Name: Cytobacillus oceanisediminis H2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1303

Type strain:

Species: Cytobacillus oceanisediminis

Strain Designation: H2

Culture col. no.: DSM 24771, CGMCC 1.10115, JCM 16506, BCRC 80336, CIP 110262

Strain history: CIP <- 2011, J. Zhang, Beijing Inst. Technol, Beijing, China: strain H2

NCBI tax ID(s): 665099 (species)

SI-ID 374225

CGMCC 1.10115, JCM 16506, DSM 24771, CIP 110262

Special Collections

Section

Cytobacillus oceanisediminis H2 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from marine sediment.

Gram-positive
rod-shaped
spore-forming
aerobe
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	*Bacillaceae*
	Genus	*Cytobacillus*
	Species	**Cytobacillus oceanisediminis**
	Full Scientific Name (LPSN)	Cytobacillus oceanisediminis (Zhang et al. 2010) Patel and Gupta 2020

Synonym

Bacillus oceanisediminis

Information on morphological and physiological properties Morphology

[Ref.: #29741]	Gram stain	positive
[Ref.: #121382]	Gram stain	positive

[Ref.: #29741]	Cell length	02-03 µm

[Ref.: #29741]	Cell width	0.6-0.8 µm

[Ref.: #29741]	Cell shape	rod-shaped
[Ref.: #121382]	Cell shape	rod-shaped

[Ref.: #121382]	Motility	yes

[Ref.: #29741]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17755]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #17755]

Culture medium growth

[Ref.: #17755]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17755]

Culture medium composition

expand / minimize

[Ref.: #37685]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37685]

Culture medium growth

[Ref.: #37685]

Culture medium composition

expand / minimize

[Ref.: #121382]

Culture medium

CIP Medium 368

[Ref.: #121382]

Culture medium growth

[Ref.: #121382]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121382]

Culture medium

CIP Medium 72

[Ref.: #121382]

Culture medium growth

[Ref.: #121382]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #17755]	growth	30 °C
[Ref.: #29741]	growth	04-45 °C
[Ref.: #29741]	optimum	37 °C
[Ref.: #37685]	growth	30 °C
[Ref.: #67770]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #29741]			optimum	7
[Ref.: #29741]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29741]

Oxygen tolerance

aerobe

[Ref.: #29741]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %94.425

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29741]		NaCl		growth	0-13	%
[Ref.: #29741]		NaCl		optimum	0-13	%

[Ref.: #29741]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29741]	acetate ChEBI	+	carbon source
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29741]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29741]	glucose ChEBI	+	carbon source
[Ref.: #29741]	glycogen ChEBI	+	carbon source
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29741]	lactate ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29741]	malate ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29741]	nitrate ChEBI	+	reduction
[Ref.: #121382]	nitrate ChEBI	+	reduction
[Ref.: #121382]	nitrite ChEBI	+	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29741]	pyruvate ChEBI	+	carbon source
[Ref.: #29741]	raffinose ChEBI	+	carbon source
[Ref.: #29741]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29741]	succinate ChEBI	+	carbon source
[Ref.: #29741]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #29741]		indole ChEBI	yes
[Ref.: #121382]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #29741]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #29741]	catalase	+	1.11.1.6
[Ref.: #121382]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29741]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #121382]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121382]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #121382]	11739	not determinedn.d.	+/-	-	-	-	+/-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	+	+	+/-	-	+/-	+	+	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121382]	12470	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-

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

[Ref.: #17755]	Sample type/isolated from	marine sediment
[Ref.: #17755]	Geographic location (country and/or sea, region)	South China Sea
[Ref.: #17755]	Country	China
[Ref.: #17755]	Country ISO 3 Code	CHN
[Ref.: #17755]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sediment sample from the South Sea
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #121382]	Sample type/isolated from	Environment, Sediment sample
[Ref.: #121382]	Geographic location (country and/or sea, region)	South Sea
[Ref.: #121382]	Country	China
[Ref.: #121382]	Country ISO 3 Code	CHN
[Ref.: #121382]	Continent	Asia
[Ref.: #121382]	Isolation date	2008
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ292772 (>99% sequence identity) for Bacillales from Microbeatlas

Aquatic Samples	700
Soil Samples	1890
Animal Samples	1214
Plant Samples	450
Total Samples	4254

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17755]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121382]	Biosafety level	1	Risk group (French classification)

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.: #29741]	Bacillus oceanisediminis strain H2 16S ribosomal RNA gene, partial sequence	GQ292772	1393	GenBank ENA	665099 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cytobacillus oceanisediminis CGMCC 1.10115	GCA_007830235	scaffold	GenBank ENA	665099 tax ID	*
[Ref.: #66792]	Bacillus oceanisediminis strain CGMCC 1.10115	665099.9	wgs	PATRIC	665099 tax ID	*
[Ref.: #66792]	Bacillus oceanisediminis CGMCC 1.10115	2596583545	draft	JGI IMG/M	665099 tax ID	*

[Ref.: #17755]	GC-content	44.8 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #29741]	GC-content	44.8 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cytobacillus oceanisediminis CGMCC 1.10115 NCBI: GCA_007830235.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	73.306	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.17	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	66.191	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	94.425	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.733	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	80.124	no

Availability in culture collections External links

[Ref.: #17755]

Culture collection no.

DSM 24771, CGMCC 1.10115, JCM 16506, BCRC 80336, CIP 110262

[Ref.: #70954]

SI-ID 374225

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Falsibacillus albus sp. nov., isolated from mangrove soil.	Shi SB, Liu C, Jiang MG, Li GD, Yang LF, Wu JF, Jiang LQ, Zhang K, Shen NK, Jiang CL, Jiang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.003328	2019	*
Phylogeny	Bacillus oryzisoli sp. nov., isolated from rice rhizosphere.	Zhang XX, Gao JS, Zhang L, Zhang CW, Ma XT, Zhang J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001215	2016	*
Phylogeny	Bacillus taiwanensis sp. nov., isolated from a soil sample from Taiwan.	Liu B, Liu GH, Sengonca C, Schumann P, Wang MK, Xiao RF, Zheng XF, Chen Z	Int J Syst Evol Microbiol	10.1099/ijs.0.000222	2015	*
Phylogeny	Bacillus oceanisediminis sp. nov., isolated from marine sediment.	Zhang J, Wang J, Fang C, Song F, Xin Y, Qu L, Ding K	Int J Syst Evol Microbiol	10.1099/ijs.0.019851-0	2010	*
Phylogeny	Cytobacillus pseudoceanisediminis sp. nov., A Novel Facultative Methylotrophic Bacterium with High Heavy Metal Resistance Isolated from the Deep Underground Saline Spring.	Tarasov K, Yakhnenko A, Zarubin M, Gangapshev A, Potekhina NV, Avtukh AN, Kravchenko E	Curr Microbiol	10.1007/s00284-022-03141-8	2022	*

References

#17755

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24771

#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 )

#29741

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26123 (see below)

#37685 ; Curators of the CIP;

#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;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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) .

#70954

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID374225.1 )

#121382 Collection of Institut Pasteur ; Curators of the CIP; CIP 110262

#26123

IJSEM 2924 2010 ( DOI 10.1099/ijs.0.019851-0 , PubMed 20118297 )

* These data were automatically processed and therefore are not curated

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Cytobacillus oceanisediminis CGMCC 1.10115

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