Amorphus coralli R5 Sph 026, RS.Sph.026 | Type strain | DSM 19760, LMG 24307 | BacDiveID:17873

Strain identifier

BacDive ID: 17873

Type strain:

Species: Amorphus coralli

Strain Designation: R5 Sph 026, RS.Sph.026

Culture col. no.: DSM 19760, LMG 24307

Strain history: <- D. Zeevi Ben Yosef, Ben-Gurion-Univ., Beer-Sheva, Israel; R5 Sph 026 <- E. Ben Dov

NCBI tax ID(s): 1120983 (strain), 340680 (species)

SI-ID 310961

LMG 24307, DSM 19760

Section

Amorphus coralli R5 Sph 026 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Coral mucus Fungia granulosa.

Gram-negative
rod-shaped
aerobe
mesophilic
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Amorphaceae*
	Genus	*Amorphus*
	Species	**Amorphus coralli**
	Full Scientific Name (LPSN)	Amorphus coralli Zeevi Ben Yosef et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32416]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.969

[Ref.: #32416]	Cell width	0.5-3 µm

[Ref.: #32416]	Cell shape	rod-shaped

[Ref.: #32416]	Motility	no

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

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

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8300]			growth	28 °C
[Ref.: #32416]			growth	25-30 °C
[Ref.: #32416]			optimum	25-30 °C

[Ref.: #8300]	Temperature range	mesophilic
[Ref.: #32416]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32416]			optimum	7.5-8
[Ref.: #32416]			growth	7.5-8

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

[Ref.: #32416]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32416]		NaCl		growth	03-04	%
[Ref.: #32416]		NaCl		optimum	03-04	%

Observation

aggregates in chains

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32416]		arabinose ChEBI	+	carbon source
[Ref.: #32416]		glucose ChEBI	+	carbon source
[Ref.: #32416]		histidine ChEBI	+	carbon source
[Ref.: #32416]		maltose ChEBI	+	carbon source
[Ref.: #32416]		mannitol ChEBI	+	carbon source
[Ref.: #32416]		mannose ChEBI	+	carbon source
[Ref.: #32416]		ornithine ChEBI	+	carbon source
[Ref.: #32416]		propionate ChEBI	+	carbon source
[Ref.: #32416]		sorbitol ChEBI	+	carbon source
[Ref.: #32416]		succinate ChEBI	+	carbon source

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

[Ref.: #8300]	Sample type/isolated from	Coral mucus Fungia granulosa
[Ref.: #8300]	Host species	Fungia granulosa
[Ref.: #8300]	Geographic location (country and/or sea, region)	Red Sea, Gulf of Eilat
[Ref.: #8300]	Country	Israel
[Ref.: #8300]	Country ISO 3 Code	ISR
[Ref.: #8300]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Cnidaria (Corals)
#Host Body Product	#Oral cavity and Airways	#Mucus

What are isolation sources categories?

Global distribution of 16S sequence DQ097300 (>99% sequence identity) for Amorphus coralli subclade from Microbeatlas

Aquatic Samples	899
Soil Samples	296
Animal Samples	119
Plant Samples	84
Total Samples	1398

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

Biosafety level

1

Risk group (German classification)
According to TRBA 466

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.: #8300]	Amorphus coralli strain RS.Sph.026 16S ribosomal RNA gene, partial sequence	DQ097300	1438	ENA	340680 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Amorphus coralli DSM 19760	GCA_000374525	scaffold	GenBank	1120983 tax ID	*
[Ref.: #66792]	Amorphus coralli DSM 19760	1120983.3	wgs	PATRIC	1120983 tax ID	*
[Ref.: #66792]	Amorphus coralli DSM 19760	2517572147	draft	JGI IMG/M	1120983 tax ID	*

[Ref.: #8300]	GC-content	62.1 mol%	fluorimetric
[Ref.: #8300]	GC-content	67.1 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #32416]	GC-content	67.1 mol%

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: Amorphus coralli DSM 19760 DSM 19760 NCBI: GCA_000374525.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amorphus coralli DSM 19760 DSM 19760 NCBI: GCA_000374525.1
[Ref.: #69480]	motile	no	85.934	yes
[Ref.: #69480]	flagellated	no	95.213	yes
[Ref.: #69480]	gram-positive	no	98.18	no
[Ref.: #69480]	anaerobic	no	96.066	yes
[Ref.: #69480]	aerobic	yes	88.902	yes
[Ref.: #69480]	halophile	no	69.72	no
[Ref.: #69480]	spore-forming	no	96.426	yes
[Ref.: #69480]	glucose-util	yes	88.623	yes
[Ref.: #69480]	thermophile	no	93.877	yes
[Ref.: #69480]	glucose-ferment	no	93.157	no

Availability in culture collections External links

Culture collection no.

DSM 19760, LMG 24307

SI-ID 310961

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales.	Zeevi Ben Yosef D, Ben-Dov E, Kushmaro A	Int J Syst Evol Microbiol	10.1099/ijs.0.65462-0	2008	*
Phylogeny	Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima.	Hwang JM, Chung EJ, Park JA, Jeong JH, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.048959-0	2013	*
Phylogeny	Amorphus orientalis sp. nov., an exopolysaccharide-producing bacterium isolated from salt mine sediment.	Wang YX, Liu JH, Chen YG, Zhang XX, Wang ZG, Chen Y, Tian SP, Hu B, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.015735-0	2009	*

References

#8300

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19760

#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 )

#32416

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 #28639 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#86862

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-ID310961.1 )

#28639

IJSEM 2704 2008 ( DOI 10.1099/ijs.0.65462-0 , PubMed 19060044 )

* These data were automatically processed and therefore are not curated

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