Name: Lancefieldella rimae D140H-11A
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3041

Type strain:

Species: Lancefieldella rimae

Strain Designation: D140H-11A

Culture col. no.: DSM 7090, ATCC 49626, CCUG 31168, VPI D140H-11A, JCM 10299, CIP 109880, IFO 15546, LMG 11476, NBRC 15546, NCFB 2896

Strain history: CIP <- 2008, JCM <- I. Olsen, Oslo Univ, Norway <- DSM <- ATCC <- VPI D140H-11A: strain 10299

NCBI tax ID(s): 553184 (strain), 1383 (species)

SI-ID 92323

LMG 11476, ATCC 49626, CCUG 31168, DSM 7090, NCFB 2896, JCM 10299, NCIMB 702896, IFO15546, NBRC 15546, KCTC 5042, CIP 109880

Special Collections

Other strains from Lancefieldella rimae

Section

Lancefieldella rimae D140H-11A is an anaerobe, Gram-positive, motile bacterium that was isolated from human gingival crevice.

Gram-positive
motile
oval-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	*Actinomycetota*
	Class	*Coriobacteriia*
	Order	*Coriobacteriales*
	Family	*Atopobiaceae*
	Genus	*Lancefieldella*
	Species	**Lancefieldella rimae**
	Full Scientific Name (LPSN)	Lancefieldella rimae (Olsen et al. 1991) Nouioui et al. 2018

	Synonym	Lactobacillus rimae
	Synonym	Atopobium rimae

Information on morphological and physiological properties Morphology

[Ref.: #122239]	Gram stain	positive

[Ref.: #122239]	Cell shape	oval-shaped

[Ref.: #122239]	Motility	yes

[Ref.: #50459]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2980]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #2980]

Culture medium growth

[Ref.: #2980]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2980]

Culture medium composition

expand / minimize

[Ref.: #37299]

Culture medium

MEDIUM 6 - Columbia agar with 10 % horse blood

[Ref.: #37299]

Culture medium growth

[Ref.: #37299]

Culture medium composition

expand / minimize

[Ref.: #122239]

Culture medium

CIP Medium 6

[Ref.: #122239]

Culture medium growth

[Ref.: #122239]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122239]

Culture medium

CIP Medium 10

[Ref.: #122239]

Culture medium growth

[Ref.: #122239]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #2980]	growth	37 °C
[Ref.: #37299]	growth	37 °C
[Ref.: #50459]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2980]	Oxygen tolerance	anaerobe
[Ref.: #50459]	Oxygen tolerance	anaerobe
[Ref.: #122239]	Oxygen tolerance	anaerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	+	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #122239]	nitrate ChEBI	-	reduction
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #122239]	nitrite ChEBI	-	reduction
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #122239]		indole ChEBI	no
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

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

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym, API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym, API rID32A
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym, API rID32A
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API rID32A
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68380]	arginine dihydrolase	+	3.5.3.6	* from API rID32A
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	+	3.2.1.21	* from API rID32A
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API rID32A
[Ref.: #122239]	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.: #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.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym, API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API rID32A
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122239]	oxidase	-
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #122239]	urease	-	3.5.1.5
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
[Ref.: #68382]	valine arylamidase	-		* from API zym
	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.: #2980]	12574	-	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-

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.: #122239]	12187	-	-	+	+	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #2980]	Sample type/isolated from	human gingival crevice

[Ref.: #50459]	Sample type/isolated from	Human gingival crevice

[Ref.: #67770]	Sample type/isolated from	Human gingival crevices

[Ref.: #122239]	Sample type/isolated from	Human, Gingival crevice
[Ref.: #122239]	Geographic location (country and/or sea, region)	Oslo
[Ref.: #122239]	Country	Norway
[Ref.: #122239]	Country ISO 3 Code	NOR
[Ref.: #122239]	Continent	Europe
[Ref.: #122239]	Isolation date	1991
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Gingiva
#Host Body-Site	#Oral cavity and airways	#Tooth

What are isolation sources categories?

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

[Ref.: #2980]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #122239]	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.: #2980]	A.rimae 16S rRNA	X67149	1349	GenBank ENA	1383 tax ID
[Ref.: #67770]	Atopobium rimae gene for 16S ribosomal RNA, partial sequence, strain: JCM 10299	AB540986	1474	GenBank ENA	1383 tax ID
[Ref.: #20218]	Atopobium rimae 16S ribosomal RNA gene, partial sequence	AF292371	1445	GenBank ENA	1383 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Lancefieldella rimae DSM 7090	GCA_001438885	scaffold	GenBank ENA	1383 tax ID
[Ref.: #67770]	Lancefieldella rimae ATCC 49626	GCA_000174015	contig	GenBank ENA	553184 tax ID
[Ref.: #66792]	Atopobium rimae ATCC 49626	553184.4	wgs	PATRIC	553184 tax ID	*
[Ref.: #66792]	Atopobium rimae ATCC 49626 strain SRR9217479-mag-bin.11	553184.9	wgs	PATRIC	553184 tax ID	*
[Ref.: #66792]	Atopobium rimae strain DSM 7090	1383.3	wgs	PATRIC	1383 tax ID	*
[Ref.: #66792]	Atopobium rimae DSM 7090	2834436906	draft	JGI IMG/M	1383 tax ID	*

[Ref.: #2980]	GC-content	45.0 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	45 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #2980]

Culture collection no.

DSM 7090, ATCC 49626, CCUG 31168, VPI D140H-11A, JCM 10299, CIP 109880, IFO 15546, LMG 11476, NBRC 15546, NCFB 2896

[Ref.: #72561]

SI-ID 92323

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus uli sp. nov. and Lactobacillus rimae sp. nov. from the human gingival crevice and emended descriptions of lactobacillus minutus and Streptococcus parvulus.	Olsen I, Johnson JL, Moore LV, Moore WE	Int J Syst Bacteriol	10.1099/00207713-41-2-261	1991	*

References

#2980

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7090

#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 )

#37299 ; Curators of the CIP;
#50459 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 31168

#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;

#68380

Automatically annotated from API rID32A .

#68382

Automatically annotated from API zym .

#72561

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-ID92323.1 )

#122239 Collection of Institut Pasteur ; Curators of the CIP; CIP 109880
* These data were automatically processed and therefore are not curated

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