Hallerella succinigenes (DSM 104698, UW S3, JCM 34256)

Name: Hallerella succinigenes (DSM 104698, UW S3, JCM 34256)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 139940

Type strain

Strain Designation UW S3, UWS3

Culture col. no. DSM 104698 UW S3 JCM 34256 UWS3

NCBI tax ID(s) 1896222

Special Collections DSMZ JCM Pig Literature strains DZIF

History DSMZ <- A. Neumann; Univ. of Wisconsin, Dept. of Bacteriology, Madison, Wisc., USA; UW S3 {2016} JCM <-- B. Abt; DSMZ, Germany; DSM 104698 (=UWS3) <-- A. Neumann; Univ. of Wisconsin, USA; UWS3.

Links

Hallerella succinigenes UW S3 is an obligate anaerobe, rod-shaped bacterium that was isolated from Pig cecum.

rod-shaped obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405682

JCM34256,DSM 104698

@ref 20215

Last LPSN update 2026-05-29 08:39:36

Domain Bacteria

Phylum Fibrobacterota

Class Fibrobacteria

Order Fibrobacterales

Family Fibrobacteraceae

Genus Hallerella

Species Hallerella succinigenes

Full scientific name Hallerella succinigenes Wylensek et al. 2021

Morphology

Cell morphology

@ref	Cell length	Cell shape	Gram stain	Confidence
69645	1-2 µm	rod-shaped
125439			negative	95.432

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
42548	MDM (MODIFIED DEHORITY MEDIUM) (DSMZ Medium 1668)	Medium recipe at MediaDive	Name: MDM (modified dehority medium) (DSMZ Medium 1668) Composition: L-Cysteine HCl 1.0 g/l Tryptone 1.0 g/l Yeast extract 1.0 g/l K2HPO4 0.013608 g/l NaHCO3 0.013442 g/l NaCl 0.00935 g/l NH4Cl 0.00321 g/l MgCl2 x 2 H2O 0.001942 g/l ZnCl2 0.000546 g/l NiCl2 x 6 H2O 0.000474 g/l CoCl2 0.000208 g/l MgCl2 0.00019 g/l CaCl2 0.000178 g/l Na2WO4 x 2 H2O 0.000132 g/l Na2 MoO4 x 2 H2O 9.6e-05 g/l Na2SeO3 7e-05 g/l FeSO4 x 7 H2O 5.6e-05 g/l Distilled water
69645	Gifu Anaerobic Medium, modi?ed
69645	Wilkins-Chalgren Anaerobe broth		supplemented with L-cysteine and DTT (0.05% and 0.02% (w/v), respectively)
69645	modified YCFA

Culture temp

@ref	Growth	Type	Temperature (°C)
42548	positive	growth	37
67770	positive	growth	37
69645	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
69645	obligate anaerobe
125439	facultative anaerobe	90.297

Spore formation

@ref	Spore formation	Confidence
125439		99.884

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	-	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	-	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	-	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
69645	17234 ChEBI	glucose	+	assimilation
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite
69645	30089 ChEBI	acetate
69645	15740 ChEBI	formate
68380	35581 ChEBI	indole	from API rID32A
68367	35581 ChEBI	indole	from API 20A
69645	30031 ChEBI	succinate

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

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
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68367	gelatinase	-		from API 20A
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	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
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
42548	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
42548	-	-	-	-	-	-	+/-	-	-	+/-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-

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	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
42548	Pig cecum	Madison, WI	USA	USA	North America
67770	Cecum of a pig in Madison	Wisconsin	USA	USA	North America
69645	Pig caecum	Madison, Wisconsin	USA	USA	North America	Modified Dehority Medium (DSMZ medium 1668)	supplemented with 10 g cellobiose	5 days	37	anaerobic

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42548	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM279767v1 assembly for Hallerella succinigenes UWS3	contig	GCA_002797675	1896222.3	2747842507	1896222	75.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42548	Hallerella succinigenes strain UWS3 16S ribosomal RNA gene, partial sequence	MN537467	1521		2652275

GC content

@ref	GC-content (mol%)	Method
67770	49.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM279767v1 assembly for Hallerella succinigenes UWS3
NCBI: GCA_002797675

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.30	no
125439	motility	BacteriaNetⓘ	no	71.92	no
125439	gram_stain	BacteriaNetⓘ	negative	95.43	no
125439	spore_formation	BacteriaNetⓘ	no	99.88	no

Literature

References

#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 )
#42548	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104698
#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;
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#69645	David Wylensek, Thomas C. A. Hitch, Thomas Riedel, Afrizal Afrizal, Neeraj Kumar, Esther Wortmann, Tianzhe Liu, Saravanan Devendran, Till R. Lesker, Sara B. Hernández, Viktoria Heine, Eva M. Buhl, Paul M. D'Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R. Parreira, Birte Abt, Heidi L. Doden, Lindsey Ly, João M. P. Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P. Neumann, Garret Suen, Tomas de Wouters, Sascha Rohn, Ilias Lagkouvardos, Emma Allen-Vercoe, Cathrin Spröer, Boyke Bunk, Anja J. Taverne-Thiele, Marcel Giesbers, Jerry M. Wells, Klaus Neuhaus, Angelika Schnieke, Felipe Cava, Nicola Segata, Lothar Elling, Till Strowig, Jason M. Ridlon, Tobias A. M. Gulder, Jörg Overmann, Thomas Clavel: A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nat. Commun. 11: 2020 ( DOI 10.1038/s41467-020-19929-w )
#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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