Scrofimicrobium canadense (DSM 105338, WB03_NA08, JCM 34392)

Name: Scrofimicrobium canadense (DSM 105338, WB03_NA08, JCM 34392)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159351

Type strain

Strain Designation WB03_NA08

Culture col. no. DSM 105338 WB03_NA08 JCM 34392

NCBI tax ID(s) 2652290

Special Collections DSMZ JCM Pig Literature strains DZIF

History DSMZ <- E. Allen-Vercoe, Dept. Molecular and Cellular Biology, College of Biological Science, University of Guelph; JCM <-- B. Abt; DSMZ, Germany; DSM 105338 (=WB03_NA08) <-- E. Allen-Vercoe; Univ. of Guelph, Canada.

Links

Scrofimicrobium canadense WB03_NA08 is a facultative anaerobe, Gram-positive, rod-shaped bacterium that was isolated from wild boar.

Gram-positive rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397303

JCM 34392,DSM 105338

@ref 20215

Last LPSN update 2026-05-29 08:44:10

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Actinomycetales

Family Actinomycetaceae

Genus Scrofimicrobium

Species Scrofimicrobium canadense

Full scientific name Scrofimicrobium canadense Wylensek et al. 2021

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Confidence
125438				94.35
125439				96.856
69645	positive	1-2 µm	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
66174	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)	Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
69645	Nutrient agar (NA)
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)
66174	positive	growth	37
67770	positive	growth	37
69645	positive	growth	37

Physiology and metabolism

Oxygen tolerance

69645

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		96.955

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	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
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
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	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite
69645	30089 ChEBI	acetate
69645	15740 ChEBI	formate
68367	35581 ChEBI	indole	from API 20A
69645	24996 ChEBI	lactate
69645	30031 ChEBI	succinate

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68367	gelatinase	-		from API 20A
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
66174	-	-	+	-	-	+/-	+	-	+	+	-	+/-	+	+	+	+	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure	Latitude	Longitude
66174	wild boar	Stratford, Ontario	Canada	CAN	North America					43.3667	-80.9833 43.3667/-80.9833
67770	Feces of a farmed wild boar in Moserville	Ontario	Canada	CAN	North America
69645	Wild boar feces	Moserville, Ontario	Canada	CAN	North America	Nutrient Agar	3-4 days	37	aerobic

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM969661v1 assembly for Scrofimicrobium canadense WB03_NA08	contig	GCA_009696615	2606625.3	2964161494	2652290	65.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66174	Scrofimicrobium canadense strain WB03_NA08 16S ribosomal RNA gene, partial sequence	MN537492	1444		2652290

GC content

@ref	GC-content (mol%)	Method
67770	53.6	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM969661v1 assembly for Scrofimicrobium canadense WB03_NA08
BV-BRC: 2606625.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	69.73	no
125439	gram_stain	BacteriaNetⓘ	positive	75.04	no
125439	motility	BacteriaNetⓘ	no	96.86	no
125439	spore_formation	BacteriaNetⓘ	no	96.96	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomycetaceae bacterium WB03_NA08
PATRIC: 2606625.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.93	no
125438	anaerobic	anaerobicⓘ	no	79.50	yes
125438	spore-forming	spore-formingⓘ	no	82.51	no
125438	aerobic	aerobicⓘ	no	77.72	yes
125438	thermophilic	thermophileⓘ	no	95.15	yes
125438	flagellated	motile2+ⓘ	no	94.35	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 )
#66174	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105338
#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 .
#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 )
#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 )

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