Sedimentibacter acidaminivorans (DSM 24004, JCM 17293, MO-SEDI)

Name: Sedimentibacter acidaminivorans (DSM 24004, JCM 17293, MO-SEDI)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132448

Type strain

Strain Designation MO-SEDI

Culture col. no. DSM 24004 JCM 17293 MO-SEDI

NCBI tax ID(s) 913099

Special Collections DSMZ JCM Literature strains

History DSMZ <- S. Sakai, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; MO-SEDI <- H. Imachi {2010} JCM <-- S. Sakai; JAMSTEC, Japan; MO-SEDI.

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Sedimentibacter acidaminivorans MO-SEDI is an obligate anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from marine subsurface sediment.

Gram-negative rod-shaped colony-forming obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405231

JCM 17293,DSM 24004

@ref 20215

Last LPSN update 2026-05-29 08:37:51

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Tissierellales

Family Sedimentibacteraceae

Genus Sedimentibacter

Species Sedimentibacter acidaminivorans

Full scientific name Sedimentibacter acidaminivorans Imachi et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43751	negative	0.4-1.4 µm	0.4-0.6 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43751	0.2-0.3 mm	Brownish	circular	30 days	Basal medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43751	Basal medium
24237	SEDIMENTIBACTER ACIDAMINIVORANS MEDIUM (DSMZ Medium 1616)		Medium recipe at MediaDive	Name: SEDIMENTIBACTER ACIDAMINIVORANS MEDIUM (DSMZ Medium 1616) Composition: NaCl 19.9203 g/l MgCl2 x 7 H2O 3.98406 g/l Na-pyruvate 2.73904 g/l Na2CO3 1.49402 g/l Yeast extract 0.996016 g/l CaCl2 x 2 H2O 0.996016 g/l NH4Cl 0.537849 g/l Na2S x 9 H2O 0.298805 g/l L-Cysteine HCl x H2O 0.298805 g/l KH2PO4 0.0996016 g/l HCl 0.00249004 g/l FeCl2 x 4 H2O 0.00149402 g/l NaOH 0.000498008 g/l Sodium resazurin 0.000498008 g/l Pyridoxine hydrochloride 0.000199203 g/l CoCl2 x 6 H2O 0.000189243 g/l (DL)-alpha-Lipoic acid 9.96016e-05 g/l MnCl2 x 4 H2O 9.96016e-05 g/l Calcium D-(+)-pantothenate 9.96016e-05 g/l p-Aminobenzoic acid 9.96016e-05 g/l Nicotinic acid 9.96016e-05 g/l Riboflavin 9.96016e-05 g/l Thiamine HCl 9.96016e-05 g/l ZnCl2 6.97211e-05 g/l Biotin 3.98406e-05 g/l Folic acid 3.98406e-05 g/l Na2MoO4 x 2 H2O 3.58566e-05 g/l NiCl2 x 6 H2O 2.39044e-05 g/l H3BO3 5.9761e-06 g/l Na2WO4 x 2 H2O 3.98406e-06 g/l Na2SeO3 x 5 H2O 2.98805e-06 g/l CuCl2 x 2 H2O 1.99203e-06 g/l Vitamin B12 1.99203e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24237	positive	growth	30
43751	positive	growth	4-37
43751	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
43751	positive	optimum	7-7.5
43751	positive	growth	6-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43751	obligate anaerobe
125438	anaerobe	91.24
125439	facultative anaerobe	95.906

Spore formation

43751

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43751	NaCl	positive	growth	0-60 g/L
43751	NaCl	positive	optimum	20 g/L

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43751	16449 ChEBI	alanine	-	assimilation
43751	22599 ChEBI	arabinose	-	assimilation
43751	29016 ChEBI	arginine	+	growth
43751	22653 ChEBI	asparagine	-	assimilation
43751	35391 ChEBI	aspartate	-	assimilation
43751	16150 ChEBI	benzoate	-	assimilation
43751	17968 ChEBI	butyrate	-	assimilation
43751	17057 ChEBI	cellobiose	-	assimilation
43751	35899 ChEBI	crotonate	-	assimilation
43751	15356 ChEBI	cysteine	-	assimilation
43751	33403 ChEBI	elemental sulfur	-	assimilation
43751	16236 ChEBI	ethanol	-	assimilation
43751	29806 ChEBI	fumarate	-	assimilation
43751	17234 ChEBI	glucose	-	assimilation
43751	17754 ChEBI	glycerol	-	assimilation
43751	15428 ChEBI	glycine	+	growth
43751	27570 ChEBI	histidine	-	assimilation
43751	24898 ChEBI	isoleucine	+	growth
43751	24996 ChEBI	lactate	-	assimilation
43751	17716 ChEBI	lactose	-	assimilation
43751	25017 ChEBI	leucine	+	growth
43751	25094 ChEBI	lysine	+	growth
43751	17306 ChEBI	maltose	-	assimilation
43751	29864 ChEBI	mannitol	-	assimilation
43751	37684 ChEBI	mannose	-	assimilation
43751	6731 ChEBI	melezitose	+	growth
43751	16811 ChEBI	methionine	+	growth
43751	17632 ChEBI	nitrate	-	assimilation
43751	16301 ChEBI	nitrite	-	assimilation
43751	28044 ChEBI	phenylalanine	+	growth
43751	26271 ChEBI	proline	-	assimilation
43751	17272 ChEBI	propionate	-	assimilation
43751	15361 ChEBI	pyruvate	+	growth
43751	16634 ChEBI	raffinose	-	assimilation
43751	26546 ChEBI	rhamnose	-	assimilation
43751	17814 ChEBI	salicin	-	assimilation
43751	17822 ChEBI	serine	-	assimilation
43751	64243 ChEBI	sodium L-glutamate	-	assimilation
43751	30911 ChEBI	sorbitol	-	assimilation
43751	17992 ChEBI	sucrose	-	assimilation
43751	16189 ChEBI	sulfate	-	assimilation
43751	17359 ChEBI	sulfite	-	assimilation
43751	26986 ChEBI	threonine	-	assimilation
43751	27082 ChEBI	trehalose	-	assimilation
43751	27897 ChEBI	tryptophan	+	growth
43751	18186 ChEBI	tyrosine	-	assimilation
43751	27266 ChEBI	valine	+	growth
43751	18222 ChEBI	xylose	-	assimilation
43751		yeast extract (0.01 %, w/v)	+	required for growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43751	35581 ChEBI	indole
43751	15138 ChEBI	sulfide

Enzymes

@ref	Value	Activity	Ec
43751	arginine arylamidase	+
43751	arginine dihydrolase	+	3.5.3.6
43751	esterase (C 4)	+
43751	esterase Lipase (C 8)	+
43751	glycin arylamidase	-
43751	histidine arylamidase	-
43751	leucyl glycin arylamidase	+	3.4.11.1
43751	naphthol-AS-BI-phosphohydrolase	+
43751	phenylalanine arylamidase	-
43751	proline-arylamidase	-	3.4.11.5
43751	serine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Environmental	#Microbial community	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24237	marine subsurface sediment	north-western Pacific Ocean off the Shimokita Peninsula	Japan	JPN	Asia	41.1773	142.201 41.1773/142.201
43751	A methanogenic microbial community, which was originally obtained from marine subsurface sediments collected from off the Shimokita Peninsula	Shimokita Peninsula	Japan	JPN	Asia	41.177	142.201 41.177/142.201
67770	Marine subsurface sediments obtained off the Shimokita Peninsula		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB598276 (>99% sequence identity) for Sedimentibacter acidaminivorans subclade from Microbeatlas

Aquatic Samples	113
Soil Samples	11
Animal Samples	1
Plant Samples	2
Total Samples	127

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24237	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1787395v1 assembly for Sedimentibacter acidaminivorans DSM 24004	contig	GCA_017873955	913099.3	2913419208	913099	70.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24237	Sedimentibacter sp. MO-SED gene for 16S rRNA, partial sequence	AB598275	1438		913099
24237	Sedimentibacter sp. MO-SED gene for 16S rRNA, partial sequence	AB598276	1609		913099

GC content

@ref	GC-content (mol%)	Method
43751	32	high performance liquid chromatography (HPLC)
24237	32.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1787395v1 assembly for Sedimentibacter acidaminivorans DSM 24004
NCBI: GCA_017873955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.91	no
125439	gram_stain	BacteriaNetⓘ	positive	57.44	no
125439	motility	BacteriaNetⓘ	yes	73.81	no
125439	spore_formation	BacteriaNetⓘ	yes	76.77	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sedimentibacter acidaminivorans strain DSM 24004
PATRIC: 913099.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.04	no
125438	anaerobic	anaerobicⓘ	yes	91.24	yes
125438	aerobic	aerobicⓘ	no	94.58	yes
125438	spore-forming	spore-formingⓘ	yes	54.21	yes
125438	thermophilic	thermophileⓘ	no	90.44	yes
125438	flagellated	motile2+ⓘ	yes	71.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sedimentibacter acidaminivorans sp. nov., an anaerobic, amino-acid-utilizing bacterium isolated from marine subsurface sediment.	Imachi H, Sakai S, Kubota T, Miyazaki M, Saito Y, Takai K	Int J Syst Evol Microbiol	10.1099/ijsem.0.000878	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 )
#24237	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24004
#43751	Hiroyuki Imachi, Sanae Sakai, Takaaki Kubota, Masayuki Miyazaki, Yayoi Saito, Ken Takai: Sedimentibacter acidaminivorans sp. nov., an anaerobic, amino-acid-utilizing bacterium isolated from marine subsurface sediment. IJSEM 66: 1293 - 1300 2016 ( DOI 10.1099/ijsem.0.000878 , PubMed 26739306 )
#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;
#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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Sedimentibacter acidaminivorans (DSM 24004, JCM 17293, MO-SEDI)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017873955

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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