Olsenella umbonata (DSM 22620, CCUG 58604, JCM 16156)

Name: Olsenella umbonata (DSM 22620, CCUG 58604, JCM 16156)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3062

Type strain

Strain Designation lac31

Culture col. no. DSM 22620 CCUG 58604 JCM 16156 KCTC 15140 lac31

NCBI tax ID(s) 604330

Special Collections DSMZ CCUG JCM KCTC

History DSMZ <- M. Kraatz, Faculty Vet. Med., Free Univ. Berlin, Germany; lac31 JCM <-- M. Kraatz lac31. KCTC <- CCUG <- Mareike Kraatz, Faculty Vet. Med., Free Univ.(FUB), Berlin, Germany, lac31

Links

Olsenella umbonata lac31 is an obligate anaerobe, rod-shaped bacterium that was isolated from jejunal mucosa of a domestic pig.

rod-shaped obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405938

JCM 16156,KCTC 15140,DSM 22620,CCUG 58604

@ref 20215

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

Domain Bacteria

Phylum Actinomycetota

Class Coriobacteriia

Order Coriobacteriales

Family Atopobiaceae

Genus Olsenella

Species Olsenella umbonata

Full scientific name Olsenella umbonata Kraatz et al. 2011

Synonyms (1)

Parafannyhessea umbonata

BacDive ID	Other strains from **Olsenella umbonata** (3)	Type strain
3061	O. umbonata A2, DSM 22619, CCUG 58212, JCM 16157
159566	O. umbonata CA-693-APC-4B, DSM 105184
159567	O. umbonata WB01-CNA04-AN, DSM 105334

Morphology

Cell morphology

@ref	Cell shape	Motility	Gram stain
67771	rod-shaped
67771			positive

Colony morphology

61724

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16369	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

Culture temp

@ref	Growth	Type	Temperature (°C)
16369	positive	growth	37
61724	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16369	obligate anaerobe
61724	anaerobe
67771	anaerobe
125438	anaerobe	91.761

Spore formation

@ref	Spore formation	Confidence
67771
125439		99.284

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
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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	+	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
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
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
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
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

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
16369	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body-Site	#Gastrointestinal tract	#Small intestine

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
16369	jejunal mucosa of a domestic pig		Berlin-Dahlem, Institute of Animal Nutrition	Germany	DEU	Europe
61724	Pig jejunal mucosa,healthy 62-day old animal	2006-12-25	Berlin	Germany	DEU	Europe
67770	Mucosal jejunum of a pig		Berlin	Germany	DEU	Europe
67771	From the mucosal jejunum of a pig, healthy 62 day old animal		Institute of Animal Nutrition, Berlin-Dahlem	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence LC519857 (>99% sequence identity) for Olsenella umbonata subclade from Microbeatlas

Aquatic Samples	902
Soil Samples	512
Animal Samples	12522
Plant Samples	255
Total Samples	14191

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16369	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2636416177 annotated assembly for Parafannyhessea umbonata DSM 22620	chromosome	GCA_900105025	604330.5	2636416177	604330	89.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16369	Olsenella umbonata partial 16S rRNA gene, type strain lac31T	FN178463	1428		604330
67771	Olsenella umbonata JCM 16156 gene for 16S rRNA, partial sequence	LC519857	1456		604330

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2636416177 annotated assembly for Parafannyhessea umbonata DSM 22620
NCBI: GCA_900105025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	86.27	no
125439	gram_stain	BacteriaNetⓘ	negative	68.38	no
125439	motility	BacteriaNetⓘ	yes	61.59	no
125439	spore_formation	BacteriaNetⓘ	no	99.28	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Olsenella umbonata strain DSM 22620
PATRIC: 604330.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	80.34	yes
125438	anaerobic	anaerobicⓘ	yes	91.76	yes
125438	spore-forming	spore-formingⓘ	no	73.57	yes
125438	aerobic	aerobicⓘ	no	94.69	no
125438	thermophilic	thermophileⓘ	no	86.48	no
125438	flagellated	motile2+ⓘ	no	89.13	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Taxono-genomics description of Olsenella lakotia SW165 ^T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken.	Wongkuna S, Ghimire S, Janvilisri T, Doerner K, Chankhamhaengdecha S, Scaria J.	F1000Res	10.12688/f1000research.25823.1	2020
Phylogeny	Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu.	Lu LF, Yang Y, Zheng L, Zhang R, Liu GQ, Tu TY, Xu T, Luo X, Ran MF, Zhang LQ, Wang ST, Shen CH, Zhang YG	Int J Syst Evol Microbiol	10.1099/ijsem.0.005192	2021
Phylogeny	Olsenella faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces.	Han KI, Lee KC, Eom MK, Kim JS, Suh MK, Park SH, Lee JH, Kang SW, Park JE, Oh BS, Yu SY, Choi SH, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.003469	2019
Phylogeny	Parolsenella catena gen. nov., sp. nov., isolated from human faeces.	Sakamoto M, Iino T, Hamada M, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002645	2018
Phylogeny	Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces.	Li X, Jensen RL, Hojberg O, Canibe N, Jensen BB	Int J Syst Evol Microbiol	10.1099/ijs.0.000083	2015
Phylogeny	Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae.	Morinaga K, Kusada H, Sakamoto S, Murakami T, Toyoda A, Mori H, Meng XY, Takashino M, Murotomi K, Tamaki H	Int J Syst Evol Microbiol	10.1099/ijsem.0.005596	2022
Phylogeny	Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa.	Kraatz M, Wallace RJ, Svensson L	Int J Syst Evol Microbiol	10.1099/ijs.0.022954-0	2010

References

#16369	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22620
#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 )
#61724	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58604
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 )

Content

About us

Olsenella umbonata (DSM 22620, CCUG 58604, JCM 16156)

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 rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900105025

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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