Lancefieldella rimae (DSM 7090, ATCC 49626, CCUG 31168)

Name: Lancefieldella rimae (DSM 7090, ATCC 49626, CCUG 31168)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3041

Type strain

Strain Designation D140H-11A

Culture col. no. DSM 7090 ATCC 49626 CCUG 31168 D140H-11A VPI D140H-11A 6 more

NCBI tax ID(s) 553184 1383

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- ATCC <- VPI, D140H-11A JCM <-- DSM 7090 <-- ATCC 49626 <-- VPI D140H-11A. CIP <- 2008, JCM <- I. Olsen, Oslo Univ, Norway <- DSM <- ATCC <- VPI D140H-11A: strain 10299

Links

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

Gram-positive motile oval-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92323

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

@ref 20215

Last LPSN update 2026-05-29 08:25:37

Domain Bacteria

Phylum Actinomycetota

Class Coriobacteriia

Order Coriobacteriales

Family Atopobiaceae

Genus Lancefieldella

Species Lancefieldella rimae

Full scientific name Lancefieldella rimae (Olsen et al. 1991) Nouioui et al. 2018

Synonyms (2)

Lactobacillus rimae
Atopobium rimae

BacDive ID	Other strains from **Lancefieldella rimae** (2)	Type strain
149981	L. rimae CCUG 38789
151900	L. rimae CCUG 45151 A

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
122239	positive	oval-shaped
125439	negative			98.369

Colony morphology

50459

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2980	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
37299	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122239	CIP Medium 6	Medium recipe at CIP
122239	CIP Medium 10	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2980	positive	growth	37
37299	positive	growth	37
50459	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
2980	anaerobe
50459	anaerobe
122239	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.877

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	+	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
122239	17632 ChEBI	nitrate	-	reduction
122239	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
122239	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	+	3.5.3.6	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
122239	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68382	leucine arylamidase	-	3.4.11.1	from API zym
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122239	oxidase	-
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	+	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
122239	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122239	-	-	+	+	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
2980	-	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Gingiva
#Host Body-Site	#Oral cavity and airways	#Tooth

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
2980	human gingival crevice	Homo sapiens
50459	Human gingival crevice	Homo sapiens
67770	Human gingival crevices	Homo sapiens
122239	Human, Gingival crevice	Homo sapiens	Oslo	Norway	NOR	Europe	1991

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2980	2	Risk group (German classification) According to TRBA 466
122239	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM17401v1 assembly for Lancefieldella rimae ATCC 49626	contig	GCA_000174015	553184.4	643886019	553184	77.42
67770	ASM143888v1 assembly for Lancefieldella rimae DSM 7090	scaffold	GCA_001438885	1383.3	2834436906	1383	75
66792	SRR9217479-mag-bin.11 assembly for Lancefieldella rimae ATCC 49626	contig	GCA_905373575	553184.9		553184	45.67

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Atopobium rimae 16S ribosomal RNA gene, partial sequence	AF292371	1445	1383
2980	A.rimae 16S rRNA	X67149	1349	1383
67770	Atopobium rimae gene for 16S ribosomal RNA, partial sequence, strain: JCM 10299	AB540986	1474	1383

GC content

@ref	GC-content (mol%)	Method
2980	45.0	thermal denaturation, midpoint method (Tm)
67770	45	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM17401v1 assembly for Lancefieldella rimae ATCC 49626
BV-BRC: 553184.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	89.61	no
125439	gram_stain	BacteriaNetⓘ	negative	98.37	no
125439	motility	BacteriaNetⓘ	yes	75.25	no
125439	spore_formation	BacteriaNetⓘ	no	99.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Pathogenicity	Heat-killed Lancefieldella Rimae Induces Bone Resorption by Promoting Osteoclast Differentiation.	Park J, Lim Y, Park C, Kum KY, Yun CH, Park OJ, Han SH.	J Endod	10.1016/j.joen.2024.08.014	2024
	Splenic abscess caused by Lancefieldella rimae successfully managed with percutaneous drainage and antibiotics: A case report.	Inagaki K, Hashimoto M, Hashimoto N, Suzuki K, Koyanagi N, Kitahara R, Iimuro K, Suzuki A, Furusawa S, Tsuji M, Akahori T.	Radiol Case Rep	10.1016/j.radcr.2024.07.099	2024
	A Case of Post-Endobronchial Ultrasound Polymicrobial Pericarditis and Mediastinitis in Metastatic Renal Cell Carcinoma.	Sekowski V, Hanna W.	Case Rep Oncol	10.1159/000544053	2025
	Exploring the plausible genetic relationship of salivary and tongue microbiome with periodontitis: A mendelian randomization study.	Li J, Wang S, Luo P, Li Z, Gopinath D.	Saudi Dent J	10.1007/s44445-025-00087-y	2025
	Mediastinitis after endobronchial ultrasound with transbronchial needle aspiration resulting in postpneumonectomy empyema.	Robinson NL, Watkins RD, Tapias LF.	JTCVS Tech	10.1016/j.xjtc.2024.03.012	2024
Genetics	Novel potential biomarkers for predicting childhood caries via metagenomic analysis.	Zhang H, Zheng X, Huang Y, Zou Y, Zhang T, Repo MA, Yin M, You Y, Jie Z, Xu WA.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1522970	2025
	Exploring Relationships Within the Microbiome of Root Canal Infections and the Influence of Associated Clinical Parameters.	Mominkhan D, Brito LCN, Yakubu AR, Larson E, Martin L, Patel M, Tavares WLF, Ribeiro-Sobrinho A, Teles F.	Int Endod J	10.1111/iej.70011	2025
	Newly identified pathogens in periodontitis: evidence from an association and an elimination study.	Veras EL, Castro Dos Santos N, Souza JGS, Figueiredo LC, Retamal-Valdes B, Barao VAR, Shibli J, Bertolini M, Faveri M, Teles F, Duarte P, Feres M.	J Oral Microbiol	10.1080/20002297.2023.2213111	2023
	Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.	Meng L, Jin H, Yulug B, Altay O, Li X, Hanoglu L, Cankaya S, Coskun E, Idil E, Nogaylar R, Ozsimsek A, Shoaie S, Turkez H, Nielsen J, Zhang C, Boren J, Uhlen M, Mardinoglu A.	Alzheimers Res Ther	10.1186/s13195-024-01578-6	2024
	Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic.	Dieckow S, Szafranski SP, Grischke J, Qu T, Doll-Nikutta K, Steglich M, Yang I, Haussler S, Stiesch M.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00624-3	2024
	Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.	Stoyancheva G, Mihaylova N, Gerginova M, Krumova E.	Int J Mol Sci	10.3390/ijms262110796	2025
Genetics	Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis.	Chen C, Zhang Y, Yao X, Yan Q, Li S, Zhong Q, Liu Z, Tang F, Liu C, Li H, Zhu D, Lan W, Ling Y, Lu D, Xu H, Ning Q, Wang Y, Jiang Z, Zhang Q, Gu G, Sun L, Wang N, Wang G, Zhang A, Ullah H, Sun W, Ma W.	BMC Microbiol	10.1186/s12866-023-03097-0	2023
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 .
#122239	Collection of Institut Pasteur ; Curators of the CIP; CIP 109880
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Lancefieldella rimae (DSM 7090, ATCC 49626, CCUG 31168)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000174015

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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