Bacillus yapensis (MCCC 1A14143, JCM 33181, XXST-01)

Name: Bacillus yapensis (MCCC 1A14143, JCM 33181, XXST-01)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164475

Type strain

Strain Designation XXST-01

Culture col. no. MCCC 1A14143 JCM 33181 XXST-01

NCBI tax ID(s) 2492960

Special Collections JCM Literature strains

History JCM <-- X. Tang; Third Inst. of State Oceanic Admin., China; XXST-01.

Links

Bacillus yapensis XXST-01 is a spore-forming, Gram-positive, motile bacterium that forms circular colonies and was isolated from Deep-sea sediment at 6300 m of the Yap Trench.

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

Name and taxonomic classification

SI-ID 394720

JCM 33181

@ref 20215

Last LPSN update 2026-05-29 08:45:25

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Bacillus

Species Bacillus yapensis

Full scientific name Bacillus yapensis Xu et al. 2025

Synonyms (1)

"Robertmurraya yapensis"

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
68084	positive	3.1 µm	0.7 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony shape	Incubation period	Medium used
68084	2.0-4.0 mm	circular	2 days	Trypticase Soy Agar (TSA)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	37
68084	positive	growth	10-45
68084	positive	optimum	37

Culture pH

@ref	Ability	Type	PH	PH range
68084	positive	optimum	7
68084	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	92.932

Spore formation

@ref	Type of spore	Spore formation
68084	endospore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68084	NaCl	positive	growth	0.0-6.0 %
68084	NaCl	positive	optimum	0.0-0.5 %

Observation

@ref	Observation
67770	quinones: MK-7
68084	The polar lipids are diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified phospholipid (PL) and four unidentified aminophospholipids (APL)
68084	The predominant ubiquinone is MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68084	17057 ChEBI	cellobiose	+	builds acid from
68084	62968 ChEBI	cellulose	-	hydrolysis
68084	15824 ChEBI	D-fructose	+	builds acid from
68084	17634 ChEBI	D-glucose	+	assimilation
68084	17634 ChEBI	D-glucose	+	builds acid from
68084	16024 ChEBI	D-mannose	+	builds acid from
68084		esculin ferric citrate	+	builds acid from
68084	28066 ChEBI	gentiobiose	+	builds acid from
68084	17306 ChEBI	maltose	+	assimilation
68084	17306 ChEBI	maltose	+	builds acid from
68084	37684 ChEBI	mannose	+	assimilation
68084	17632 ChEBI	nitrate	+	reduction
68084	32032 ChEBI	potassium gluconate	+/-	builds acid from
68084	17814 ChEBI	salicin	+	builds acid from
68084		skimmed milk	-	hydrolysis
68084	28017 ChEBI	starch	-	hydrolysis
68084	28017 ChEBI	starch	+	builds acid from
68084	53424 ChEBI	tween 20	-	hydrolysis
68084	53423 ChEBI	tween 40	-	hydrolysis
68084	53425 ChEBI	tween 60	-	hydrolysis
68084	53426 ChEBI	tween 80	-	hydrolysis

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68084	15688 ChEBI	acetoin	+

Enzymes

@ref	Value	Activity	Ec
68084	acid phosphatase	+/-	3.1.3.2
68084	alkaline phosphatase	+/-	3.1.3.1
68084	alpha-chymotrypsin	+/-	3.4.21.1
68084	alpha-fucosidase	+	3.2.1.51
68084	alpha-glucosidase	+	3.2.1.20
68084	alpha-mannosidase	+/-	3.2.1.24
68084	beta-glucosidase	+	3.2.1.21
68084	catalase	+	1.11.1.6
68084	cytochrome oxidase	+	1.9.3.1
68084	esterase (C 4)	+
68084	esterase Lipase (C 8)	+
68084	naphthol-AS-BI-phosphohydrolase	+/-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country
67770	Deep-sea sediment at 6300 m of the Yap Trench			Pacific Ocean
68084	sediment collected at a water depth of 6300 m	2017-06	West Pacific Yap Trench

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM396625v1 assembly for Bacillus yapensis XXST-01	contig	GCA_003966255	2492960.4	2885763063	2492960	68.6
68084	ASM528020v1 assembly for Bacillus yapensis XXST-01	contig	GCA_005280205	2492960.5	8119698258	2492960	68.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68084	Bacillus yapensis 16S ribosomal RNA gene, partial sequence	MK243676	1458		2492960

GC content

@ref	GC-content (mol%)	Method
67770	38.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM396625v1 assembly for Bacillus yapensis XXST-01
NCBI: GCA_003966255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.93	no
125439	gram_stain	BacteriaNetⓘ	variable	53.76	no
125439	motility	BacteriaNetⓘ	yes	73.97	no
125439	spore_formation	BacteriaNetⓘ	yes	89.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Proposal to Transfer Bacillus yapensis to the Genus Robertmurraya as Robertmurraya yapensis comb. nov.	Dong Z, Hou J, Quadri SR, Quach NT, Narsing Rao MP, Wu Y.	Curr Microbiol	10.1007/s00284-025-04292-0	2025
Phylogeny	Bacillus yapensis sp. nov., a novel piezotolerant bacterium isolated from deep-sea sediment of the Yap Trench, Pacific Ocean.	Xu X, Yu L, Xu G, Wang Q, Wei S, Tang X	Antonie Van Leeuwenhoek	10.1007/s10482-019-01348-7	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 )
#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;
#68084	Xiashutong Xu, Libo Yu, Guangxin Xu, Qilin Wang, Shiping Wie, Xixiang Tang: Bacillus yapensis sp. nov., a novel piezotolerant bacterium isolated from deep-sea sediment of the Yap Trench, Pacific Ocean. Antonie Van Leeuwenhoek 113: 389 - 396 2020 ( DOI 10.1007/s10482-019-01348-7 )
#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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Bacillus yapensis (MCCC 1A14143, JCM 33181, XXST-01)

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 tests

Enzymes

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003966255

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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