Name: Phascolarctobacterium succinatutens A177
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158153

Type strain:

Species: Phascolarctobacterium succinatutens

Strain Designation: A177

Culture col. no.: DSM 22533, JCM 16074, YIT 12067

Strain history: Y. Watane A177 (=YIT 12067).

NCBI tax ID(s): 626939 (strain), 626940 (species)

SI-ID 406749

DSM 22533

Other strains from Phascolarctobacterium succinatutens

P. succinatutens B 162, DSM 22521, JCM 16075, YIT ...

Section

Phascolarctobacterium succinatutens A177 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces .

Gram-negative
anaerobe
mesophilic
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	*Bacillota*
	Class	*Negativicutes*
	Order	*Acidaminococcales*
	Family	*Acidaminococcaceae*
	Genus	*Phascolarctobacterium*
	Species	**Phascolarctobacterium succinatutens**
	Full Scientific Name (LPSN)	Phascolarctobacterium succinatutens Watanabe et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.722

Information on culture and growth conditions Culture and growth conditions

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Culture medium

PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #64739]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #64739]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

anaerobe Confidence in %99.358

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.539
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[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]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	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]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	d-mannose degradation	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #64739]	Sample type/isolated from	human faeces (healthy Japanese adult)
[Ref.: #64739]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #64739]	Country	Japan
[Ref.: #64739]	Country ISO 3 Code	JPN
[Ref.: #64739]	Continent	Asia

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

Isolation sources categories

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

What are isolation sources categories?

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Global distribution of 16S sequence AB490811 (>99% sequence identity) for Phascolarctobacterium succinatutens subclade from Microbeatlas

Aquatic Samples	3216
Soil Samples	672
Animal Samples	71670
Plant Samples	343
Total Samples	75901

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

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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.: #64739]	Phascolarctobacterium succinatutens YIT 12067 gene for 16S rRNA, partial sequence	AB490811	1610	ENA	626939 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phascolarctobacterium succinatutens YIT 12067	GCA_000188175	scaffold	GenBank	626939 tax ID
[Ref.: #66792]	Phascolarctobacterium succinatutens YIT 12067	626939.3	wgs	PATRIC	626939 tax ID	*
[Ref.: #66792]	Phascolarctobacterium succinatutens YIT 12067 strain Phascolarctobacterium succinatutens 82G5	626939.32	complete	PATRIC	626939 tax ID	*
[Ref.: #66792]	Phascolarctobacterium succinatutens YIT 12067 ERS2913222	2836699358	complete	JGI IMG/M	626939 tax ID	*
[Ref.: #66792]	Phascolarctobacterium succinatutens YIT 12067	649989983	draft	JGI IMG/M	626939 tax ID	*

[Ref.: #64739]	GC-content	47 mol%	sequence analysis
[Ref.: #64739]	GC-content	46.5 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Phascolarctobacterium succinatutens YIT 12067 strain Phascolarctobacterium succinatutens 82G5 PATRIC: 626939.32
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phascolarctobacterium succinatutens YIT 12067 strain Phascolarctobacterium succinatutens 82G5 PATRIC: 626939.32
[Ref.: #69480]	gram-positive	no	95.663	no
[Ref.: #69480]	anaerobic	yes	99.999	no
[Ref.: #69480]	halophile	no	93.871	no
[Ref.: #69480]	spore-forming	no	78.295	no
[Ref.: #69480]	glucose-util	no	53.429	no
[Ref.: #69480]	thermophile	no	97.99	no
[Ref.: #69480]	flagellated	no	95.452	no
[Ref.: #69480]	aerobic	no	98.267	no
[Ref.: #69480]	motile	no	85.836	no
[Ref.: #69480]	glucose-ferment	no	66.404	no

Availability in culture collections External links

[Ref.: #64739]

Culture collection no.

DSM 22533, JCM 16074, YIT 12067

[Ref.: #110986]

SI-ID 406749

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phascolarctobacterium wakonense sp. nov., isolated from common marmoset (Callithrix jacchus) faeces.	Shigeno Y, Kitahara M, Shime M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.003407	2019	*
Phylogeny	Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces.	Watanabe Y, Nagai F, Morotomi M	Appl Environ Microbiol	10.1128/AEM.06035-11	2011	*

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 )

#64739

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22533

#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 )

#110986

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-ID406749.1 )

* These data were automatically processed and therefore are not curated

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Phascolarctobacterium succinatutens YIT 12067 strain Phascolarctobacterium succinatutens 82G5

Phascolarctobacterium succinatutens YIT 12067 strain Phascolarctobacterium succinatutens 82G5

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