Catenibacillus scindens (DSM 106146, CCUG 71490, JCM 33534)

Name: Catenibacillus scindens (DSM 106146, CCUG 71490, JCM 33534)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 139755

Type strain

Strain Designation CG19-1

Culture col. no. DSM 106146 CCUG 71490 JCM 33534 CG19-1

NCBI tax ID(s) 673271

Special Collections DSMZ CCUG JCM Literature strains

Links

Catenibacillus scindens CG19-1 is an anaerobe, mesophilic, Gram-positive prokaryote that forms circular colonies and was isolated from healthy human feces.

Gram-positive rod-shaped colony-forming anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406272

JCM 33534,DSM 106146,CCUG 71490

@ref 20215

Last LPSN update 2025-12-16 10:03:25

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Catenibacillus

Species Catenibacillus scindens

Full scientific name Catenibacillus scindens Braune and Blaut 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
66717	positive	1.0-2.0 µm	0.6-1.0 µm	rod-shaped

Colony morphology

@ref	Type of hemolysis	Colony size	Colony color	Colony shape	Incubation period	Medium used
66717	gamma	0.5 mm	matte greyish	circular	4 days	sheep-blood agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
42366	RCM MEDIUM (N2/CO2) (DSMZ Medium 634c)	Medium recipe at MediaDive	Name: RCM MEDIUM (N2/CO2) (DSMZ Medium 634c) Composition: dehydrated RCM medium 38.0 g/l Sodium carbonate 1.0 g/l Sodium resazurin 0.0005 g/l Distilled water
66717	reinforced clostridial medium (RCM mod)		contained (g/l): yeast extract (3.0), meat extract (10), peptone (10), glucose (5.0), soluble starch (1.0), NaCl (5.0), sodium acetate (5.0) and cysteine hydrochloride (0.5)
66717	sheep-blood agar		at 37° C
66717	starch-free RCM mod.		supplemented with 40 mM pyruvate
66717	starch-free RCMmod.

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
42366	positive	growth	37	mesophilic
66717	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66717	anaerobe
125439	facultative anaerobe	93.3

Spore formation

@ref	Spore formation	Confidence
66717
125439		90.9

Murein

@ref	Murein short key	Type
66717	A21.04	A4ß L-Orn-D-Asp

Observation

@ref	Observation
66717	Capsules, slime or polyphosphate granules are not produced.
66717	Doubling time at optimal growth is 2.7 h.
66717	using a gas phase of N 2 /CO 2 (80 : 20, v/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66717	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
66717	90249 ChEBI	2-naphthyl tetradecanoate	-	hydrolysis
66717	19950 ChEBI	3-O-methylgallate	-	reduction
66717	90128 ChEBI	4-nitrophenyl 6-O-phosphono-beta-D-galactoside	-	hydrolysis
66717	546840 ChEBI	4-nitrophenyl alpha-D-galactoside	-	hydrolysis
66717	91122 ChEBI	4-nitrophenyl alpha-D-glucopyranoside	-	hydrolysis
66717	90253 ChEBI	4-nitrophenyl alpha-L-fucoside	-	hydrolysis
66717	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	-	hydrolysis
66717	90259 ChEBI	4-nitrophenyl beta-D-glucopyranoside	-	hydrolysis
66717	90146 ChEBI	4-nitrophenyl beta-D-glucuronide	-	hydrolysis
66717	90148 ChEBI	4-nitrophenyl beta-D-xylopyranoside	-	hydrolysis
66717	90255 ChEBI	4-nitrophenyl beta-L-fucoside	-	hydrolysis
66717	90260 ChEBI	4-nitrophenyl beta-lactoside	-	hydrolysis
66717	90343 ChEBI	4-Nitrophenyl N-acetyl-beta-D-glucosaminide	-	hydrolysis
66717	17440 ChEBI	4-nitrophenyl phosphate	-	hydrolysis
66717	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
66717	37572 ChEBI	alpha-L-arabinofuranoside	-	hydrolysis
66717	27613 ChEBI	amygdalin	-	builds acid from
66717	22605 ChEBI	arabinitol	-	builds acid from
66717	22599 ChEBI	arabinose	-	builds acid from
66717	18305 ChEBI	arbutin	-	builds acid from
66717	17968 ChEBI	butyrate	+	fermentation
66717	17968 ChEBI	butyrate	-	hydrolysis
66717	17057 ChEBI	cellobiose	-	builds acid from
66717	15354 ChEBI	choline	-	hydrolysis
66717	15824 ChEBI	D-fructose	-	builds acid from
66717	12936 ChEBI	D-galactose	-	builds acid from
66717	8391 ChEBI	D-gluconate	-	builds acid from
66717	17634 ChEBI	D-glucose	-	builds acid from
66717	62318 ChEBI	D-lyxose	-	builds acid from
66717	16899 ChEBI	D-mannitol	-	builds acid from
66717	16024 ChEBI	D-mannose	-	builds acid from
66717	16988 ChEBI	D-ribose	-	builds acid from
66717	17924 ChEBI	D-sorbitol	-	builds acid from
66717	16443 ChEBI	D-tagatose	-	builds acid from
66717	17113 ChEBI	erythritol	-	builds acid from
66717	4853 ChEBI	esculin	-	builds acid from
66717	29749 ChEBI	ferulate	-	growth
66717	29749 ChEBI	ferulate	+	reduction
66717	33984 ChEBI	fucose	-	builds acid from
66717	16813 ChEBI	galactitol	-	builds acid from
66717		gamma-L-glutamate-4-nitroanilide	-	hydrolysis
66717	5291 ChEBI	gelatin	-	hydrolysis
66717	28066 ChEBI	gentiobiose	-	builds acid from
66717	17234 ChEBI	glucose	+	growth
66717	17754 ChEBI	glycerol	-	builds acid from
66717	90347 ChEBI	glycine 2-naphthylamide	-	hydrolysis
66717	28087 ChEBI	glycogen	-	builds acid from
66717	15443 ChEBI	inulin	-	builds acid from
66717		L-alanine 4-nitroanilide	-	hydrolysis
66717	90611 ChEBI	L-alanyl-L-alanine 2-naphthylamide	-	hydrolysis
66717	90350 ChEBI	L-arginine-2-naphthylamide	-	hydrolysis
66717	90426 ChEBI	L-cysteine 2-naphthylamide	-	hydrolysis
66717	90727 ChEBI	L-glutamyl-L-glutamic acid 2-naphthylamide	-	hydrolysis
66717	90447 ChEBI	L-histidine 2-naphthylamide	-	hydrolysis
66717	90476 ChEBI	L-leucine 2-naphthylamide	-	hydrolysis
66717	90741 ChEBI	L-leucylglycine 2-naphthylamide	-	hydrolysis
66717	90478 ChEBI	L-lysine 2-naphthylamide	-	hydrolysis
66717	90599 ChEBI	L-phenylalanine 2-naphthylamide	-	hydrolysis
66717	90600 ChEBI	L-proline 2-naphthylamide	-	hydrolysis
66717		L-proline-4-nitroanilide	-	hydrolysis
66717	90601 ChEBI	L-pyroglutamic acid 2-naphthylamide	-	hydrolysis
66717	62345 ChEBI	L-rhamnose	-	builds acid from
66717	90603 ChEBI	L-serine 2-naphthylamide	-	hydrolysis
66717	17266 ChEBI	L-sorbose	-	builds acid from
66717	90607 ChEBI	L-tyrosine 2-naphthylamide	-	hydrolysis
66717	90608 ChEBI	L-valine 2-naphthylamide	-	hydrolysis
66717	17716 ChEBI	lactose	-	builds acid from
66717	17306 ChEBI	maltose	-	builds acid from
66717	6731 ChEBI	melezitose	-	builds acid from
66717	28053 ChEBI	melibiose	-	builds acid from
66717	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
66717	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
66717	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
66717	17268 ChEBI	myo-inositol	-	builds acid from
66717	61631 ChEBI	N-acetyl-beta-D-glucosaminide	-	hydrolysis
66717	59640 ChEBI	N-acetylglucosamine	-	builds acid from
66717	91062 ChEBI	N-benzoyl-DL-arginine 2-naphthylamide	-	hydrolysis
66717	90730 ChEBI	N-glutaryl-L-phenylalanine 2-naphthylamide	-	hydrolysis
66717	17632 ChEBI	nitrate	-	reduction
66717	25646 ChEBI	octanoate	-	hydrolysis
66717	16634 ChEBI	raffinose	-	builds acid from
66717	15963 ChEBI	ribitol	-	builds acid from
66717	17814 ChEBI	salicin	-	builds acid from
66717	50144 ChEBI	sodium pyruvate	+	growth
66717	28017 ChEBI	starch	-	builds acid from
66717	17992 ChEBI	sucrose	-	builds acid from
66717	132111 ChEBI	syringate	-	growth
66717	132111 ChEBI	syringate	-	reduction
66717	27082 ChEBI	trehalose	-	builds acid from
66717	78019 ChEBI	triphenyltetrazolium chloride	-	reduction
66717	32528 ChEBI	turanose	-	builds acid from
66717	16632 ChEBI	vanillate	-	growth
66717	16632 ChEBI	vanillate	-	reduction
66717	17151 ChEBI	xylitol	-	builds acid from
66717	18222 ChEBI	xylose	-	builds acid from

Enzymes

@ref	Value	Activity	Ec
66717	acid phosphatase	-	3.1.3.2
66717	alanine aminopeptidase	-
66717	alkaline phosphatase	-	3.1.3.1
66717	arginine dihydrolase	-	3.5.3.6
66717	beta-mannosidase	-	3.2.1.25
66717	carbohydrates	-	1.14.14.9
66717	catalase	-	1.11.1.6
66717	cytochrome oxidase	-	1.9.3.1
66717	glutamate decarboxylase	-	4.1.1.15
66717	L-arginine arylamidase	-
66717	leucine arylamidase	-	3.4.11.1
66717	tryptophanase	-	4.1.99.1
66717	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

66717

Fatty acid	Percentage
C16:0	26.3
C18:1 w9c	21
C18:1 w9c DMA	8.8
C18:0 12OH	7.8
C16:0 DMA	6.1
C18:0 DMA	5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
42366	healthy human feces	Bergholz-Rehbrücke	Germany	DEU	Europe
66717	from faeces of a healthy human	Nuthetal	Germany	DEU	Europe	reinforced clostridial medium (RCM mod )	contained (g/L): yeast extract (3.0), meat extract (10), peptone (10), glucose (5.0), soluble starch (1.0), NaCl (5.0), sodium acetate (5.0) and cysteine hydrochloride (0.5)	24-48 h	37
67770	Feces of a healthy human	Nuthetal	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence FJ711049 (>99% sequence identity) for Catenibacillus scindens subclade from Microbeatlas

Aquatic Samples	92
Soil Samples	5
Animal Samples	1760
Plant Samples
Total Samples	1857

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1420211v1 assembly for Catenibacillus scindens DSM 106146	scaffold	GCA_014202115	673271.3	2861335840	673271	66.13

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42366	Intestinal bacterium CG19-1 16S ribosomal RNA gene, partial sequence	FJ711049	1454		673271
66717	Intestinal bacterium CG19-1 16S ribosomal RNA gene, partial sequence	FJ711049.1	1454		673271

GC content

@ref	GC-content (mol%)	Method
42366	47.1
67770	47.1	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: Catenibacillus scindens DSM 106146
NCBI: GCA_014202115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	90.90	no
125439	motility	BacteriaNetⓘ	yes	76.20	no
125439	gram_stain	BacteriaNetⓘ	variable	58.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Catenibacillus scindens DSM 106146
NCBI: GCA_014202115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	77.32	no
125438	anaerobic	anaerobicⓘ	yes	83.54	yes
125438	aerobic	aerobicⓘ	no	89.30	yes
125438	spore-forming	spore-formingⓘ	no	55.97	yes
125438	thermophilic	thermophileⓘ	no	91.96	no
125438	flagellated	motile2+ⓘ	no	74.63	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Flavonoid-Modifying Capabilities of the Human Gut Microbiome-An In Silico Study.	Goris T, Cuadrat RRC, Braune A.	Nutrients	10.3390/nu13082688	2021
Phylogeny	Anaerolentibacter hominis gen. nov. sp. nov., Diplocloster hominis sp. nov. and Pilosibacter fragilis gen. nov. sp. nov., isolated from human faeces.	Yan Y, Zhao QH, Xu C, Wei RQ, Jiang H, Liu SJ.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006359	2024
Phylogeny	Catenibacillus scindens gen. nov., sp. nov., a C-deglycosylating human intestinal representative of the Lachnospiraceae.	Braune A, Blaut M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003001	2018

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 )
#42366	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106146
#66717	Annett Braune, Michael Blaut: Catenibacillus scindens gen. nov., sp. nov., a C-deglycosylating human intestinal representative of the Lachnospiraceae. IJSEM 68: 3356 - 3361 2018 ( DOI 10.1099/ijsem.0.003001 , PubMed 30179152 )
#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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Catenibacillus scindens (DSM 106146, CCUG 71490, JCM 33534)

Name and taxonomic classification