Dolosigranulum pigrum (CIP 104051, ATCC 51524, IFO 15550)

Name: Dolosigranulum pigrum (CIP 104051, ATCC 51524, IFO 15550)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 135725

Type strain

Strain Designation R-91/1468, R91/1468

Culture col. no. CIP 104051 ATCC 51524 IFO 15550 NCFB 2975 LMG 19521 7 more

NCBI tax ID(s) 883103 29394

Special Collections CCUG KCTC CIP

History <- CIP <- NCFB 2975 <- Public Health Labs, Colindale, UK <- FW Gay, R91/1468 CIP <- 1997, NCFB <- PHLS: strain R91/1468

Links

Dolosigranulum pigrum R-91/1468 is an anaerobe, Gram-positive bacterium of the family Carnobacteriaceae.

Gram-positive anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 8240

LMG 15126,ATCC 51524,CCUG 33392,CIP 104051,IFO 15550,LMG 19521,NCFB 2975,NCIMB 702975,NBRC 15550,KCTC 15002

@ref 20215

Last LPSN update 2026-02-09 11:32:29

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Carnobacteriaceae

Genus Dolosigranulum

Species Dolosigranulum pigrum

Full scientific name Dolosigranulum pigrum Aguirre et al. 1994

BacDive ID	Other strains from **Dolosigranulum pigrum** (20)	Type strain
146489	D. pigrum CCUG 31310
146490	D. pigrum CCUG 31311
147218	D. pigrum CCUG 33081 A
147338	D. pigrum
148437	D. pigrum CCUG 35446
151115	D. pigrum CCUG 43300
151133	D. pigrum CCUG 43342
152321	D. pigrum CCUG 46432
152472	D. pigrum CCUG 46892
153692	D. pigrum CCUG 50662
153741	D. pigrum CCUG 50829
154512	D. pigrum CCUG 53977
154554	D. pigrum CCUG 54395
154558	D. pigrum CCUG 54405
155689	D. pigrum CCUG 59012
155760	D. pigrum CCUG 59224
156212	D. pigrum CCUG 60739
156838	D. pigrum CCUG 65991
156987	D. pigrum CCUG 68179
157175	D. pigrum CCUG 70055

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
67771	positive
34923	positive	coccus-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
34923	MEDIUM 74 - for Dolosigranulum pigrum		Distilled water make up to (1000.000 ml);Todd hewitt broth (30.000 g)
34923	CIP Medium 90			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
34923	positive	growth	37
34923	positive	growth	25-30
34923	negative	growth	10
34923	negative	growth	37
34923	negative	growth	41
34923	negative	growth	45
51495	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
51495	anaerobe
51495	microaerophile
67771	anaerobe
34923	facultative anaerobe
125439	facultative anaerobe	97.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
34923	NaCl		growth	6.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
34923	4853 ChEBI	esculin	-	hydrolysis
34923	606565 ChEBI	hippurate	-	hydrolysis
34923	17632 ChEBI	nitrate	-	reduction
34923	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
34923	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
34923	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
34923	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
34923	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
34923	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
34923	gamma-glutamyltransferase	-	2.3.2.2
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
34923	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
34923	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
34923	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
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	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	threonine metabolism	70	7 of 10
66794	degradation of sugar alcohols	68.75	11 of 16
66794	formaldehyde oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	purine metabolism	63.83	60 of 94
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	degradation of hexoses	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	pyrimidine metabolism	60	27 of 45
66794	methylglyoxal degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	phenylalanine metabolism	53.85	7 of 13
66794	non-pathway related	52.63	20 of 38
66794	oxidative phosphorylation	50.55	46 of 91
66794	ketogluconate metabolism	50	4 of 8
66794	gluconeogenesis	50	4 of 8
66794	methionine metabolism	50	13 of 26
66794	cysteine metabolism	50	9 of 18
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	lipid metabolism	48.39	15 of 31
66794	glutamate and glutamine metabolism	46.43	13 of 28
66794	leucine metabolism	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	alanine metabolism	44.83	13 of 29
66794	d-mannose degradation	44.44	4 of 9
66794	NAD metabolism	44.44	8 of 18
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	glutathione metabolism	42.86	6 of 14
66794	degradation of pentoses	42.86	12 of 28
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	cellulose degradation	40	2 of 5
66794	starch degradation	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	urea cycle	38.46	5 of 13
66794	isoleucine metabolism	37.5	3 of 8
66794	arginine metabolism	37.5	9 of 24
66794	tryptophan metabolism	36.84	14 of 38
66794	d-xylose degradation	36.36	4 of 11
66794	octane oxidation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	valine metabolism	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	myo-inositol biosynthesis	30	3 of 10
66794	propionate fermentation	30	3 of 10
66794	citric acid cycle	28.57	4 of 14
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	histidine metabolism	27.59	8 of 29
66794	vitamin B6 metabolism	27.27	3 of 11
66794	flavin biosynthesis	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	lysine metabolism	23.81	10 of 42
66794	isoprenoid biosynthesis	23.08	6 of 26
66794	nitrate assimilation	22.22	2 of 9
66794	lipid A biosynthesis	22.22	2 of 9

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
34923	-	-	+	+	-	+	-	-	-	+	+	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Organ	#Spinal Cord
#Host	#Human	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
34923			United Kingdom	GBR	Europe
51495	Human spinal cord,removed at autopsy	Colchester	United Kingdom	GBR	Europe
67771	From human spinal cord, removed at autopsy	Colchester	United Kingdom	GBR	Europe
34923	Human, Acute multiple sclerosis	Colchester General Hospital	United Kingdom	GBR	Europe	1988

Taxonmaps

69479

Global distribution of 16S sequence GU395995 (>99% sequence identity) for Dolosigranulum pigrum subclade from Microbeatlas

Aquatic Samples	2385
Soil Samples	1684
Animal Samples	28449
Plant Samples	728
Total Samples	33246

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
34923	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Dolo_pigr_ATCC_51524_V1 assembly for Dolosigranulum pigrum ATCC 51524	scaffold	GCA_000245815	883103.3	2513237341	883103	75.71

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67771	Dolosigranulum pigrum strain 33929-06 16S ribosomal RNA gene, partial sequence	GU395995	1375	29394
124043	Dolosigranulum pigrum gene for 16S rRNA, partial sequence, strain: NBRC 15550.	AB680900	1472	29394
124043	Dolosigranulum pigrum NBRC 15550 gene for 16S rRNA, partial sequence.	LC752391	588	29394
124043	D.pigrum 16S rRNA gene (partial)	X70907	1523	29394
124043	Dolosigranulum pigrum strain CCUG 33392 16S-23S ribosomal RNA intergenic spacer, complete sequence.	JQ012770	253	29394

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dolosigranulum pigrum ATCC 51524
NCBI: GCA_000245815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	87.60	no
125439	motility	BacteriaNetⓘ	yes	60.10	no
125439	gram_stain	BacteriaNetⓘ	variable	72.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dolosigranulum pigrum ATCC 51524 ATCC 51524
NCBI: GCA_000245815.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.30	no
125438	anaerobic	anaerobicⓘ	no	87.12	no
125438	aerobic	aerobicⓘ	no	91.51	yes
125438	spore-forming	spore-formingⓘ	no	81.57	no
125438	thermophilic	thermophileⓘ	no	92.45	yes
125438	flagellated	motile2+ⓘ	no	86.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Quantitative assessment of individual populations within polymicrobial biofilms.	Lopes SP, Azevedo NF, Pereira MO.	Sci Rep	10.1038/s41598-018-27497-9	2018
Genetics	Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome.	Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP.	mSystems	10.1128/msystems.00425-21	2021
Genetics	Whole-Genome Shotgun Sequencing for Nasopharyngeal Microbiome in Pre-school Children With Recurrent Wheezing.	Song Y, Hou J, Kwok JSL, Weng H, Tang MF, Wang MH, Leung ASY, Tao KP, Wong GWK, Chan RWY, Tsui SKW, Leung TF.	Front Microbiol	10.3389/fmicb.2021.792556	2021
Metabolism	Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota.	Brugger SD, Eslami SM, Pettigrew MM, Escapa IF, Henke MT, Kong Y, Lemon KP.	mSphere	10.1128/msphere.00852-20	2020
Genetics	Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains.	Chaves-Moreno D, Wos-Oxley ML, Jauregui R, Medina E, Oxley AP, Pieper DH.	PLoS One	10.1371/journal.pone.0145861	2015
Phylogeny	Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study.	Xu H, Tian J, Hao W, Zhang Q, Zhou Q, Shi W, Qin M, He X, Chen F.	Front Microbiol	10.3389/fmicb.2018.02009	2018
	Complete Genome Sequence of Dolosigranulum pigrum from a Patient with Interstitial Lung Disease Using Single-Molecule Real-Time Sequencing Technology.	Mukhopadhyay R, Joaquin J, Hogue R, Fitzgerald S, Jospin G, Mars K, Eisen JA, Chaturvedi V.	Genome Announc	10.1128/genomea.00317-17	2017
	Internal and external microbiota of home-caught Anopheles coluzzii (Diptera: Culicidae) from Côte d'Ivoire, Africa: Mosquitoes are filthy.	Chen K, Ponnusamy L, Mouhamadou CS, Fodjo BK, Sadia GC, Affoue FPK, Deguenon JM, Roe RM.	PLoS One	10.1371/journal.pone.0278912	2022
Phylogeny	Phenotypic and phylogenetic characterization of some Gemella-like organisms from human infections: description of Dolosigranulum pigrum gen. nov., sp. nov.	Aguirre M, Morrison D, Cookson BD, Gay FW, Collins MD	J Appl Bacteriol	10.1111/j.1365-2672.1993.tb01602.x	1993

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 )
#34923	Collection of Institut Pasteur ; Curators of the CIP; CIP 104051
#51495	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 33392
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Dolosigranulum pigrum (CIP 104051, ATCC 51524, IFO 15550)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000245815

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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