Name: Phaeobacter inhibens T5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13731

Type strain:

Species: Phaeobacter inhibens

Strain Designation: T5

Culture col. no.: DSM 16374, CIP 109289, LMG 22475

Strain history: CIP <- 2006, DSMZ <- T. Martens, T5 <- T. Brinkhoff

NCBI tax ID(s): 999548 (strain), 221822 (species)

SI-ID 131523

LMG 22475, DSM 16374, CIP 109289, CECT 7251

Other strains from Phaeobacter inhibens

P. inhibens DSM 17395
P. inhibens 2.10, DSM 24588
P. inhibens CIP 109852
P. inhibens P10, 01/009, DSM 29965

Section

Phaeobacter inhibens T5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water sample.

Gram-negative
motile
ovoid-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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Phaeobacter*
	Species	**Phaeobacter inhibens**
	Full Scientific Name (LPSN)	Phaeobacter inhibens Martens et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31517]	Gram stain	negative
[Ref.: #120118]	Gram stain	negative

[Ref.: #31517]	Cell length	1.4-1.9 µm

[Ref.: #31517]	Cell width	0.6-0.8 µm

[Ref.: #31517]	Cell shape	ovoid-shaped
[Ref.: #120118]	Cell shape	rod-shaped

[Ref.: #31517]	Motility	yes
[Ref.: #120118]	Motility	no

[Ref.: #6411]

Incubation period

1-2 days

[Ref.: #31517]

Pigment production

yes

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6411]

Culture medium

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

[Ref.: #6411]

Culture medium growth

[Ref.: #6411]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6411]

Culture medium composition

expand / minimize

[Ref.: #37502]

Culture medium

Marine agar (MA)

[Ref.: #37502]

Culture medium growth

[Ref.: #37502]

Culture medium composition

expand / minimize

[Ref.: #120118]

Culture medium

CIP Medium 13

[Ref.: #120118]

Culture medium growth

[Ref.: #120118]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6411]	growth	25 °C
[Ref.: #31517]	growth	04-36 °C
[Ref.: #31517]	optimum	27-29 °C
[Ref.: #37502]	growth	20 °C

[Ref.: #6411]	Temperature range	mesophilic
[Ref.: #31517]	Temperature range	mesophilic
[Ref.: #37502]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #31517]			optimum	7.5
[Ref.: #31517]			growth	6-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31517]	Oxygen tolerance	aerobe
[Ref.: #120118]	Oxygen tolerance	obligate aerobe

[Ref.: #31517]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31517]		NaCl		growth	0.05-8.6	%
[Ref.: #31517]		NaCl		optimum	2.96-3.94	%

[Ref.: #31517]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #31517]	alanine ChEBI	+	carbon source
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #31517]	arginine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE, API 20E
[Ref.: #31517]	asparagine ChEBI	+	carbon source
[Ref.: #31517]	aspartate ChEBI	+	carbon source
[Ref.: #31517]	cellobiose ChEBI	+	carbon source
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68368]	D-mannitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31517]	fructose ChEBI	+	carbon source
[Ref.: #31517]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE, API 20E
[Ref.: #31517]	glucose ChEBI	+	carbon source
[Ref.: #31517]	glycerol ChEBI	+	carbon source
[Ref.: #31517]	glycine ChEBI	+	carbon source
[Ref.: #31517]	histidine ChEBI	+	carbon source
[Ref.: #68368]	L-arabinose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #31517]	leucine ChEBI	+	carbon source
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #31517]	mannose ChEBI	+	carbon source
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #120118]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #120118]	nitrite ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #31517]	proline ChEBI	+	carbon source
[Ref.: #31517]	propionate ChEBI	+	carbon source
[Ref.: #31517]	ribose ChEBI	+	carbon source
[Ref.: #31517]	sorbitol ChEBI	+	carbon source
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #31517]	threonine ChEBI	+	carbon source
[Ref.: #31517]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE, API 20E
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE, API 20E
[Ref.: #31517]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #120118]	indole ChEBI	no
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68369]	indole ChEBI	no	* from API 20NE, API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68369]		indole ChEBI		-	* from API 20NE, API 20E

	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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE, API 20E
[Ref.: #68368]	beta-galactosidase	-	3.2.1.23	* from API 20E, API zym
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE, API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #6411]	catalase	+	1.11.1.6
[Ref.: #31517]	catalase	+	1.11.1.6
[Ref.: #120118]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31517]	cytochrome oxidase	+	1.9.3.1
[Ref.: #6411]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE, API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #120118]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #120118]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE, API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #6411]	16846	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	+/-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #6411]	23751	-	-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	+/-	+	+/-	-	+	+	+/-	+/-	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.: #120118]	11770	-	+	+	+	-	+	+	-	-	-	+	+	+	-	-	+	-	-	-	-

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

[Ref.: #6411]	Sample type/isolated from	water sample
[Ref.: #6411]	Geographic location (country and/or sea, region)	Wadden Sea
[Ref.: #6411]	Country	Germany
[Ref.: #6411]	Country ISO 3 Code	DEU
[Ref.: #6411]	Continent	Europe

[Ref.: #120118]	Sample type/isolated from	Environment, Water, tidal mud flat
[Ref.: #120118]	Geographic location (country and/or sea, region)	Wadden Sea
[Ref.: #120118]	Country	Germany
[Ref.: #120118]	Country ISO 3 Code	DEU
[Ref.: #120118]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC176240 (>99% sequence identity) for Phaeobacter from Microbeatlas

Aquatic Samples	6774
Soil Samples	318
Animal Samples	295
Plant Samples	82
Total Samples	7469

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

[Ref.: #6411]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120118]	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.: #6411]	Phaeobacter inhibens DSM 16374 16S ribosomal RNA gene, partial sequence	KC176240	1380	ENA	999548 tax ID
[Ref.: #6411]	Phaeobacter inhibens DSM 16374 16S ribosomal RNA gene, partial sequence	AY177712	1386	ENA	999548 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phaeobacter inhibens DSM 16374	GCA_000473105	scaffold	GenBank	999548 tax ID	*
[Ref.: #66792]	Phaeobacter inhibens DSM 16374	999548.6	wgs	PATRIC	999548 tax ID	*
[Ref.: #66792]	Phaeobacter inhibens T5, DSM 16374	2574179718	complete	JGI IMG/M	999548 tax ID	*

[Ref.: #6411]

GC-content

55.7 mol%

Availability in culture collections External links

[Ref.: #6411]

Culture collection no.

DSM 16374, CIP 109289, LMG 22475

[Ref.: #82913]

SI-ID 131523

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench.	Ding W, Liu P, Xu Y, Fang J, Cao J	FEMS Microbiol Lett	10.1093/femsle/fnaa004	2019	*
Phylogeny	Phaeobacter marinintestinus sp. nov., isolated from the intestine of a sea cucumber (Apostichopus japonicus).	Lee MH, Song EJ, Seo MJ, Hyun DW, Bae JW, Lee SY, Roh SW, Nam YD	Antonie Van Leeuwenhoek	10.1007/s10482-014-0318-x	2014	*
Phylogeny	Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395.	Buddruhs N, Pradella S, Goker M, Pauker O, Pukall R, Sproer C, Schumann P, Petersen J, Brinkhoff T	Int J Syst Evol Microbiol	10.1099/ijs.0.053900-0	2013	*
Phylogeny	Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera.	Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T	Int J Syst Evol Microbiol	10.1099/ijs.0.63724-0	2006	*

References

#6411

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16374

#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 )

#31517

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 #27812 (see below)

#37502 ; 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) .

#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 )

#68368

Automatically annotated from API 20E .

#68369

Automatically annotated from API 20NE .

#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 .

#82913

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-ID131523.1 )

#120118 Collection of Institut Pasteur ; Curators of the CIP; CIP 109289

#27812

IJSEM 1293 2006 ( DOI 10.1099/ijs.0.63724-0 , PubMed 16738106 )

* These data were automatically processed and therefore are not curated

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