Name: Pseudoramibacter alactolyticus DO-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5452

Type strain:

Species: Pseudoramibacter alactolyticus

Strain Designation: DO-4

Culture col. no.: DSM 3980, ATCC 23263, CCUG 52346, CIP 107831, JCM 6480, VPI 0416, KCTC 15024

Strain history: CIP <- 2003, ATCC <- W.E. Moore <- A. Prevot: strain DO-4

NCBI tax ID(s): 887929 (strain), 113287 (species)

SI-ID 37975

ATCC 23263, DSM 3980, JCM 6480, CIP 106365, CCUG 52346, CIP 107831, KCTC 15024

Other strains from Pseudoramibacter alactolyticus

P. alactolyticus 1218, CIP 107834, ATCC 23264
P. alactolyticus CCUG 12259
P. alactolyticus CCUG 15972
P. alactolyticus CCUG 27985

Section

Pseudoramibacter alactolyticus DO-4 is an anaerobe, mesophilic bacterium that was isolated from purulent pleurisy.

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	*Clostridia*
	Order	*Eubacteriales*
	Family	*Eubacteriaceae*
	Genus	*Pseudoramibacter*
	Species	**Pseudoramibacter alactolyticus**
	Full Scientific Name (LPSN)	Pseudoramibacter alactolyticus (Prévot and Taffanel 1942) Willems and Collins 1996

	Synonym	"Ramibacterium* alactolyticum"*
	Synonym	Eubacterium alactolyticum

Information on morphological and physiological properties Morphology

[Ref.: #116171]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #116171]	Cell shape	rod-shaped

[Ref.: #116171]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %96.577

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1538]

Culture medium

AMB MEDIUM (DSMZ Medium 455)

[Ref.: #1538]

Culture medium growth

[Ref.: #1538]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1538]

Culture medium composition

expand / minimize

[Ref.: #39941]

Culture medium

MEDIUM 7 - for Actinomyces

[Ref.: #39941]

Culture medium growth

[Ref.: #39941]

Culture medium composition

expand / minimize

[Ref.: #116171]

Culture medium

CIP Medium 7

[Ref.: #116171]

Culture medium growth

[Ref.: #116171]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #116171]

Culture medium

CIP Medium 45

[Ref.: #116171]

Culture medium growth

[Ref.: #116171]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #1538]	growth	37 °C
[Ref.: #39941]	growth	37 °C
[Ref.: #59519]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #116171]	growth	37 °C

[Ref.: #1538]	Temperature range	mesophilic
[Ref.: #39941]	Temperature range	mesophilic
[Ref.: #59519]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #116171]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1538]	Oxygen tolerance	anaerobe
[Ref.: #59519]	Oxygen tolerance	anaerobe
[Ref.: #116171]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.651

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.957

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116171]	cellobiose ChEBI	-	degradation
[Ref.: #116171]	D-arabinose ChEBI	-	degradation
[Ref.: #116171]	D-fructose ChEBI	-	degradation
[Ref.: #116171]	D-glucose ChEBI	+	degradation
[Ref.: #116171]	D-xylose ChEBI	-	degradation
[Ref.: #116171]	esculin ChEBI	-	hydrolysis
[Ref.: #116171]	lactose ChEBI	-	degradation
[Ref.: #116171]	maltose ChEBI	-	degradation
[Ref.: #116171]	nitrate ChEBI	-	reduction
[Ref.: #116171]	nitrate ChEBI	+	respiration
[Ref.: #116171]	nitrite ChEBI	-	reduction
[Ref.: #116171]	salicin ChEBI	-	degradation
[Ref.: #116171]	sucrose ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #67770]	acetate ChEBI	yes
[Ref.: #67770]	butyrate ChEBI	yes
[Ref.: #67770]	formate ChEBI	yes
[Ref.: #67770]	hexanoate ChEBI	yes
[Ref.: #67770]	hydrogen ChEBI	yes
[Ref.: #116171]	indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #116171]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116171]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #116171]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #116171]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116171]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116171]	10685	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	purine metabolism	61.7	58 of 94
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	52.75	48 of 91
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #1538]	Sample type/isolated from	purulent pleurisy

[Ref.: #59519]	Sample type/isolated from	Human purulent pleurisy

[Ref.: #67770]	Sample type/isolated from	Human oral cavity

[Ref.: #116171]	Sample type/isolated from	Purulent pleurisy
* marker position based on {}

Isolation sources categories

#Infection	#Inflammation	-
#Host Body-Site	#Oral cavity and airways	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC037208 (>99% sequence identity) for Pseudoramibacter alactolyticus subclade from Microbeatlas

Aquatic Samples	21
Soil Samples	11
Animal Samples	531
Plant Samples	14
Total Samples	577

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

[Ref.: #1538]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #116171]	Biosafety level	1	Risk group (French classification)

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.: #67770]	Pseudoramibacter alactolyticus gene for 16S ribosomal RNA, partial sequence, strain: JCM 6480	LC037208	1487	ENA	113287 tax ID
[Ref.: #20218]	Pseudoramibacter alactolyticus gene for 16S rRNA, strain: 23263	AB036759	1480	ENA	887929 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudoramibacter alactolyticus ATCC 23263	GCA_000185505	scaffold	GenBank	887929 tax ID
[Ref.: #66792]	Pseudoramibacter alactolyticus ATCC 23263	887929.3	wgs	PATRIC	887929 tax ID	*
[Ref.: #66792]	Pseudoramibacter alactolyticus ATCC 23263	649989993	draft	JGI IMG/M	887929 tax ID	*

[Ref.: #67770]

GC-content

61 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: Pseudoramibacter alactolyticus ATCC 23263 ATCC 23263 NCBI: GCA_000185505.1
[Ref.: #69481]	spore-forming	no	88	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoramibacter alactolyticus ATCC 23263 PATRIC: 887929.3
[Ref.: #69480]	motile	no	93.318	no
[Ref.: #69480]	flagellated	no	96.613	no
[Ref.: #69480]	gram-positive	yes	75.95	no
[Ref.: #69480]	anaerobic	yes	99.435	yes
[Ref.: #69480]	halophile	no	72.474	no
[Ref.: #69480]	spore-forming	no	82.1	no
[Ref.: #69480]	thermophile	no	96.215	yes
[Ref.: #69480]	glucose-util	yes	87.981	no
[Ref.: #69480]	aerobic	no	99.009	yes
[Ref.: #69480]	glucose-ferment	yes	67.172	no

Availability in culture collections External links

[Ref.: #1538]

Culture collection no.

DSM 3980, ATCC 23263, CCUG 52346, CIP 107831, JCM 6480, VPI 0416, KCTC 15024

[Ref.: #74940]

SI-ID 37975

References

#1538

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3980

#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 )

#39941 ; Curators of the CIP;
#59519 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52346

#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;

#68382

Automatically annotated from API zym .

#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 )

#74940

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-ID37975.1 )

#116171 Collection of Institut Pasteur ; Curators of the CIP; CIP 107831
* These data were automatically processed and therefore are not curated

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Pseudoramibacter alactolyticus ATCC 23263 ATCC 23263

Pseudoramibacter alactolyticus ATCC 23263

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Change proposal