Name: Microscilla marina SIO-8
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3813

Type strain:

Species: Microscilla marina

Strain Designation: SIO-8

Culture col. no.: DSM 4236, ATCC 23134, NCMB 1400

Strain history: <- NCMB <- ATCC <- R.A. Lewin, SIO-8

NCBI tax ID(s): 313606 (strain), 1027 (species)

SI-ID 10158

LMG 13022, ATCC 23134, DSM 4236, LMG 18923, NCIMB 1400, NCMB 1400, IFO15650, IFO 16560, IFO 16042, NBRC 16560, NBRC 16042

Special Collections

DSMZ

Section

Microscilla marina SIO-8 is an obligate aerobe, chemoorganotroph, motile bacterium that was isolated from marine aquarium outflow.

motile
rod-shaped
chemoorganotroph
obligate 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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Microscillaceae*
	Genus	*Microscilla*
	Species	**Microscilla marina**
	Full Scientific Name (LPSN)	Microscilla marina Pringsheim 1951 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %95.36

[Ref.: #43350]	Cell length	10-100 µm

[Ref.: #43350]	Cell shape	rod-shaped

[Ref.: #43350]	Motility	yes

[Ref.: #43350]	Flagellum arrangement	gliding

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1623]

Culture medium

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

[Ref.: #1623]

Culture medium growth

[Ref.: #1623]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #1623]			growth	25 °C
[Ref.: #43350]			maximum	35 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43350]

Oxygen tolerance

obligate aerobe

[Ref.: #43350]

Nutrition type

chemoorganotroph

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43350]	agar ChEBI	-	degradation
[Ref.: #43350]	alginate ChEBI	-	degradation
[Ref.: #43350]	carboxymethylcellulose ChEBI	+	degradation
[Ref.: #43350]	cellulose ChEBI	-	degradation
[Ref.: #43350]	chitin ChEBI	-	degradation
[Ref.: #43350]	gelatin ChEBI	+	degradation
[Ref.: #43350]	glucose ChEBI	-	assimilation
[Ref.: #43350]	glutamate ChEBI	-	nitrogen source
[Ref.: #43350]	nitrate ChEBI	-	nitrogen source
[Ref.: #43350]	nitrate ChEBI	-	reduction
[Ref.: #43350]	peptone	+	nitrogen source
[Ref.: #43350]	starch ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	histidine metabolism	79.31	23 of 29
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	lysine metabolism	78.57	33 of 42
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	isoprenoid biosynthesis	73.08	19 of 26
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	carotenoid biosynthesis	68.18	15 of 22
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	oxidative phosphorylation	56.04	51 of 91
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	vitamin B12 metabolism	47.06	16 of 34
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	chlorophyll metabolism	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #1623]	Sample type/isolated from	marine aquarium outflow
[Ref.: #1623]	Geographic location (country and/or sea, region)	California, La Jolla
[Ref.: #1623]	Country	USA
[Ref.: #1623]	Country ISO 3 Code	USA
[Ref.: #1623]	Continent	North America
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	#Water reservoir (Aquarium/pool)
#Engineered	#Waste	#Wastewater
#Environmental	#Aquatic	#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB078080 (>99% sequence identity) for Microscilla marina subclade from Microbeatlas

Aquatic Samples	1071
Soil Samples	283
Animal Samples	213
Plant Samples	63
Total Samples	1630

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

[Ref.: #1623]

Biosafety level

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.: #1623]	Microscilla marina gene for 16S rRNA, strain:IFO 16560	AB078080	1455	GenBank ENA	1027 tax ID
[Ref.: #20218]	Microscilla marina 16S ribosomal RNA	M58793	1451	GenBank ENA	1027 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microscilla marina ATCC 23134	GCA_000169175	contig	GenBank ENA	313606 tax ID	*
[Ref.: #66792]	Microscilla marina ATCC 23134	313606.3	wgs	PATRIC	313606 tax ID	*
[Ref.: #66792]	Microscilla marina ATCC 23134	2636416090	draft	JGI IMG/M	313606 tax ID	*
[Ref.: #66792]	Microscilla marina ATCC 23134	640196209	draft	JGI IMG/M	313606 tax ID	*

[Ref.: #1623]	GC-content	42.3 mol%
[Ref.: #43350]	GC-content	42 mol%	Buoyant density centrifugation (BD)
[Ref.: #1623]	GC-content	40.6 mol%	sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Microscilla marina ATCC 23134 PATRIC: 313606.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microscilla marina ATCC 23134 PATRIC: 313606.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.36	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.089	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.404	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.447	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	89.367	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	79.75	yes

Availability in culture collections External links

[Ref.: #1623]

Culture collection no.

DSM 4236, ATCC 23134, NCMB 1400

[Ref.: #73324]

SI-ID 10158

References

#1623

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4236

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#43350

; 4: 409 - 409 ISBN 978 ( DOI 10.1007/978-0-387-68572-4 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#73324

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-ID10158.1 )

* These data were automatically processed and therefore are not curated

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Microscilla marina ATCC 23134

Microscilla marina ATCC 23134

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