Avibacterium endocarditidis (CIP 109717, DSM 18224, CCUG 52860)

Name: Avibacterium endocarditidis (CIP 109717, DSM 18224, CCUG 52860)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11693

Type strain

Strain Designation 20186H4H1

Culture col. no. CIP 109717 DSM 18224 CCUG 52860 20186H4H1

NCBI tax ID(s) 380674

Special Collections DSMZ CCUG CIP Literature strains

Links

Avibacterium endocarditidis 20186H4H1 is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from chicken, valvular endocarditis.

Gram-negative rod-shaped aerobe mesophilic animal pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 309431

CCUG 52860,DSM 18224,CIP 109717

@ref 20215

Last LPSN update 2025-12-16 09:49:39

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Avibacterium

Species Avibacterium endocarditidis

Full scientific name Avibacterium endocarditidis Bisgaard et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32050	negative	rod-shaped
119025	negative	rod-shaped
125439	negative		98.3
125438			92.376
125438	negative		98.5

Colony morphology

59690

Incubation period1 day

Pigmentation

32050

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7440	COLUMBIA BLOOD AGAR (DSMZ Medium 429)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
37433	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)
119025	CIP Medium 72	Medium recipe at CIP
119025	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7440	positive	growth	37	mesophilic
32050	positive	optimum	37	mesophilic
37433	positive	growth	37	mesophilic
59690	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32050	aerobe
59690	aerobe
119025	facultative anaerobe
125439	obligate aerobe	99.1

Spore formation

@ref	Spore formation	Confidence
125439		97.5
125438		93.547

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68377	15824 ChEBI	D-fructose	+	builds acid from	from API NH
68377	17634 ChEBI	D-glucose	+	builds acid from	from API NH
32050	23652 ChEBI	dextrin	+	carbon source
32050	28757 ChEBI	fructose	+	carbon source
32050	28260 ChEBI	galactose	+	carbon source
32050	24265 ChEBI	gluconate	+	carbon source
32050	17234 ChEBI	glucose	+	carbon source
32050	17754 ChEBI	glycerol	+	carbon source
32050	25115 ChEBI	malate	+	carbon source
32050	17306 ChEBI	maltose	+	carbon source
68377	17306 ChEBI	maltose	+	builds acid from	from API NH
32050	29864 ChEBI	mannitol	+	carbon source
32050	506227 ChEBI	N-acetylglucosamine	+	carbon source
32050	17632 ChEBI	nitrate	+	reduction
119025	17632 ChEBI	nitrate	+	reduction
119025	16301 ChEBI	nitrite	+	reduction
68377	18257 ChEBI	ornithine	-	degradation	from API NH
32050	16634 ChEBI	raffinose	+	carbon source
32050	33942 ChEBI	ribose	+	carbon source
32050	30911 ChEBI	sorbitol	+	carbon source
32050	17992 ChEBI	sucrose	+	carbon source
32050	27082 ChEBI	trehalose	+	carbon source
68377	27897 ChEBI	tryptophan	-	energy source	from API NH
68377	16199 ChEBI	urea	-	hydrolysis	from API NH

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68377	35581 ChEBI	indole		from API NH
119025	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68377	35581 ChEBI	indole	-	from API NH

Enzymes

@ref	Value	Activity	Ec
32050	acid phosphatase	+	3.1.3.2
32050	alkaline phosphatase	+	3.1.3.1
68377	alkaline phosphatase	+	3.1.3.1	from API NH
32050	alpha-galactosidase	+	3.2.1.22
32050	catalase	+	1.11.1.6
119025	catalase	+	1.11.1.6
32050	cytochrome oxidase	+	1.9.3.1
68377	ornithine decarboxylase	-	4.1.1.17	from API NH
119025	oxidase	+
68377	tryptophan deaminase	-	4.1.99.1	from API NH
32050	urease	+	3.5.1.5
119025	urease	-	3.5.1.5
68377	urease	-	3.5.1.5	from API NH

API NH

@ref	PEN	GLU	FRU	MAL	SAC	ODC	URE	LIP	PAL	beta GAL	ProA	GGT	IND
7440	+	+	+	+	-	-	-	+	+	-	+	-	-
7440	-	+	+	+	+	-	-	-	+	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Inflammation	-
#Host	#Birds	#Chicken

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
7440	chicken, valvular endocarditis			Denmark	DNK	Europe
59690	Adult broiler parent hen,valvular endocarditis	2004	Copenhagen,RVAU	Denmark	DNK	Europe
119025	Valvular endocarditis, adult broiler parent		Copenhagen	Denmark	DNK	Europe	2004

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
7440		2	Risk group (German classification) According to TRBA 466
119025		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
66792	ASM292114v1 assembly for Avibacterium endocarditidis 20186H4H1	scaffold	GCA_002921145	380674.10	2842990487	380674	26.07

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7440	Avibacterium endocarditidis strain 20186H4H1 16S ribosomal RNA gene, partial sequence	DQ465412	1218		380674

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Avibacterium endocarditidis 20186H4H1
NCBI: GCA_002921145

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.50	no
125439	motility	BacteriaNetⓘ	no	72.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Avibacterium endocarditidis 20186H4H1
NCBI: GCA_002921145.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	93.45	no
125438	aerobic	aerobicⓘ	no	84.53	no
125438	spore-forming	spore-formingⓘ	no	93.55	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	92.38	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Avibacterium endocarditidis sp. nov., isolated from valvular endocarditis in chickens.	Bisgaard M, Christensen JP, Bojesen AM, Christensen H	Int J Syst Evol Microbiol	10.1099/ijs.0.64879-0	2007

References

#7440	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18224
#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 )
#32050	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28300 (see below)
#37433	; Curators of the CIP;
#59690	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52860
#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) .
#68377	Automatically annotated from API NH .
#119025	Collection of Institut Pasteur ; Curators of the CIP; CIP 109717
#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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Avibacterium endocarditidis (CIP 109717, DSM 18224, CCUG 52860)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API NH

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002921145

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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