phytomed		2014
Phylogeny	Identification of the traditional and non-traditional sulfate-reducing bacteria associated with corroded ship hull.	Alasvand Zarasvand K, Ravishankar Rai V.	3 Biotech	10.1007/s13205-016-0507-6	2016
	Beneficial effects of L-arginine on 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced neuronal degeneration in substantia nigra of Balb/c mice.	Hami J, Hosseini M, Nezhad SV, Shahi S, Lotfi N, Ehsani H, Sadeghi A.	Adv Biomed Res	10.4103/2277-9175.187374	2016
	Ultrastructural and morphometrical study of preimplantation endometrium in superovulated mice treated with progesterone or Sildenafil.	Roshangar L, Soleimani-Rad J, Rashedee B, Mazochian H, Nikzad B, Soleimani Rad S.	Iran J Reprod Med		2013
Pathogenicity	[Immunocontraceptive effect of a synthetic chimeric peptide of sperm].	He W, Liang Z, Wu Y, Shi C, Jia Z, Zhou W, Li Y.	Zhonghua Yi Xue Za Zhi		2002
Metabolism	A Small Molecule Antagonist of PD-1/PD-L1 Interactions Acts as an Immune Checkpoint Inhibitor for NSCLC and Melanoma Immunotherapy.	Wang Y, Gu T, Tian X, Li W, Zhao R, Yang W, Gao Q, Li T, Shim JH, Zhang C, Liu K, Lee MH.	Front Immunol	10.3389/fimmu.2021.654463	2021
Pathogenicity	Inhibitory effects of Euphorbia supina on Propionibacterium acnes-induced skin inflammation in vitro and in vivo.	Lim HJ, Jeon YD, Kang SH, Shin MK, Lee KM, Jung SE, Cha JY, Lee HY, Kim BR, Hwang SW, Lee JH, Sugita T, Cho O, Myung H, Jin JS, Lee YM.	BMC Complement Altern Med	10.1186/s12906-018-2320-8	2018
Metabolism	The use of Euphorbia hirta L. (Euphorbiaceae) in diarrhea and constipation involves calcium antagonism and cholinergic mechanisms.	Ali MZ, Mehmood MH, Saleem M, Saleem M, Gilani AH.	BMC Complement Med Ther	10.1186/s12906-019-2793-0	2020
	Green tea (Camellia sinesis) ameliorates female Schistosoma mansoni-induced changes in the liver of Balb/C mice.	Bin Dajem SM, Shati AA, Adly MA, Ahmed OM, Ibrahim EH, Mostafa OM.	Saudi J Biol Sci	10.1016/j.sjbs.2011.06.003	2011
	Ontogeny of susceptibility to the convulsant, Ro 5-4864, and its relationship to audiogenic seizure susceptibility in inbred mice.	Seale TW, Roderick TH, Skolnick P.	Life Sci	10.1016/0024-3205(87)90583-2	1987
	T-cell regulation of erythropoiesis during acute lymphoblastic leukemia.	Bacon ER, Sing AP, Troutner JC, Reinisch CL.	Exp Hematol		1985
Pathogenicity	Inflammation enhances IL-2 driven differentiation of cytolytic CD4 T cells.	Workman AM, Jacobs AK, Vogel AJ, Condon S, Brown DM.	PLoS One	10.1371/journal.pone.0089010	2014
	Btk regulates localization, in vivo activation, and class switching of anti-DNA B cells.	Halcomb KE, Musuka S, Gutierrez T, Wright HL, Satterthwaite AB.	Mol Immunol	10.1016/j.molimm.2008.08.278	2008
Metabolism	Encephalitogenic T cells that stably express both T-bet and ROR gamma t consistently produce IFNgamma but have a spectrum of IL-17 profiles.	Abromson-Leeman S, Bronson RT, Dorf ME.	J Neuroimmunol	10.1016/j.jneuroim.2009.07.007	2009
Metabolism	Erythropoietin over-expression protects against diet-induced obesity in mice through increased fat oxidation in muscles.	Hojman P, Brolin C, Gissel H, Brandt C, Zerahn B, Pedersen BK, Gehl J.	PLoS One	10.1371/journal.pone.0005894	2009
	Sequence-specific antitumor activity of a phosphorothioate oligodeoxyribonucleotide targeted to human C-raf kinase supports an antisense mechanism of action in vivo.	Monia BP, Sasmor H, Johnston JF, Freier SM, Lesnik EA, Muller M, Geiger T, Altmann KH, Moser H, Fabbro D.	Proc Natl Acad Sci U S A	10.1073/pnas.93.26.15481	1996
	Multifunctional CD4 cells expressing gamma interferon and perforin mediate protection against lethal influenza virus infection.	Brown DM, Lee S, Garcia-Hernandez Mde L, Swain SL.	J Virol	10.1128/jvi.07172-11	2012
Phylogeny	Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment.	Zhang G, Jiao K, Xie F, Pei S, Jiang L.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003344	2019
Phylogeny	Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp.	Shivani Y, Subhash Y, Sasikala C, Ramana CV.	Int J Syst Evol Microbiol	10.1099/ijsem.0.001574	2017
Metabolism	Thiomonas islandica sp. nov., a moderately thermophilic, hydrogen- and sulfur-oxidizing betaproteobacterium isolated from a hot spring.	Vesteinsdottir H, Reynisdottir DB, Orlygsson J.	Int J Syst Evol Microbiol	10.1099/ijs.0.015511-0	2011
Phylogeny	Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru.	Finster KW, Kjeldsen KU	Antonie Van Leeuwenhoek	10.1007/s10482-009-9403-y	2009
Phylogeny	Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids.	Takii S, Hanada S, Hase Y, Tamaki H, Uyeno Y, Sekiguchi Y, Matsuura K	Int J Syst Evol Microbiol	10.1099/ijs.0.65750-0	2008

References

#6996	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17456
#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 )
#25150	Y. S. Shivani, Y.,Sasikala, C.,Ramana, C. V.: Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp. IJSEM 67: 87 - 93 2017 ( DOI 10.1099/ijsem.0.001574 , PubMed 27902290 )
#28810	IJSEM 2433 2008 ( DOI 10.1099/ijs.0.65750-0 , PubMed 18842870 )
#32597	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 #28810
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Halodesulfovibrio marinisediminis (DSM 17456, JCM 14577, NBRC 101113)

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

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900129975

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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