Abiotrophia defectiva (DSM 9849, ATCC 49176, CIP 103242)

Name: Abiotrophia defectiva (DSM 9849, ATCC 49176, CIP 103242)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 219

Type strain

Culture col. no. DSM 9849 ATCC 49176 CIP 103242 SC 10 CCUG 27639

NCBI tax ID(s) 592010 46125

Special Collections DSMZ CIP CCUG

History DSMZ <- A. Bouvet, SC10 <- J.F. Acar CIP <- 1988, A. Bouvet, Hôtel Dieu Hosp., Paris, France: strain SC 10 <- J.F. Acar, Broussais Hosp., France

Links

Abiotrophia defectiva DSM 9849 is an anaerobe, Gram-positive, coccus-shaped bacterium that was isolated from blood of bacterial endocarditis patient.

Gram-positive coccus-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92499

LMG 14740,ATCC 49176,CCUG 27639,CCUG 27804,CIP 103242,DSM 9849,CCM 4672,CIP 103.242,KCTC 3662

@ref 20215

Last LPSN update 2026-05-29 08:24:58

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Aerococcaceae

Genus Abiotrophia

Species Abiotrophia defectiva

Full scientific name Abiotrophia defectiva (Bouvet et al. 1989) Kawamura et al. 1995

Synonyms (1)

Streptococcus defectivus

BacDive ID	Other strains from **Abiotrophia defectiva** (38)	Type strain
135184	A. defectiva CIP 103895
135892	A. defectiva C4, CIP 103892
135893	A. defectiva PE7, CIP 103893, ATCC 700209
135894	A. defectiva D5, CIP 103894
144952	A. defectiva CCUG 27280 A
145171	A. defectiva CCUG 27805
145172	A. defectiva CCUG 27806
145173	A. defectiva CCUG 27807
145174	A. defectiva CCUG 27808
145313	A. defectiva CCUG 28152
145981	A. defectiva CCUG 30076
146223	A. defectiva CCUG 30642
146761	A. defectiva CCUG 32076
147157	A. defectiva CCUG 32966 B
147409	A. defectiva CCUG 33542
148055	A. defectiva CCUG 34739
148519	A. defectiva CCUG 35584
149144	A. defectiva CCUG 36937
149662	A. defectiva CCUG 38140
149983	A. defectiva CCUG 38793
150007	A. defectiva CCUG 38830
150039	A. defectiva CCUG 38904
150104	A. defectiva CCUG 38998
150280	A. defectiva CCUG 39479
150286	A. defectiva CCUG 39499
150539	A. defectiva CCUG 41537
152179	A. defectiva CCUG 45983
152186	A. defectiva CCUG 46001
152516	A. defectiva CCUG 46990 B
152552	A. defectiva CCUG 47045
152579	A. defectiva CCUG 47112
153374	A. defectiva CCUG 49368
154020	A. defectiva CCUG 52016
154929	A. defectiva CCUG 55745
155280	A. defectiva CCUG 57181
155432	A. defectiva CCUG 57749
155940	A. defectiva CCUG 59700
156779	A. defectiva CCUG 65103

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
118863	positive	coccus-shaped
125438				91.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3744	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
40579	MEDIUM 27 - for Capnocytophaga gingivalis and Abiotrophia genus		Distilled water make up to (489.000 ml);Horse serum (200.000 ml);Brain heart infusion (37.000 g);Maltose 10 % solution - M0173 (200.000 ml);Cysteine hydrochloride 5% solution - M0172 (111.000 ml)
118863	CIP Medium 27	Medium recipe at CIP
118863	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3744	positive	growth	37
40579	positive	growth	37
118863	positive	growth	25-41
118863	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3744	anaerobe
118863	facultative anaerobe
125439	obligate anaerobe	97.424

Spore formation

@ref	Spore formation	Confidence
125439		99.278

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118863	NaCl		growth	6.5 %

Murein

@ref	Murein short key	Type
3744	A11	A1alpha L-Lys-direct

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68381	40585 ChEBI	alpha-cyclodextrin	-	builds acid from	from API rID32STR
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68381	29016 ChEBI	arginine	-	hydrolysis	from API rID32STR
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68381	18333 ChEBI	D-arabitol	-	builds acid from	from API rID32STR
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68381	16899 ChEBI	D-mannitol	-	builds acid from	from API rID32STR
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68381	16988 ChEBI	D-ribose	-	builds acid from	from API rID32STR
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
118863	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68381	28087 ChEBI	glycogen	-	builds acid from	from API rID32STR
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
68381	606565 ChEBI	hippurate	-	hydrolysis	from API rID32STR
118863	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68381	30849 ChEBI	L-arabinose	-	builds acid from	from API rID32STR
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	+	builds acid from	from API 50CH acid
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68381	6731 ChEBI	melezitose	-	builds acid from	from API rID32STR
68381	28053 ChEBI	melibiose	-	builds acid from	from API rID32STR
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68381	320055 ChEBI	methyl beta-D-glucopyranoside	-	builds acid from	from API rID32STR
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
118863	17632 ChEBI	nitrate	-	reduction
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
118863	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68381	16634 ChEBI	raffinose	-	builds acid from	from API rID32STR
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68381	30911 ChEBI	sorbitol	-	builds acid from	from API rID32STR
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68381	16199 ChEBI	urea	-	hydrolysis	from API rID32STR
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68381	15688 ChEBI	acetoin		from API rID32STR
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68381	15688 ChEBI	acetoin	-		from API rID32STR
118863	15688 ChEBI	acetoin	-
68380	35581 ChEBI	indole		-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
118863	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68381	alkaline phosphatase	-	3.1.3.1	from API rID32STR
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68381	arginine dihydrolase	-	3.5.3.6	from API rID32STR
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
118863	beta-galactosidase	-	3.2.1.23
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68381	beta-glucosidase	-	3.2.1.21	from API rID32STR
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68381	beta-glucuronidase	-	3.2.1.31	from API rID32STR
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68381	beta-mannosidase	-	3.2.1.25	from API rID32STR
118863	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118863	gamma-glutamyltransferase	-	2.3.2.2
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68381	glycyl tryptophan arylamidase	-		from API rID32STR
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68382	leucine arylamidase	-	3.4.11.1	from API zym
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
118863	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68381	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32STR
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118863	ornithine decarboxylase	-	4.1.1.17
118863	oxidase	-
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
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
68381	urease	-	3.5.1.5	from API rID32STR
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	90.91	20 of 22
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	ppGpp biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	photosynthesis	71.43	10 of 14
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	purine metabolism	64.89	61 of 94
66794	phenylalanine metabolism	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	pyrimidine metabolism	60	27 of 45
66794	glycolysis	58.82	10 of 17
66794	methionine metabolism	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	oxidative phosphorylation	57.14	52 of 91
66794	degradation of sugar alcohols	56.25	9 of 16
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	NAD metabolism	55.56	10 of 18
66794	lipid metabolism	54.84	17 of 31
66794	non-pathway related	52.63	20 of 38
66794	tetrahydrofolate metabolism	50	7 of 14
66794	myo-inositol biosynthesis	50	5 of 10
66794	isoleucine metabolism	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	sulfopterin metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	degradation of pentoses	46.43	13 of 28
66794	vitamin B1 metabolism	46.15	6 of 13
66794	valine metabolism	44.44	4 of 9
66794	serine metabolism	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	tryptophan metabolism	42.11	16 of 38
66794	cellulose degradation	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glutamate and glutamine metabolism	39.29	11 of 28
66794	alanine metabolism	37.93	11 of 29
66794	gluconeogenesis	37.5	3 of 8
66794	C4 and CAM-carbon fixation	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	metabolism of disaccharids	36.36	4 of 11
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	leucine metabolism	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	propionate fermentation	30	3 of 10
66794	citric acid cycle	28.57	4 of 14
66794	proline metabolism	27.27	3 of 11
66794	vitamin B6 metabolism	27.27	3 of 11
66794	flavin biosynthesis	26.67	4 of 15
66794	arginine metabolism	25	6 of 24
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	histidine metabolism	24.14	7 of 29
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	tyrosine metabolism	21.43	3 of 14
66794	glutathione metabolism	21.43	3 of 14

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118863	-	+	+	+	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
118863	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
3744	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
3744	-	-	+	+	-	-	-	-	-	+	+	-	-	+	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-

API rID32STR

@ref	ADH (Arg)	beta GLU	beta GAR	beta GUR	alpha GAL	PAL	RIB	MAN	SOR	LAC	TRE	RAF	SAC	LARA	DARL	Acid from alpha-cyclodextrinCDEX	Acetoin production (Voges Proskauer test)VP	Alanyl-Phenylalanyl-Proline arylamidaseAPPA	beta GAL	Pyrrolidonyl arylamidasePyrA	N-Acetyl-glucosaminidasebeta NAG	Glycyl-tryptophan arylamidaseGTA	HIP	GLYG	PUL	MAL	MEL	MLZ	Acidification of methyl beta-D-glucopyranosideMbeta DG	TAG	beta MAN	URE
3744	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
3744	-	-	+	-	+	-	-	-	-	+	+	-	+	-	-	-	-	+	+	+	-	-	-	-	+/-	+	-	-	-	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Infection	#Inflammation	-
#Infection	#Patient	-
#Host Body Product	#Fluids	#Blood

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent	Latitude	Longitude
3744	blood of bacterial endocarditis patient	Homo sapiens	France	FRA	Europe	46.7111	1.7191 46.7111/1.7191
118863	Human, Blood	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence D50541 (>99% sequence identity) for Abiotrophia defectiva subclade from Microbeatlas

Aquatic Samples	4201
Soil Samples	3195
Animal Samples	121237
Plant Samples	1336
Total Samples	129969

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3744	2	Risk group (German classification) According to TRBA 466
118863	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
124043	ASM1326741v1 assembly for Abiotrophia defectiva FDAARGOS_785	complete	GCA_013267415	46125.34	8062750990	46125	94.64
124043	ASM3704134v1 assembly for Abiotrophia defectiva ATCC 49176	complete	GCA_037041345	592010.15		592010	92.43
66792	ASM16007v2 assembly for Abiotrophia defectiva ATCC 49176	scaffold	GCA_000160075	592010.4	2562617177	592010	65.48

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Abiotrophia defectiva strain ATCC 49176 16S-23S ribosomal RNA intergenic spacer, partial sequence	AY351327	235	592010
3744	Abiotrophia defectiva (Streptococcus defectivus) DNA for 16S rRNA	D50541	1411	592010
124043	Abiotrophia defectiva strain CCUG 27639 16S-23S ribosomal RNA intergenic spacer, complete sequence.	JQ012763	231	46125

GC content

3744

GC-content (mol%)46.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1326741v1 assembly for Abiotrophia defectiva FDAARGOS_785
NCBI: GCA_013267415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	97.42	no
125439	gram_stain	BacteriaNetⓘ	positive	69.23	no
125439	motility	BacteriaNetⓘ	no	85.82	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: Abiotrophia defectiva strain FDAARGOS_785 strain Not applicable
PATRIC: 46125.34

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.26	no
125438	anaerobic	anaerobicⓘ	no	88.47	no
125438	spore-forming	spore-formingⓘ	no	86.27	no
125438	aerobic	aerobicⓘ	no	95.57	yes
125438	thermophilic	thermophileⓘ	no	96.71	yes
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbial Characteristics of the Extrinsic Black Stain in Primary Dentition.	Bai X, Dong X, Liu J, Wu Q, Zhao W, Li G, Zhang S.	Int Dent J	10.1016/j.identj.2025.103988	2025
	Secretome analysis and virulence assessment in Abiotrophia defectiva.	Bhardwaj RG, Khalaf ME, Karched M.	J Oral Microbiol	10.1080/20002297.2024.2307067	2024
Phylogeny	Orthopedic Device-Related Infections Due to Emerging Pathogens Diagnosed by a Combination of Microbiological Approaches: Case Series and Literature Review.	Quirino A, Marascio N, Scarlata GGM, Cicino C, Pavia G, Pantanella M, Carlisi G, Mercurio M, Familiari F, Rotundo S, Olivadese V, La Gamba V, Serapide F, Gasparini G, Matera G.	Diagnostics (Basel)	10.3390/diagnostics12123224	2022
	Metatranscriptomic analysis shows functional alterations in subgingival biofilm in young smokers with periodontitis: a pilot study.	Casarin RCV, Silva RVCD, Paz HES, Stolf CS, Carvalho LM, Noronha MF, Sallum AW, Monteiro MF.	J Appl Oral Sci	10.1590/1678-7757-2024-0031	2024
Genetics	The media composition as a crucial element in high-throughput metabolic network reconstruction.	Borer B, Magnusdottir S.	Interface Focus	10.1098/rsfs.2022.0070	2023
	Laboratory Diagnosis of 37 Cases of Bartonella Endocarditis Based on Enzyme Immunoassay and Real-Time PCR.	Shapira L, Rasis M, Binsky Ehrenreich I, Maor Y, Katchman EA, Treves A, Velan A, Halutz O, Graidy-Varon M, Leibovitch C, Maisler N, Ephros M, Giladi M.	J Clin Microbiol	10.1128/jcm.02217-20	2021
Phylogeny	Use of groESL as a target for identification of Abiotrophia, Granulicatella, and Gemella species.	Hung WC, Tseng SP, Chen HJ, Tsai JC, Chang CH, Lee TF, Hsueh PR, Teng LJ.	J Clin Microbiol	10.1128/jcm.00787-10	2010
	The Evaluation of the Effects of Two Probiotic Strains on the Oral Ecosystem: A Randomized Clinical Trial.	Volgenant CMC, van der Waal SV, Brandt BW, Buijs MJ, van der Veen MH, Rosema NAM, Fiebich BL, Rose T, Schmitter T, Gajfulin M, Crielaard W, Zaura E.	Front Oral Health	10.3389/froh.2022.825017	2022
Phylogeny	Bloodstream and endovascular infections due to Abiotrophia defectiva and Granulicatella species.	Senn L, Entenza JM, Greub G, Jaton K, Wenger A, Bille J, Calandra T, Prod'hom G.	BMC Infect Dis	10.1186/1471-2334-6-9	2006
Enzymology	Identification of Abiotrophia adiacens and Abiotrophia defectiva by 16S rRNA gene PCR and restriction fragment length polymorphism analysis.	Ohara-Nemoto Y, Tajika S, Sasaki M, Kaneko M.	J Clin Microbiol	10.1128/jcm.35.10.2458-2463.1997	1997
Phylogeny	Identification of clinically relevant viridans streptococci by an oligonucleotide array.	Chen CC, Teng LJ, Kaiung S, Chang TC.	J Clin Microbiol	10.1128/jcm.43.4.1515-1521.2005	2005
Pathogenicity	Real-time PCR assay for detection of fluoroquinolone resistance associated with grlA mutations in Staphylococcus aureus.	Lapierre P, Huletsky A, Fortin V, Picard FJ, Roy PH, Ouellette M, Bergeron MG.	J Clin Microbiol	10.1128/jcm.41.7.3246-3251.2003	2003
Metabolism	Eubacterial SpoVG homologs constitute a new family of site-specific DNA-binding proteins.	Jutras BL, Chenail AM, Rowland CL, Carroll D, Miller MC, Bykowski T, Stevenson B.	PLoS One	10.1371/journal.pone.0066683	2013
Enzymology	Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species.	Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG.	J Clin Microbiol	10.1128/jcm.42.8.3686-3695.2004	2004
Enzymology	Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples.	Maheux AF, Bissonnette L, Boissinot M, Bernier JL, Huppe V, Picard FJ, Berube E, Bergeron MG.	Appl Environ Microbiol	10.1128/aem.02337-10	2011
	Development of a PCR assay for rapid detection of enterococci.	Ke D, Picard FJ, Martineau F, Menard C, Roy PH, Ouellette M, Bergeron MG.	J Clin Microbiol	10.1128/jcm.37.11.3497-3503.1999	1999
Pathogenicity	New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci.	Huletsky A, Giroux R, Rossbach V, Gagnon M, Vaillancourt M, Bernier M, Gagnon F, Truchon K, Bastien M, Picard FJ, van Belkum A, Ouellette M, Roy PH, Bergeron MG.	J Clin Microbiol	10.1128/jcm.42.5.1875-1884.2004	2004
Phylogeny	Molecular characterization of subject-specific oral microflora during initial colonization of enamel.	Diaz PI, Chalmers NI, Rickard AH, Kong C, Milburn CL, Palmer RJ, Kolenbrander PE.	Appl Environ Microbiol	10.1128/aem.72.4.2837-2848.2006	2006
Phylogeny	Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes.	Blower TR, Short FL, Rao F, Mizuguchi K, Pei XY, Fineran PC, Luisi BF, Salmond GP.	Nucleic Acids Res	10.1093/nar/gks231	2012
	Characterization of the Tn916-like transposon Tn3872 in a strain of abiotrophia defectiva (Streptococcus defectivus) causing sequential episodes of endocarditis in a child.	Poyart C, Quesne G, Acar P, Berche P, Trieu-Cuot P.	Antimicrob Agents Chemother	10.1128/aac.44.3.790-793.2000	2000
Metabolism	Cytokine induction of peripheral blood mononuclear cells by biofilms and biofilm supernatants of Granulicatella and Abiotrophia spp.	Bhardwaj RG, Al-Khabbaz A, Karched M.	Microb Pathog	10.1016/j.micpath.2017.11.037	2018
	The Effect of Benzyl Isothiocyanate on the Expression of Genes Encoding NADH Oxidase and Fibronectin-Binding Protein in Oral Streptococcal Biofilms.	Alhandal H, Almesaileikh E, Bhardwaj RG, Al Khabbaz A, Karched M.	Front Oral Health	10.3389/froh.2022.863723	2022
Pathogenicity	Granulicatella and Abiotrophia species from human clinical specimens.	Christensen JJ, Facklam RR	J Clin Microbiol	10.1128/JCM.39.10.3520-3523.2001	2001
Phylogeny	Abiotrophia elegans sp. nov., a possible pathogen in patients with culture-negative endocarditis.	Roggenkamp A, Abele-Horn M, Trebesius KH, Tretter U, Autenrieth IB, Heesemann J.	J Clin Microbiol	10.1128/jcm.36.1.100-104.1998	1998

References

#3744	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9849
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#40579	; Curators of the CIP;
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#68371	Automatically annotated from API 50CH acid .
#68380	Automatically annotated from API rID32A .
#68381	Automatically annotated from API rID32STR .
#68382	Automatically annotated from API zym .
#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 .
#118863	Collection of Institut Pasteur ; Curators of the CIP; CIP 103242
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Abiotrophia defectiva (DSM 9849, ATCC 49176, CIP 103242)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 50CHac

API rID32A

API rID32STR

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013267415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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