Slackia exigua (DSM 15923, ATCC 700122, JCM 11022)

Name: Slackia exigua (DSM 15923, ATCC 700122, JCM 11022)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3064

Type strain

Strain Designation S-7

Culture col. no. DSM 15923 ATCC 700122 JCM 11022 KCTC 5966 CCUG 44588 3 more

NCBI tax ID(s) 649764 84109

Special Collections DSMZ CCUG JCM KCTC CIP

Links

Slackia exigua S-7 is an anaerobe, mesophilic, rod-shaped prokaryote that was isolated from human necrotic pulp.

rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 43783

NCTC 12994,KCTC 5966,ATCC 700122,CIP 105133,CCUG 44588,JCM 11022,DSM 15923

@ref 20215

Last LPSN update 2025-12-16 09:47:27

Domain Bacillati

Phylum Actinomycetota

Class Coriobacteriia

Order Eggerthellales

Family Eggerthellaceae

Genus Slackia

Species Slackia exigua

Full scientific name Slackia exigua (Poco et al. 1996) Wade et al. 1999

Synonyms (1)

Eubacterium exiguum

BacDive ID	Other strains from **Slackia exigua** (5)	Type strain
148973	S. exigua CCUG 36663
150195	S. exigua CCUG 39259
155074	S. exigua CCUG 56394
155076	S. exigua CCUG 56395 B
156663	S. exigua CCUG 63980

Morphology

Cell morphology

@ref	Cell shape	Motility
67771	rod-shaped
67771
119153	rod-shaped
125439

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6186	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
119153	CIP Medium 20	Medium recipe at CIP
119153	CIP Medium 72	Medium recipe at CIP
6186	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6186	positive	growth	37	mesophilic
56394	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6186	anaerobe
56394	anaerobe
67771	anaerobe

Spore formation

@ref	Spore formation
67771
125439

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
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	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	chorismate metabolism	88.89	8 of 9
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	threonine metabolism	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	vitamin B1 metabolism	69.23	9 of 13
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	glycolysis	64.71	11 of 17
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoleucine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	purine metabolism	61.7	58 of 94
66794	methylglyoxal degradation	60	3 of 5
66794	pyrimidine metabolism	60	27 of 45
66794	histidine metabolism	58.62	17 of 29
66794	propanol degradation	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	glutamate and glutamine metabolism	53.57	15 of 28
66794	oxidative phosphorylation	50.55	46 of 91
66794	methionine metabolism	50	13 of 26
66794	arginine metabolism	50	12 of 24
66794	butanoate fermentation	50	2 of 4
66794	tetrahydrofolate metabolism	50	7 of 14
66794	isoprenoid biosynthesis	50	13 of 26
66794	citric acid cycle	50	7 of 14
66794	sulfopterin metabolism	50	2 of 4
66794	gluconeogenesis	50	4 of 8
66794	suberin monomers biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	non-pathway related	47.37	18 of 38
66794	leucine metabolism	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	cysteine metabolism	44.44	8 of 18
66794	d-mannose degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	propionate fermentation	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	tryptophan metabolism	39.47	15 of 38
66794	sulfate reduction	38.46	5 of 13
66794	lysine metabolism	38.1	16 of 42
66794	carnitine metabolism	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	tyrosine metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	serine metabolism	33.33	3 of 9
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	flavin biosynthesis	33.33	5 of 15
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	pentose phosphate pathway	27.27	3 of 11
66794	CMP-KDO biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	ascorbate metabolism	22.73	5 of 22
66794	degradation of pentoses	21.43	6 of 28

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
6186	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	+	-	+	+	-	+	+	+/-	+/-	-	+
6186	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	+	+	-	+/-	+	-	+	-	+/-
6186	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Infection	#Inflammation
#Host	#Human
#Host Body-Site	#Oral cavity and airways

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6186	human necrotic pulp	Japan	JPN	Asia
56394	Human necrotic pulp of tooth
67770	Human oral lesion
67771	From human necrotic pulp	Japan	JPN	Asia
119153	Human, Necrotic pulp of tooth

Taxonmaps

69479

Global distribution of 16S sequence NR_024952 (>99% sequence identity) for Slackia exigua subclade from Microbeatlas

Aquatic Samples	124
Soil Samples	198
Animal Samples	11626
Plant Samples	92
Total Samples	12040

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6186	2	Risk group (German classification) According to TRBA 466
119153	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
67770	51765_F02 assembly for Slackia exigua NCTC12994	contig	GCA_900450505	84109.4	2833514366	84109	78.71
67770	ASM16287v1 assembly for Slackia exigua ATCC 700122	scaffold	GCA_000162875	649764.3	645951837	649764	73.98

Genome browser: GCA_900450505

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Slackia exigua 16S ribosomal RNA gene, complete sequence	AF101240	1465	649764
67770	Slackia exigua gene for 16S ribosomal RNA, partial sequence, strain: JCM 11022	LC007113	1474	84109
67771	Slackia exigua ATCC 700122 16S ribosomal RNA, partial sequence	NR_024952	1465	649764

GC content

@ref	GC-content (mol%)	Method
67770	60	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Slackia exigua ATCC 700122
NCBI: GCA_000162875

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	yes	63.80	no
125439	gram_stain	BacteriaNetⓘ	negative	95.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	74.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Slackia exigua ATCC 700122
PATRIC: 649764.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.29	no
125438	anaerobic	anaerobicⓘ	yes	85.44	no
125438	spore-forming	spore-formingⓘ	no	82.58	yes
125438	aerobic	aerobicⓘ	no	88.48	no
125438	thermophilic	thermophileⓘ	no	92.40	yes
125438	flagellated	motile2+ⓘ	no	88.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.	Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus EP, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.04.006	2020
	Complete genome sequence for Slackia exigua strain SB208, isolated from a human colonic adenocarcinoma.	Lewis KN, Zepeda-Rivera MA, Baryiames AA, Jones DS, LaCourse KD, Bullman S, Johnston CD.	Microbiol Resour Announc	10.1128/mra.00445-25	2025
	Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset.	Kharrat N, Assidi M, Abu-Elmagd M, Pushparaj PN, Alkhaldy A, Arfaoui L, Naseer MI, El Omri A, Messaoudi S, Buhmeida A, Rebai A.	Bioinformation	10.6026/97320630015372	2019
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Phylogeny	Characterization of Slackia exigua isolated from human wound infections, including abscesses of intestinal origin.	Kim KS, Rowlinson MC, Bennion R, Liu C, Talan D, Summanen P, Finegold SM.	J Clin Microbiol	10.1128/jcm.01576-09	2010
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
Phylogeny	Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus.	Shao ZQ, Zhang YM, Pan XZ, Wang B, Chen JQ.	PLoS One	10.1371/journal.pone.0060116	2013
Enzymology	Crystal structure and biochemical properties of putrescine carbamoyltransferase from Enterococcus faecalis: Assembly, active site, and allosteric regulation.	Shi D, Yu X, Zhao G, Ho J, Lu S, Allewell NM, Tuchman M.	Proteins	10.1002/prot.24042	2012
Enzymology	Cultivation of a Synergistetes strain representing a previously uncultivated lineage.	Vartoukian SR, Palmer RM, Wade WG.	Environ Microbiol	10.1111/j.1462-2920.2009.02135.x	2010
	Evidence of horizontal transfer of symbiotic genes from a Bradyrhizobium japonicum inoculant strain to indigenous diazotrophs Sinorhizobium (Ensifer) fredii and Bradyrhizobium elkanii in a Brazilian Savannah soil.	Barcellos FG, Menna P, da Silva Batista JS, Hungria M.	Appl Environ Microbiol	10.1128/aem.01823-06	2007
Phylogeny	Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses.	Baudoux AC, Hendrix RW, Lander GC, Bailly X, Podell S, Paillard C, Johnson JE, Potter CS, Carragher B, Azam F.	Environ Microbiol	10.1111/j.1462-2920.2011.02685.x	2012
Metabolism	Isolation of a human intestinal bacterium capable of daidzein and genistein conversion.	Matthies A, Blaut M, Braune A.	Appl Environ Microbiol	10.1128/aem.01795-08	2009
Metabolism	Degradation of arginine by Slackia exigua ATCC 700122 and Cryptobacterium curtum ATCC 700683.	Uematsu H, Sato N, Djais A, Hoshino E	Oral Microbiol Immunol	10.1111/j.1399-302X.2006.00307.x	2006
Phylogeny	The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov.	Wade WG, Downes J, Dymock D, Hiom SJ, Weightman AJ, Dewhirst FE, Paster BJ, Tzellas N, Coleman B	Int J Syst Bacteriol	10.1099/00207713-49-2-595	1999
Genetics	Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool.	Bilen M, Cadoret F, Richez M, Tomei E, Daoud Z, Raoult D, Fournier PE.	New Microbes New Infect	10.1016/j.nmni.2017.11.001	2018

References

#6186	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15923
#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 )
#56394	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 44588
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68380	Automatically annotated from API rID32A .
#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 .
#119153	Collection of Institut Pasteur ; Curators of the CIP; CIP 105133
#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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Slackia exigua (DSM 15923, ATCC 700122, JCM 11022)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900450505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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