Peribacillus cavernae (DSM 105484, CCTCC AB 2015055, KCTC 33637)

Name: Peribacillus cavernae (DSM 105484, CCTCC AB 2015055, KCTC 33637)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140140

Type strain

Strain Designation L5

Culture col. no. DSM 105484 CCTCC AB 2015055 KCTC 33637 L5

NCBI tax ID(s) 1674310

Special Collections DSMZ KCTC Literature strains

History <- Korean Collection for Type Cultures, Biological Resources Center, Korea Institute of Bioscience and Biotechnology (KRIBB); KCTC 33637 <- Liling Feng, Huzhong Agricultural Univ., China

Links

Peribacillus cavernae L5 is an obligate aerobe, spore-forming, psychrophilic prokaryote that forms circular colonies and was isolated from From soil of Tenglong cave.

spore-forming Gram-positive motile rod-shaped colony-forming obligate aerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400881

KCTC 33637,DSM 105484

@ref 20215

Last LPSN update 2026-02-09 11:33:32

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Peribacillus

Species Peribacillus cavernae

Full scientific name Peribacillus cavernae (Feng et al. 2016) Patel and Gupta 2020

Synonyms (1)

Bacillus cavernae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
43772	positive	1-6 µm	0.3-0.8 µm	rod-shaped	polar
67771				rod-shaped
67771	positive

Colony morphology

@ref	Colony color	Colony shape	Medium used
43772	Pink	circular	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43772	Reasoner's 2A agar (R2A)
42747	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
43772	LB (Luria-Bertani) MEDIUM
43772	MacConkey agar
43772	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
42747	positive	growth	30	mesophilic
43772	positive	growth	4	psychrophilic
43772	negative	growth	40
43772	positive	growth	4-32
43772	positive	optimum	28	mesophilic
67771	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
43772	positive	optimum	7
43772	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
43772	obligate aerobe
67771	aerobe

Spore formation

@ref	Spore description	Type of spore	Confidence
43772	Oval, central position	spore
67771		spore
125438			93.934

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
43772		NaCl	positive	growth	0-1 %(w/v)
43772	non-halophilic	NaCl	positive	optimum	0 %(w/v)

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43772	16651 ChEBI	(S)-lactate	+	assimilation
43772		casein	-	hydrolysis
43772	17057 ChEBI	cellobiose	+	assimilation
43772	16947 ChEBI	citrate	-	assimilation
43772	17108 ChEBI	D-arabinose	-	builds acid from
43772	17108 ChEBI	D-arabinose	+	assimilation
43772	15824 ChEBI	D-fructose	-	builds acid from
43772	15824 ChEBI	D-fructose	+	assimilation
43772	17634 ChEBI	D-glucose	+	assimilation
43772	17634 ChEBI	D-glucose	+	builds acid from
43772	16899 ChEBI	D-mannitol	+	builds acid from
43772	16024 ChEBI	D-mannose	+	assimilation
43772	16988 ChEBI	D-ribose	-	builds acid from
43772	16988 ChEBI	D-ribose	+	assimilation
43772	17924 ChEBI	D-sorbitol	+	assimilation
43772	65327 ChEBI	D-xylose	-	builds acid from
43772	4853 ChEBI	esculin	+	builds acid from
43772	5291 ChEBI	gelatin	+	hydrolysis
43772	17234 ChEBI	glucose	-	fermentation
43772	29987 ChEBI	glutamate	+	assimilation
43772	17754 ChEBI	glycerol	-	builds acid from
43772	28087 ChEBI	glycogen	+	assimilation
43772	17295 ChEBI	L-phenylalanine	+	assimilation
43772	17115 ChEBI	L-serine	+	assimilation
43772	16857 ChEBI	L-threonine	+	assimilation
43772	17716 ChEBI	lactose	+	assimilation
43772	17306 ChEBI	maltose	-	builds acid from
43772	17306 ChEBI	maltose	+	assimilation
43772	17632 ChEBI	nitrate	-	reduction
43772	25646 ChEBI	octanoate	+	assimilation
43772	15611 ChEBI	sarcosine	+	assimilation
43772	64103 ChEBI	sodium butyrate	+	assimilation
43772	28017 ChEBI	starch	-	hydrolysis
43772	53424 ChEBI	tween 20	-	hydrolysis
43772	53423 ChEBI	tween 40	+	hydrolysis
43772	53425 ChEBI	tween 60	+	hydrolysis
43772	53426 ChEBI	tween 80	+	hydrolysis
43772	31011 ChEBI	valerate	+	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite
43772	15688 ChEBI	acetoin
43772	16136 ChEBI	hydrogen sulfide
43772	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
43772	15688 ChEBI	acetoin	-
43772	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
43772	acid phosphatase	-	3.1.3.2
43772	alkaline phosphatase	+	3.1.3.1
43772	alpha-chymotrypsin	-	3.4.21.1
43772	alpha-galactosidase	-	3.2.1.22
43772	alpha-glucosidase	-	3.2.1.20
43772	alpha-mannosidase	-	3.2.1.24
43772	arginine dihydrolase	-	3.5.3.6
43772	beta-D-fucosidase	-	3.2.1.38
43772	beta-galactosidase	-	3.2.1.23
43772	beta-glucosidase	-	3.2.1.21
43772	beta-glucuronidase	-	3.2.1.31
43772	catalase	+	1.11.1.6
43772	cystine arylamidase	-	3.4.11.3
43772	cytochrome oxidase	-	1.9.3.1
43772	esterase (C 4)	+
43772	esterase Lipase (C 8)	+
43772	leucine arylamidase	-	3.4.11.1
43772	lipase (C 14)	-
43772	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43772	naphthol-AS-BI-phosphohydrolase	+
43772	trypsin	-	3.4.21.4
43772	valine arylamidase	-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	propanol degradation	100	7 of 7
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	vitamin B1 metabolism	100	13 of 13
66794	pentose phosphate pathway	100	11 of 11
66794	kanosamine biosynthesis II	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	aspartate and asparagine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	glycine betaine biosynthesis	100	5 of 5
66794	citric acid cycle	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	leucine metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	NAD metabolism	83.33	15 of 18
66794	Entner Doudoroff pathway	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenol degradation	80	16 of 20
66794	peptidoglycan biosynthesis	80	12 of 15
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	pyrimidine metabolism	73.33	33 of 45
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	coenzyme M biosynthesis	70	7 of 10
66794	starch degradation	70	7 of 10
66794	alanine metabolism	68.97	20 of 29
66794	lipid metabolism	67.74	21 of 31
66794	enterobactin biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	vitamin B12 metabolism	64.71	22 of 34
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	myo-inositol biosynthesis	60	6 of 10
66794	arachidonate biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	degradation of hexoses	55.56	10 of 18
66794	lysine metabolism	54.76	23 of 42
66794	vitamin B6 metabolism	54.55	6 of 11
66794	androgen and estrogen metabolism	50	8 of 16
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	degradation of pentoses	46.43	13 of 28
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	3-phenylpropionate degradation	40	6 of 15
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	allantoin degradation	33.33	3 of 9
66794	octane oxidation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	lipid A biosynthesis	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	ginsenoside metabolism	31.25	5 of 16
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

43772

Fatty acid	Percentage
C20:0	29.5
C16:0	17.7
C18:0	13.1
C12:0	13
C14:0	10.8
C20:1ω7c	4
C17:1 iso ω5c	2.3
iso-C19:1	1.6
C11:0 iso 3OH	1.5
C20:1ω9c	1.3
C17:0 anteiso	1.3
C18:1ω9c	1.3
C19:0	1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67771	From soil of Tenglong cave	Hubei	China	CHN	Asia
42747	cave soil	Tenglong, Enshi city, Hubei province	China	CHN	Asia
43772	Soil of Tenglong cave	Enshi City, Hubei Province	China	CHN	Asia	30.564	109.641 30.564/109.641

Taxonmaps

69479

Global distribution of 16S sequence KT186244 (>99% sequence identity) for Bacillus from Microbeatlas

Aquatic Samples	18
Soil Samples	38
Animal Samples	14
Plant Samples	1
Total Samples	71

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42747	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3081318v1 assembly for Peribacillus cavernae DSM 105484	contig	GCA_030813185	1674310.7	2926509544	1674310	67.07
66792	ASM398913v1 assembly for Peribacillus cavernae L5	scaffold	GCA_003989135	1674310.3		1674310	64.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42747	Bacillus cavernae strain L5 16S ribosomal RNA gene, partial sequence	KT186244	1472		1674310

GC content

@ref	GC-content (mol%)	Method
67771	45.6	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: Peribacillus cavernae L5
NCBI: GCA_003989135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	86.30	no
125439	motility	BacteriaNetⓘ	yes	79.10	no
125439	gram_stain	BacteriaNetⓘ	variable	86.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Peribacillus cavernae L5
NCBI: GCA_003989135.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	78.93	yes
125438	anaerobic	anaerobicⓘ	no	96.73	yes
125438	aerobic	aerobicⓘ	yes	81.47	yes
125438	spore-forming	spore-formingⓘ	yes	93.93	no
125438	thermophilic	thermophileⓘ	no	88.69	yes
125438	flagellated	motile2+ⓘ	yes	76.77	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bacillus glennii sp. nov. and Bacillus saganii sp. nov., isolated from the vehicle assembly building at Kennedy Space Center where the Viking spacecraft were assembled.	Seuylemezian A, Ott L, Wolf S, Fragante J, Yip O, Pukall R, Schumann P, Vaishampayan P.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003714	2020
Phylogeny	Bacillus cavernae sp. nov. isolated from cave soil.	Feng L, Liu D, Sun X, Wang G, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000794	2015

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 )
#42747	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105484
#43772	Liling Feng, Dongmei Liu, Xuelian Sun, Gejiao Wang, Mingshun Li: Bacillus cavernae sp. nov. isolated from cave soil. IJSEM 66: 801 - 806 2016 ( DOI 10.1099/ijsem.0.000794 , PubMed 26612584 )
#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;
#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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Peribacillus cavernae (DSM 105484, CCTCC AB 2015055, KCTC 33637)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030813185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media

Fatty acid profile