Name: Paenibacillus crassostreae LPB0068
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158760

Type strain:

Species: Paenibacillus crassostreae

Strain Designation: LPB0068

Culture col. no.: KACC 18694, JCM 31183

Strain history: H. Yi; Korea Univ., South Korea; LPB0068.

NCBI tax ID(s): 1763538 (species)

Section

Paenibacillus crassostreae LPB0068 is a facultative anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from pacific oyster .

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
facultative anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus crassostreae**
	Full Scientific Name (LPSN)	Paenibacillus crassostreae Shin et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65512]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #65512]	Cell length	1.3-2.5 µm

[Ref.: #65512]	Cell width	0.5-0.8 µm

[Ref.: #65512]	Cell shape	rod-shaped

[Ref.: #65512]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.616

[Ref.: #65512]	Colony size	1.0-1.5 mm
[Ref.: #65512]	Colony color	cream
[Ref.: #65512]	Colony shape	circular
[Ref.: #65512]	Incubation period	3 days
[Ref.: #65512]	Cultivation medium used	TSA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65512]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #65512]

Culture medium growth

		Temperature
[Ref.: #65512]	growth	4-35 °C
[Ref.: #65512]	optimum	25 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #65512]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65512]			optimum	7.0
[Ref.: #65512]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65512]

Oxygen tolerance

facultative anaerobe

[Ref.: #65512]	Spore description	endospore
[Ref.: #65512]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65512]		NaCl		growth	0-3	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65512]	adenine ChEBI	+	hydrolysis
[Ref.: #65512]	amygdalin ChEBI	+	builds acid from
[Ref.: #65512]	arginine ChEBI	-	hydrolysis
[Ref.: #65512]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #65512]	casein	-	hydrolysis
[Ref.: #65512]	cellobiose ChEBI	+	builds acid from
[Ref.: #65512]	chitin ChEBI	-	hydrolysis
[Ref.: #65512]	D-glucose ChEBI	+	builds acid from
[Ref.: #65512]	D-mannose ChEBI	+	builds acid from
[Ref.: #65512]	D-ribose ChEBI	+	builds acid from
[Ref.: #65512]	dna ChEBI	-	hydrolysis
[Ref.: #65512]	esculin ChEBI	+	builds acid from
[Ref.: #65512]	esculin ChEBI	+	hydrolysis
[Ref.: #65512]	gelatin ChEBI	-	hydrolysis
[Ref.: #65512]	gentiobiose ChEBI	+	builds acid from
[Ref.: #65512]	glucose ChEBI	-	fermentation
[Ref.: #65512]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #65512]	inulin ChEBI	+	builds acid from
[Ref.: #65512]	L-arabinose ChEBI	+	builds acid from
[Ref.: #65512]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #65512]	lactose ChEBI	+	builds acid from
[Ref.: #65512]	lysine ChEBI	-	hydrolysis
[Ref.: #65512]	maltose ChEBI	+	builds acid from
[Ref.: #65512]	melibiose ChEBI	+	builds acid from
[Ref.: #65512]	nitrate ChEBI	-	reduction
[Ref.: #65512]	ornithine ChEBI	-	hydrolysis
[Ref.: #65512]	salicin ChEBI	+	builds acid from
[Ref.: #65512]	sodium alginate ChEBI	-	hydrolysis
[Ref.: #65512]	starch ChEBI	+	builds acid from
[Ref.: #65512]	starch ChEBI	+	hydrolysis
[Ref.: #65512]	tryptophan ChEBI	-	hydrolysis
[Ref.: #65512]	tween 20 ChEBI	-	hydrolysis
[Ref.: #65512]	tween 40 ChEBI	+	hydrolysis
[Ref.: #65512]	tween 60 ChEBI	+	hydrolysis
[Ref.: #65512]	tween 80 ChEBI	-	hydrolysis
[Ref.: #65512]	urea ChEBI	-	hydrolysis
[Ref.: #65512]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65512]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65512]	acid phosphatase	-	3.1.3.2
[Ref.: #65512]	alkaline phosphatase	-	3.1.3.1
[Ref.: #65512]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65512]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65512]	alpha-galactosidase	+	3.2.1.22
[Ref.: #65512]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65512]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65512]	beta-galactosidase	+	3.2.1.23
[Ref.: #65512]	beta-glucosidase	+	3.2.1.21
[Ref.: #65512]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65512]	catalase	+	1.11.1.6
[Ref.: #65512]	cystine arylamidase	-	3.4.11.3
[Ref.: #65512]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65512]	esterase (C 4)	+
[Ref.: #65512]	esterase Lipase (C 8)	+
[Ref.: #65512]	leucine arylamidase	-	3.4.11.1
[Ref.: #65512]	lipase (C 14)	-
[Ref.: #65512]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65512]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65512]	trypsin	-	3.4.21.4
[Ref.: #65512]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65512]

Fatty acid	Percentage
C15:0 anteiso	49.6
C16:0	17.7
C14:0	14
C16:0 iso	4.1
C15:0 iso	3.9
C17:0 anteiso	3.3
C12:0	1.8
C13:0 anteiso	1.6
C18:0	1.1
C17:0 iso	1.1
C14:0 iso	1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #65512]	Sample type/isolated from	pacific oyster (Crassostrea giga)
[Ref.: #65512]	Geographic location (country and/or sea, region)	Yeongheungdo Island
[Ref.: #65512]	Country	Republic of Korea
[Ref.: #65512]	Country ISO 3 Code	KOR
[Ref.: #65512]	Continent	Asia
[Ref.: #65512]	Geographic location	37.2545°/126.4960°
[Ref.: #65512]	Enrichment culture	MA

[Ref.: #67770]	Sample type/isolated from	Pacific oyster (Crassostrea gigas)
[Ref.: #67770]	Host species	Crassostrea gigas
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Mollusca

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU057345 (>99% sequence identity) for Paenibacillus crassostreae subclade from Microbeatlas

Aquatic Samples	1011
Soil Samples	5986
Animal Samples	2252
Plant Samples	961
Total Samples	10210

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #65512]	16S rRNA gene sequence	KU057345		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paenibacillus crassostreae LPB0068	GCA_001637335	contig	GenBank	1763538 tax ID
[Ref.: #66792]	Paenibacillus crassostreae LPB0068	GCA_001857945	complete	GenBank	1763538 tax ID	*
[Ref.: #66792]	Paenibacillus crassostreae LPB0068	2744054636	draft	JGI IMG/M	1763538 tax ID	*
[Ref.: #66792]	Paenibacillus crassostreae LPB0068	2718218093	complete	JGI IMG/M	1763538 tax ID	*

[Ref.: #65512]

GC-content

40 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paenibacillus crassostreae LPB0068 NCBI: GCA_001857945.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus crassostreae LPB0068 NCBI: GCA_001857945.1
[Ref.: #69480]	flagellated	yes	84.66	no
[Ref.: #69480]	gram-positive	yes	87.548	no
[Ref.: #69480]	anaerobic	no	98.087	no
[Ref.: #69480]	aerobic	yes	78.297	no
[Ref.: #69480]	halophile	no	89.82	no
[Ref.: #69480]	spore-forming	yes	96.489	yes
[Ref.: #69480]	thermophile	no	99.449	no
[Ref.: #69480]	glucose-util	yes	89.719	no
[Ref.: #69480]	motile	yes	87.228	no
[Ref.: #69480]	glucose-ferment	no	90.552	yes

Availability in culture collections External links

[Ref.: #65512]

Culture collection no.

KACC 18694, JCM 31183

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas.	Shin SK, Kim E, Yi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.002444	2017	*

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 )

#65512

Su-Kyoung Shin, Eunji Kim and Hana Yi: Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas. IJSEM 68: 58 - 63 2018 ( DOI 10.1099/ijsem.0.002444 , PubMed 29068277 )

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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