Shimia biformata (JCM 18818, BCRC 80548, CC-AMW-C)

Name: Shimia biformata (JCM 18818, BCRC 80548, CC-AMW-C)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134055

Type strain

Strain Designation CC-AMW-C

Culture col. no. JCM 18818 BCRC 80548 CC-AMW-C

NCBI tax ID(s) 1294299

Special Collections JCM Literature strains

History C.-C. Young CC-AMW-C.

Links

Shimia biformata CC-AMW-C is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 27590

BCRC 80548,JCM 18818

@ref 20215

Last LPSN update 2026-02-09 11:32:06

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Shimia

Species Shimia biformata

Full scientific name Shimia biformata Hameed et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31147	negative	1.85 µm	0.6 µm	rod-shaped
125439	negative				96.3
125438	negative				97.833

Pigmentation

31147

Productionno

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31147	positive	growth	20-40
31147	positive	optimum	33.5
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31147	positive	optimum	7.5
31147	positive	growth	6.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31147	aerobe
125439	aerobe	91.9

Spore formation

@ref	Spore formation	Confidence
31147
125439		95
125438		94.317

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31147	NaCl	positive	growth	01-06 %
31147	NaCl	positive	optimum	3 %

Observation

@ref	Observation
31147	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31147	30089 ChEBI	acetate	+	carbon source
31147	22599 ChEBI	arabinose	+	carbon source
31147	35391 ChEBI	aspartate	+	carbon source
31147	4853 ChEBI	esculin	+	hydrolysis
31147	28757 ChEBI	fructose	+	carbon source
31147	29987 ChEBI	glutamate	+	carbon source
31147	24996 ChEBI	lactate	+	carbon source
31147	17716 ChEBI	lactose	+	carbon source
31147	17306 ChEBI	maltose	+	carbon source
31147	28053 ChEBI	melibiose	+	carbon source
31147	51850 ChEBI	methyl pyruvate	+	carbon source
31147	506227 ChEBI	N-acetylglucosamine	+	carbon source
31147	18257 ChEBI	ornithine	+	carbon source
31147	28044 ChEBI	phenylalanine	+	carbon source
31147	50048 ChEBI	phenylethylamine	+	carbon source
31147	17822 ChEBI	serine	+	carbon source
31147	30031 ChEBI	succinate	+	carbon source
31147	17748 ChEBI	thymidine	+	carbon source
31147	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31147	acid phosphatase	+	3.1.3.2
31147	alkaline phosphatase	+	3.1.3.1
31147	catalase	+	1.11.1.6
31147	cytochrome oxidase	+	1.9.3.1
31147	gelatinase	+
31147	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
31147	seawater
67770	Coastal surface seawater (~30 cm depth) at Kending	Taiwan, Province of China	TWN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1688851v1 assembly for Shimia biformata JCM 18818	scaffold	GCA_016888515	1294299.3	2995446064	1294299	72.55

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31147	Shimia biformata strain CC-AMW-C 16S ribosomal RNA gene, partial sequence	KC169813	1422		1294299

GC content

@ref	GC-content (mol%)	Method
31147	61.2
67770	61.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shimia biformata JCM 18818
NCBI: GCA_016888515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.00	no
125439	motility	BacteriaNetⓘ	yes	56.80	no
125439	gram_stain	BacteriaNetⓘ	negative	96.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shimia biformata JCM 18818
NCBI: GCA_016888515.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.83	no
125438	anaerobic	anaerobicⓘ	no	94.77	yes
125438	aerobic	aerobicⓘ	yes	83.46	yes
125438	spore-forming	spore-formingⓘ	no	94.32	yes
125438	thermophilic	thermophileⓘ	no	97.42	yes
125438	flagellated	motile2+ⓘ	no	63.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006.	Hameed A, Shahina M, Lin SY, Lai WA, Hsu YH, Liu YC, Huang YM, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.053553-0	2013

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 )
#27475	IJSEM 4533 2013 ( DOI 10.1099/ijs.0.053553-0 , PubMed 23907225 )
#31147	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 #27475
#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;
#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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Shimia biformata (JCM 18818, BCRC 80548, CC-AMW-C)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_016888515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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