Name: Succinatimonas hippei DSM 22608
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16638

Type strain:

Species: Succinatimonas hippei

Culture col. no.: DSM 22608, JCM 16073, YIT 12066, KCTC 15190

Strain history: Y. Watanae A55 (=YIT 12066).

NCBI tax ID(s): 762983 (strain), 626938 (species)

SI-ID 401773

DSM 22608

Special Collections

Section

Succinatimonas hippei DSM 22608 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from faeces from a healthy 57-year-old Japanese male.

Gram-negative
rod-shaped
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	*Aeromonadales*
	Family	*Succinivibrionaceae*
	Genus	*Succinatimonas*
	Species	**Succinatimonas hippei**
	Full Scientific Name (LPSN)	Succinatimonas hippei Morotomi et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29564]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.983

[Ref.: #29564]	Cell length	3.1 µm

[Ref.: #29564]	Cell width	0.95 µm

[Ref.: #29564]	Cell shape	rod-shaped

[Ref.: #29564]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16430]

Culture medium

WILKINS-CHALGREN ANAEROBE BROTH (N2/CO2) (DSMZ Medium 339a)

[Ref.: #16430]

Culture medium growth

[Ref.: #16430]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16430]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16430]	growth	37 °C
[Ref.: #29564]	growth	30-45 °C
[Ref.: #29564]	optimum	37.5 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #16430]	Oxygen tolerance	anaerobe
[Ref.: #29564]	Oxygen tolerance	anaerobe

[Ref.: #29564]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %94.831
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29564]	arabinose ChEBI	+	carbon source
[Ref.: #29564]	glucose ChEBI	+	carbon source
[Ref.: #29564]	maltose ChEBI	+	carbon source
[Ref.: #29564]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29564]		acid phosphatase	+	3.1.3.2

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	oxidative phosphorylation	56.04	51 of 91
[Ref.: #66794]	NAD metabolism	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	flavin biosynthesis	46.67	7 of 15
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	leucine metabolism	38.46	5 of 13
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	ubiquinone biosynthesis	28.57	2 of 7
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	lipid metabolism	25.81	8 of 31
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #16430]	Sample type/isolated from	faeces from a healthy 57-year-old Japanese male
[Ref.: #16430]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #16430]	Country	Japan
[Ref.: #16430]	Country ISO 3 Code	JPN
[Ref.: #16430]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Human feces
* marker position based on {}

Isolation sources categories

#Host	#Human	#Male
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB601002 (>99% sequence identity) for Succinatimonas hippei subclade from Microbeatlas

Aquatic Samples	416
Soil Samples	258
Animal Samples	7361
Plant Samples	102
Total Samples	8137

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16430]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #16430]	Succinatimonas hippei gene for 16S rRNA, partial sequence, strain: YIT 12066	AB490810	1469	GenBank ENA	762983 tax ID
[Ref.: #20218]	Succinatimonas hippei gene for 16S ribosomal RNA, partial sequence	AB601002	1478	GenBank ENA	762983 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Succinatimonas hippei YIT 12066	GCA_000188195	scaffold	GenBank ENA	762983 tax ID	*
[Ref.: #66792]	Succinatimonas hippei YIT 12066	762983.3	wgs	PATRIC	762983 tax ID	*
[Ref.: #66792]	Succinatimonas hippei YIT 12066	649990019	draft	JGI IMG/M	762983 tax ID	*

[Ref.: #16430]	GC-content	40.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29564]	GC-content	40.3 mol%

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: Succinatimonas hippei YIT 12066 YIT 12066 NCBI: GCA_000188195.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Succinatimonas hippei YIT 12066 YIT 12066 NCBI: GCA_000188195.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.983	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	65.451	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	92.008	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	94.831	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.846	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	72.701	yes

Availability in culture collections External links

[Ref.: #16430]

Culture collection no.

DSM 22608, JCM 16073, YIT 12066, KCTC 15190

[Ref.: #85659]

SI-ID 401773

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	CO2 -dependent growth of Succinatimonas hippei YIT 12066T isolated from human feces.	Morotomi M, Nagai F, Watanabe Y	Microbiol Immunol	10.1111/j.1348-0421.2012.00420.x	2012	*
Phylogeny	Succinatimonas hippei gen. nov., sp. nov., isolated from human faeces.	Morotomi M, Nagai F, Watanabe Y, Tanaka R	Int J Syst Evol Microbiol	10.1099/ijs.0.015958-0	2009	*

References

#16430

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22608

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#29564

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 #25959 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#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 )

#85659

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID401773.1 )

#25959

IJSEM 1788 2010 ( DOI 10.1099/ijs.0.015958-0 , PubMed 19749029 )

* These data were automatically processed and therefore are not curated

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Succinatimonas hippei YIT 12066 YIT 12066

Succinatimonas hippei YIT 12066 YIT 12066

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