Holdemanella porci (DSM 105256, LKV-472-APC-3, JCM 34391)

Name: Holdemanella porci (DSM 105256, LKV-472-APC-3, JCM 34391)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158892

Type strain

Strain Designation LKV-472-APC-3

Culture col. no. DSM 105256 LKV-472-APC-3 JCM 34391

NCBI tax ID(s) 2652276

Special Collections DSMZ JCM Pig DZIF

History DSMZ <- T. Clavel , TU Munich, Freising-Weihenstephan, Germany; LKV-472-APC-3 JCM <-- B. Abt; DSMZ, Germany; DSM 105256 (=LKV-472-APC-3) <-- T. Clavel; RWTH Aachen, Germany.

Links

Holdemanella porci LKV-472-APC-3 is a bacterium that was isolated from pig, APC, 37 weeks old, feces.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407748

JCM 34391,DSM 105256

@ref 20215

Last LPSN update 2026-05-29 08:44:04

Domain Bacteria

Phylum Bacillota

Class Erysipelotrichia

Order Erysipelotrichales

Family Erysipelotrichaceae

Genus Holdemanella

Species Holdemanella porci

Full scientific name Holdemanella porci Wylensek et al. 2021

Morphology

Cell morphology

@ref	Motility	Confidence
125438		93.95

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
65714	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
65714	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
65714	CHOPPED MEAT MEDIUM (DSMZ Medium 78)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
65714	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	93.436

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
65714	pig, APC, 37 weeks old, feces	Kranzberg (Bavaria)	Germany	DEU	Europe
67770	Feces of an APC^1311/+ pig	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence MN537482 (>99% sequence identity) for Holdemanella biformis subclade from Microbeatlas

Aquatic Samples	2953
Soil Samples	924
Animal Samples	69724
Plant Samples	187
Total Samples	73788

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
65714	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	ASM969607v1 assembly for Holdemanella porci LKV-472-APC-3	contig	GCA_009696075	1735.276	8064359004	2652276	48.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65714	Holdemanella porci strain LKV-472-APC-3 16S ribosomal RNA gene, partial sequence	MN537482	1482		2652276

GC content

@ref	GC-content (mol%)	Method
67770	34.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM969607v1 assembly for Holdemanella porci LKV-472-APC-3
NCBI: GCA_009696075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.44	no
125439	motility	BacteriaNetⓘ	no	67.16	no
125439	gram_stain	BacteriaNetⓘ	positive	72.06	no
125439	spore_formation	BacteriaNetⓘ	no	66.75	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Holdemanella biformis strain LKV-472-APC-3
PATRIC: 1735.276

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.90	no
125438	anaerobic	anaerobicⓘ	yes	85.07	no
125438	spore-forming	spore-formingⓘ	no	78.89	no
125438	aerobic	aerobicⓘ	no	96.93	no
125438	thermophilic	thermophileⓘ	no	94.87	no
125438	flagellated	motile2+ⓘ	no	93.95	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 )
#65714	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105256
#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;
#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 )

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