Propionimicrobium lymphophilum | Type strain | CCUG 27816, NCTC 11866, LMG 16728, DSM 4903, ATCC 27520, JCM 5829, VPI 7625B, CIP 103263, NCIMB 702587, NCDO 2587 | BacDiveID:12663

Strain identifier

BacDive ID: 12663

Type strain:

Species: Propionimicrobium lymphophilum

Culture col. no.: CCUG 27816, NCTC 11866, LMG 16728, DSM 4903, ATCC 27520, JCM 5829, VPI 7625B, CIP 103263, NCIMB 702587, NCDO 2587

Strain history: CIP <- 2003, JCM <- ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 7625B

NCBI tax ID(s): 1123001 (strain), 33012 (species)

SI-ID 8646

LMG 16728, ATCC 27520, CCUG 27816, CIP 103263, DSM 4903, JCM 5829, NCTC 11866, NCDO 2587, NCIMB 702587

Section

Propionimicrobium lymphophilum CCUG 27816 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from submaxillary tissue.

Gram-positive
rod-shaped
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Propionibacteriaceae*
	Genus	*Propionimicrobium*
	Species	**Propionimicrobium lymphophilum**
	Full Scientific Name (LPSN)	Propionimicrobium lymphophilum (Torrey 1916) Stackebrandt et al. 2002

	Synonym	Propionibacterium lymphophilum
	Synonym	"Bacillus* lymphophilus"*

Information on morphological and physiological properties Morphology

[Ref.: #120724]	Gram stain	positive

[Ref.: #120724]	Cell shape	rod-shaped

[Ref.: #120724]	Motility	no

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

MEDIUM 26 - for Gardnerella and Propionibacterium lymphophilum

Culture medium growth

Culture medium composition

expand / minimize

[Ref.: #120724]

Culture medium

CIP Medium 26

[Ref.: #120724]

Culture medium growth

[Ref.: #120724]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120724]

Culture medium

CIP Medium 433

[Ref.: #120724]

Culture medium growth

[Ref.: #120724]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #1870]			growth	37 °C
[Ref.: #37134]			growth	37 °C
[Ref.: #48963]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #1870]	Temperature range	mesophilic
[Ref.: #37134]	Temperature range	mesophilic
[Ref.: #48963]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1870]	Oxygen tolerance	anaerobe
[Ref.: #48963]	Oxygen tolerance	anaerobe
[Ref.: #120724]	Oxygen tolerance	anaerobe

[Ref.: #1870]	Murein short key	A11.31
[Ref.: #1870]	Murein types	A4alpha L-Lys-D-Asp

Observation

quinones: MK-9(H₄)

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]		arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #120724]		cellobiose ChEBI	-	degradation
[Ref.: #120724]		D-arabinose ChEBI	-	degradation
[Ref.: #120724]		D-fructose ChEBI	+	degradation
[Ref.: #120724]		D-glucose ChEBI	+	degradation
[Ref.: #68380]		D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #120724]		D-xylose ChEBI	-	degradation
[Ref.: #120724]		esculin ChEBI	-	hydrolysis
[Ref.: #68380]		L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #120724]		lactose ChEBI	-	degradation
[Ref.: #120724]		maltose ChEBI	+	degradation
[Ref.: #120724]		nitrate ChEBI	-	reduction
[Ref.: #68380]		nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #120724]		nitrite ChEBI	-	reduction
[Ref.: #68380]		raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #120724]		salicin ChEBI	-	degradation
[Ref.: #120724]		sucrose ChEBI	-	degradation
[Ref.: #68380]		tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]		urea ChEBI	-	hydrolysis	* from API rID32A
		Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120724]		indole ChEBI	no
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68380]		alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]		alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]		alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]		alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]		alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]		alpha-glucosidase	-	3.2.1.20	* from API rID32A
[Ref.: #120724]		amylase	-
[Ref.: #68380]		arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #120724]		beta-galactosidase	-	3.2.1.23
[Ref.: #68380]		beta-galactosidase	-	3.2.1.23	* from API rID32A
[Ref.: #68380]		beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]		beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]		beta-glucuronidase	+	3.2.1.31	* from API rID32A
[Ref.: #120724]		caseinase	-	3.4.21.50
[Ref.: #120724]		catalase	-	1.11.1.6
[Ref.: #120724]		DNase	-
[Ref.: #120724]		gelatinase	-
[Ref.: #68380]		glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]		glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]		glycin arylamidase	-		* from API rID32A
[Ref.: #68380]		histidine arylamidase	-		* from API rID32A
[Ref.: #68380]		L-arginine arylamidase	-		* from API rID32A
[Ref.: #120724]		lecithinase	-
[Ref.: #68380]		leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]		leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #120724]		lipase	-
[Ref.: #68380]		N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #120724]		oxidase	-
[Ref.: #68380]		phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]		proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #120724]		protease	-
[Ref.: #68380]		pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]		serine arylamidase	-		* from API rID32A
[Ref.: #68380]		tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #120724]		tween esterase	-
[Ref.: #68380]		tyrosine arylamidase	-		* from API rID32A
[Ref.: #120724]		urease	-	3.5.1.5
[Ref.: #68380]		urease	-	3.5.1.5	* from API rID32A
		Only first 10 entries are displayed. Click here to see all.

API® rID32A:

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

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #1870]	12566	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #1870]	Sample type/isolated from	submaxillary tissue

[Ref.: #48963]	Sample type/isolated from	Human submaxillary tissue

[Ref.: #67770]	Sample type/isolated from	Submaxillary tissue

[Ref.: #120724]	Sample type/isolated from	Human, Submaxillary tissue
* marker position based on {}

Isolation sources categories

#Host Body-Site

#Oral cavity and airways

#Mouth

What are isolation sources categories?

Global distribution of 16S sequence AJ003056 (>99% sequence identity) for Propionimicrobium lymphophilum subclade from Microbeatlas

Aquatic Samples	1384
Soil Samples	283
Animal Samples	7765
Plant Samples	77
Total Samples	9509

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

[Ref.: #1870]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #120724]	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.: #20218]	Propionibacterium lymphophilum ATCC 27520 16S rRNA gene, partial sequence	U02907	388	ENA	33012 tax ID	*
[Ref.: #20218]	Propionibacterium lymphophilum DSM 4903 16S rRNA gene	AJ003056	1502	ENA	33012 tax ID	*
[Ref.: #20218]	Propionimicrobium lymphophilum gene for 16S ribosomal RNA, partial sequence, strain: JCM 5829	AB729070	1482	ENA	33012 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Propionimicrobium lymphophilum DSM 4903	GCA_000423485	scaffold	GenBank	1123001 tax ID
[Ref.: #66792]	Propionimicrobium lymphophilum DSM 4903	1123001.3	wgs	PATRIC	1123001 tax ID	*
[Ref.: #66792]	Propionimicrobium lymphophilum DSM 4903	2523533555	draft	JGI IMG/M	1123001 tax ID	*

[Ref.: #1870]	GC-content	54.0 mol%
[Ref.: #67770]	GC-content	56 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 Diaspora project based on: Propionimicrobium lymphophilum DSM 4903 PATRIC: 1123001.3
[Ref.: #69480]	motile	no	92.858	no
[Ref.: #69480]	flagellated	no	97.516	no
[Ref.: #69480]	gram-positive	yes	90.089	no
[Ref.: #69480]	anaerobic	yes	90.534	yes
[Ref.: #69480]	aerobic	no	93.677	yes
[Ref.: #69480]	halophile	no	78.275	no
[Ref.: #69480]	spore-forming	no	93.85	no
[Ref.: #69480]	glucose-util	yes	84.281	no
[Ref.: #69480]	thermophile	no	92.036	yes
[Ref.: #69480]	glucose-ferment	yes	70.598	no

Availability in culture collections External links

Culture collection no.

CCUG 27816, NCTC 11866, LMG 16728, DSM 4903, ATCC 27520, JCM 5829, VPI 7625B, CIP 103263, NCIMB 702587, NCDO 2587

SI-ID 8646

*

References

#1870

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4903

#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 )

#37134 ; Curators of the CIP;
#48963 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 27816

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68380

Automatically annotated from API rID32A .

#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) .

#81875

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-ID8646.1 )

#120724 Collection of Institut Pasteur ; Curators of the CIP; CIP 103263
* These data were automatically processed and therefore are not curated

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