Neobacillus piezotolerans (MCCC 1A12711, JCM 32872, YLB-04)

Name: Neobacillus piezotolerans (MCCC 1A12711, JCM 32872, YLB-04)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164404

Type strain

Strain Designation YLB-04

Culture col. no. MCCC 1A12711 JCM 32872 YLB-04

NCBI tax ID(s) 2259171

Special Collections JCM Literature strains

History X. Tang; Third Inst. of State Oceanic Admin., China; YLB-04.

Links

Neobacillus piezotolerans YLB-04 is an aerobe, Gram-positive, motile bacterium that forms circular colonies and was isolated from Deep-sea sediment at 6300 m of the Yap Trench.

Gram-positive motile rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 28224

JCM 32872

@ref 20215

Last LPSN update 2026-02-09 11:39:50

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Cytobacillaceae

Genus Neobacillus

Species Neobacillus piezotolerans

Full scientific name Neobacillus piezotolerans (Yu et al. 2019) Gupta et al. 2020

Synonyms (1)

Bacillus piezotolerans

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
68177	positive	1.2-2.2 µm	0.3-0.6 µm	rod-shaped		peritrichous

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
68177	0.5-1 mm	cream	circular	1 day	LB (Luria-Bertani) MEDIUM

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	37
68177	positive	growth	15-50
68177	positive	optimum	45

Culture pH

@ref	Ability	Type	PH	PH range
68177	positive	optimum	7.5
68177	positive	growth	5-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
68177	aerobe
125439	anaerobe	91.8

Spore formation

@ref	Type of spore	Spore formation
68177	endospore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68177	NaCl	positive	growth	0-6 %(w/v)
68177	NaCl	positive	optimum	0 %(w/v)

Observation

@ref	Observation
67770	quinones: MK-7
68177	Growth occurs within the hydropressure range 0.1-50 MPa (optimum 0.1 MPa)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68177	17521 ChEBI	(-)-quinic acid	-	assimilation
68177		1 % sodium lactate	+	oxidation
68177	64552 ChEBI	2-hydroxybutyrate	-	assimilation
68177	37054 ChEBI	3-hydroxybutyrate	+	oxidation
68177	73918 ChEBI	3-O-methyl-D-glucose	-	assimilation
68177	18101 ChEBI	4-hydroxyphenylacetic acid	-	assimilation
68177	16411 ChEBI	acetic acid	-	assimilation
68177	13705 ChEBI	acetoacetate	-	assimilation
68177	17128 ChEBI	adipate	-	assimilation
68177	17925 ChEBI	alpha-D-glucose	+	oxidation
68177	17665 ChEBI	alpha-D-glucose 6-phosphate	-	assimilation
68177	27613 ChEBI	amygdalin	-	fermentation
68177	22599 ChEBI	arabinose	-	fermentation
68177	161680 ChEBI	aztreonam	+	oxidation
68177	161680 ChEBI	aztreonam	+	assimilation
68177	28860 ChEBI	beta-D-glucuronic acid	-	assimilation
68177	73706 ChEBI	bromosuccinate	-	assimilation
68177	17057 ChEBI	cellobiose	-	assimilation
68177	62968 ChEBI	cellulose	-	hydrolysis
68177	16947 ChEBI	citrate	-	assimilation
68177	18333 ChEBI	D-arabitol	-	assimilation
68177	29990 ChEBI	D-aspartate	-	assimilation
68177	15824 ChEBI	D-fructose	+	oxidation
68177	78697 ChEBI	D-fructose 6-phosphate	-	assimilation
68177	28847 ChEBI	D-fucose	-	assimilation
68177	15895 ChEBI	D-galactonic acid lactone	-	assimilation
68177	12936 ChEBI	D-galactose	-	assimilation
68177	18024 ChEBI	D-galacturonic acid	-	assimilation
68177	8391 ChEBI	D-gluconate	+	oxidation
68177	17634 ChEBI	D-glucose	+	assimilation
68177		D-lactic acid methyl ester	-	assimilation
68177	15588 ChEBI	D-malate	-	assimilation
68177	16899 ChEBI	D-mannitol	-	assimilation
68177	16024 ChEBI	D-mannose	-	assimilation
68177	33801 ChEBI	D-saccharate	-	assimilation
68177	17814 ChEBI	D-salicin	-	assimilation
68177	16523 ChEBI	D-serine	-	assimilation
68177	17924 ChEBI	D-sorbitol	-	assimilation
68177	23652 ChEBI	dextrin	-	assimilation
68177	4853 ChEBI	esculin	+/-	hydrolysis
68177	15740 ChEBI	formate	-	assimilation
68177	71321 ChEBI	fusidate	-	assimilation
68177	35390 ChEBI	galactarate	-	assimilation
68177	16865 ChEBI	gamma-aminobutyric acid	-	assimilation
68177	5291 ChEBI	gelatin	+/-	hydrolysis
68177	28066 ChEBI	gentiobiose	-	assimilation
68177	17234 ChEBI	glucose	+	fermentation
68177	32323 ChEBI	glucuronamide	-	assimilation
68177	17754 ChEBI	glycerol	+	oxidation
68177	70744 ChEBI	glycyl-L-proline	+	oxidation
68177	32735 ChEBI	guanidinium chloride	-	assimilation
68177	17120 ChEBI	hexanoate	-	assimilation
68177	17596 ChEBI	inosine	+	oxidation
68177	16977 ChEBI	L-alanine	-	assimilation
68177	30849 ChEBI	L-arabinose	-	assimilation
68177	90350 ChEBI	L-arginine-2-naphthylamide	-	assimilation
68177	29991 ChEBI	L-aspartate	-	assimilation
68177	18287 ChEBI	L-fucose	-	assimilation
68177	29985 ChEBI	L-glutamate	-	assimilation
68177	15971 ChEBI	L-histidine	-	assimilation
68177		L-lactate	-	assimilation
68177	15589 ChEBI	L-malate	-	assimilation
68177	18183 ChEBI	L-pyroglutamic acid	-	assimilation
68177	17115 ChEBI	L-serine	-	assimilation
68177	17716 ChEBI	lactose	-	assimilation
68177	6472 ChEBI	lincomycin	-	assimilation
68177	48607 ChEBI	lithium chloride	-	assimilation
68177	25115 ChEBI	malate	-	assimilation
68177	17306 ChEBI	maltose	+	assimilation
68177	28053 ChEBI	melibiose	-	fermentation
68177	28053 ChEBI	melibiose	-	assimilation
68177	37657 ChEBI	methyl D-glucoside	-	assimilation
68177	51850 ChEBI	methyl pyruvate	-	assimilation
68177	50694 ChEBI	minocycline	-	assimilation
68177	17268 ChEBI	myo-inositol	-	assimilation
68177	63154 ChEBI	N-acetyl-beta-D-mannosamine	+	oxidation
68177	28037 ChEBI	n-acetyl-D-galactosamine	-	assimilation
68177	506227 ChEBI	N-acetyl-D-glucosamine	+	oxidation
68177		n-acetyl-neuraminic acid	+	oxidation
68177	59640 ChEBI	N-acetylglucosamine	+	assimilation
68177	100147 ChEBI	nalidixic acid	+	oxidation
68177	75273 ChEBI	niaproof	-	assimilation
68177	17309 ChEBI	pectin	+	oxidation
68177	18401 ChEBI	phenylacetate	-	assimilation
68177	32032 ChEBI	potassium gluconate	-	assimilation
68177	75248 ChEBI	potassium tellurite	+	oxidation
68177	17272 ChEBI	propionate	-	assimilation
68177	16634 ChEBI	raffinose	-	assimilation
68177	26546 ChEBI	rhamnose	-	fermentation
68177	29673 ChEBI	rifamycin sv	+/-	assimilation
68177		skimmed milk	-	hydrolysis
68177	75229 ChEBI	sodium bromate	+/-	assimilation
68177	64103 ChEBI	sodium butyrate	+	oxidation
68177	64103 ChEBI	sodium butyrate	+	assimilation
68177	53258 ChEBI	sodium citrate	-	assimilation
68177	17164 ChEBI	stachyose	-	assimilation
68177	28017 ChEBI	starch	-	hydrolysis
68177	17992 ChEBI	sucrose	+	fermentation
68177	17992 ChEBI	sucrose	+	oxidation
68177	75198 ChEBI	tetrazolium blue	-	assimilation
68177	75193 ChEBI	tetrazolium violet	-	assimilation
68177	27082 ChEBI	trehalose	+	oxidation
68177	45735 ChEBI	troleandomycin	-	assimilation
68177	32528 ChEBI	turanose	-	assimilation
68177	53424 ChEBI	tween 20	-	hydrolysis
68177	53423 ChEBI	tween 40	-	hydrolysis
68177	53423 ChEBI	tween 40	-	assimilation
68177	53425 ChEBI	tween 60	-	hydrolysis
68177	53426 ChEBI	tween 80	-	hydrolysis
68177	28001 ChEBI	vancomycin	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite
68177	15688 ChEBI	acetoin
68177	16136 ChEBI	hydrogen sulfide
68177	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68177	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68177	acid phosphatase	+/-	3.1.3.2
68177	alkaline phosphatase	+	3.1.3.1
68177	alpha-chymotrypsin	+	3.4.21.1
68177	alpha-fucosidase	-	3.2.1.51
68177	alpha-galactosidase	-	3.2.1.22
68177	alpha-glucosidase	+	3.2.1.20
68177	alpha-mannosidase	-	3.2.1.24
68177	arginine dihydrolase	-	3.5.3.6
68177	beta-galactosidase	-	3.2.1.23
68177	beta-glucosidase	+/-	3.2.1.21
68177	beta-glucuronidase	+/-	3.2.1.31
68177	catalase	+	1.11.1.6
68177	cystine arylamidase	+/-	3.4.11.3
68177	cytochrome oxidase	+	1.9.3.1
68177	esterase (C 4)	+/-
68177	esterase Lipase (C 8)	+/-
68177	leucine arylamidase	+	3.4.11.1
68177	lipase (C 14)	+/-
68177	lysine decarboxylase	-	4.1.1.18
68177	N-acetyl-beta-glucosaminidase	-	3.2.1.52
68177	naphthol-AS-BI-phosphohydrolase	+/-
68177	nitrate reductase	+	1.7.99.4
68177	ornithine decarboxylase	+	4.1.1.17
68177	trypsin	+/-	3.4.21.4
68177	tryptophan deaminase	-	4.1.99.1
68177	urease	-	3.5.1.5
68177	valine arylamidase	+/-

Fatty acid profile

Metadata FA analysis

@ref

68177

Fatty acid	Percentage
C16:0	21
C15:0 iso	17.6
C15:0 anteiso	13.2
C18:0	12.7
C17:0 anteiso	6.2
C18:1 w7c/C18:1 w6c	5.1
C16:0 iso	4
C17:0 iso	3.3
C18:1 w9c	2.7
C14:0 iso	2.3
C14:0	2.2
C16:1 w7c alcohol	2.1
C17:1 iso w10c	1.4
C17:1 iso / C17:1 anteiso	1.3

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Isolation procedure
67770	Deep-sea sediment at 6300 m of the Yap Trench			Pacific Ocean
68177	sediment of hadal zones	2017-06-01	West Pacific Yap Trench	Pacific Ocean	-9.8661	-138.493 -9.8661/-138.493	marine broth	7 days	enriched at 60 MPa

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68177	ASM336280v1 assembly for Neobacillus piezotolerans YLB-04	contig	GCA_003362805	2259171.3	2957001711	2259171	68.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Neobacillus piezotolerans strain YLB-04 16S ribosomal RNA gene, partial sequence	MG913994	1443		2259171

GC content

@ref	GC-content (mol%)	Method
68177	45.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Neobacillus piezotolerans YLB-04
NCBI: GCA_003362805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	78.00	no
125439	motility	BacteriaNetⓘ	yes	62.70	no
125439	gram_stain	BacteriaNetⓘ	variable	84.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	91.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Neobacillus piezotolerans YLB-04
NCBI: GCA_003362805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	74.53	yes
125438	anaerobic	anaerobicⓘ	no	92.00	yes
125438	aerobic	aerobicⓘ	yes	75.66	yes
125438	spore-forming	spore-formingⓘ	yes	84.55	no
125438	thermophilic	thermophileⓘ	no	93.89	yes
125438	flagellated	motile2+ⓘ	yes	68.59	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench.	Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.003559	2019

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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68177	Libo Yu, Xixiang Tang, Shiping Wei, Yinkun Qiu, Xiashutong Xu, Guangxin Xu, Qilin Wang and Qian Yang: Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench. IJSEM 69: 3022 - 3030 2019 ( DOI 10.1099/ijsem.0.003559 )
#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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Neobacillus piezotolerans (MCCC 1A12711, JCM 32872, YLB-04)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003362805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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