Phaeobacter inhibens (DSM 16374, CIP 109289, LMG 22475)

Name: Phaeobacter inhibens (DSM 16374, CIP 109289, LMG 22475)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13731

Type strain

Strain Designation T5

Culture col. no. DSM 16374 CIP 109289 LMG 22475 T5

NCBI tax ID(s) 999548 221822

Special Collections DSMZ CIP Literature strains North Sea Microbiome

History <- T. Martens; T5 <- T. Brinkhoff 2006, DSMZ CIP <- 2006, DSMZ <- T. Martens, T5 <- T. Brinkhoff

Links

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

Gram-negative motile ovoid-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 131523

LMG 22475,DSM 16374,CIP 109289,CECT 7251

@ref 20215

Last LPSN update 2026-02-09 11:21:13

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Phaeobacter

Species Phaeobacter inhibens

Full scientific name Phaeobacter inhibens Martens et al. 2006

BacDive ID	Other strains from **Phaeobacter inhibens** (4)	Type strain
13730	P. inhibens DSM 17395
23227	P. inhibens 2.10, DSM 24588
137017	P. inhibens CIP 109852
158073	P. inhibens P10, 01/009, DSM 29965

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31517	negative	1.4-1.9 µm	0.6-0.8 µm	ovoid-shaped
120118	negative			rod-shaped
125439	negative				98.4

Colony morphology

6411

Incubation period1-2 days

Pigmentation

31517

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_16374_1.jpg
multimedia.multimedia content:	EM_DSM_16374_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6411	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37502	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120118	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6411	positive	growth	25	mesophilic
31517	positive	growth	04-36
31517	positive	optimum	27-29	mesophilic
37502	positive	growth	20	psychrophilic

Culture pH

@ref	Ability	Type	PH	PH range
31517	positive	optimum	7.5
31517	positive	growth	6-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31517	aerobe
120118	obligate aerobe
125439	aerobe	96.9

Spore formation

@ref	Spore formation	Confidence
31517
125439		97.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31517	NaCl	positive	growth	0.05-8.6 %
31517	NaCl	positive	optimum	2.96-3.94 %

Observation

31517

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
31517	16449 ChEBI	alanine	+	carbon source
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
31517	29016 ChEBI	arginine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
31517	22653 ChEBI	asparagine	+	carbon source
31517	35391 ChEBI	aspartate	+	carbon source
31517	17057 ChEBI	cellobiose	+	carbon source
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
31517	28757 ChEBI	fructose	+	carbon source
31517	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
31517	17234 ChEBI	glucose	+	carbon source
31517	17754 ChEBI	glycerol	+	carbon source
31517	15428 ChEBI	glycine	+	carbon source
31517	27570 ChEBI	histidine	+	carbon source
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
31517	25017 ChEBI	leucine	+	carbon source
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
31517	37684 ChEBI	mannose	+	carbon source
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
120118	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
120118	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
31517	26271 ChEBI	proline	+	carbon source
31517	17272 ChEBI	propionate	+	carbon source
31517	33942 ChEBI	ribose	+	carbon source
31517	30911 ChEBI	sorbitol	+	carbon source
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
31517	26986 ChEBI	threonine	+	carbon source
31517	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
31517	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68369	35581 ChEBI	indole	from API 20NE
120118	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68369	35581 ChEBI	indole		-	from API 20NE
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
6411	catalase	+	1.11.1.6
31517	catalase	+	1.11.1.6
120118	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31517	cytochrome oxidase	+	1.9.3.1
6411	cytochrome-c oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
120118	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
120118	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
6411	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	+/-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120118	-	+	+	+	-	+	+	-	-	-	+	+	+	-	-	+	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6411	-	-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	+/-	+	+/-	-	+	+	+/-	+/-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6411	water sample	Wadden Sea	Germany	DEU	Europe
120118	Environment, Water, tidal mud flat	Wadden Sea	Germany	DEU	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6411	1	Risk group (German classification) According to TRBA 466
120118	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM47310v1 assembly for Phaeobacter inhibens DSM 16374	scaffold	GCA_000473105	999548.6	2574179718	999548	78.15

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6411	Phaeobacter inhibens DSM 16374 16S ribosomal RNA gene, partial sequence	AY177712	1386		999548
6411	Phaeobacter inhibens DSM 16374 16S ribosomal RNA gene, partial sequence	KC176240	1380		999548

GC content

6411

GC-content (mol%)55.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phaeobacter inhibens DSM 16374
NCBI: GCA_000473105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.70	no
125439	motility	BacteriaNetⓘ	yes	77.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria.	Beiralas R, Ozer N, Segev E.	ISME Commun	10.1038/s43705-023-00311-y	2023
	The Roseobacter-Group Bacterium Phaeobacter as a Safe Probiotic Solution for Aquaculture.	Sonnenschein EC, Jimenez G, Castex M, Gram L.	Appl Environ Microbiol	10.1128/aem.02581-20	2021
	Vitamin B₁₂ is not shared by all marine prototrophic bacteria with their environment.	Sultana S, Bruns S, Wilkes H, Simon M, Wienhausen G.	ISME J	10.1038/s41396-023-01391-3	2023
	Modular Low-Copy-Number Plasmid Vectors for Rhodobacterales with Extended Host Range in Alphaproteobacteria.	Korner D, Schafer NM, Lagares A, Birmes L, Oehlmann NN, Addison H, Pohl S, Thanbichler M, Rebelein JG, Petersen J, Becker A.	ACS Synth Biol	10.1021/acssynbio.4c00062	2024
	Autecology of an oscillating population of a novel host-associated Phaeobacter species proliferating in marine bryozoans.	Bentzon-Tilia M, Henriksen NNSE, Schostag MD, Andersen AJC, Melchiorsen J, Strube ML, Gram L.	ISME Commun	10.1093/ismeco/ycaf178	2025
	Phosphate Limitation Triggers the Dissolution of Precipitated Iron by the Marine Bacterium Pseudovibrio sp. FO-BEG1.	Romano S, Bondarev V, Kolling M, Dittmar T, Schulz-Vogt HN.	Front Microbiol	10.3389/fmicb.2017.00364	2017
	Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens.	Dogs M, Voget S, Teshima H, Petersen J, Davenport K, Dalingault H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Standfest S, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Klenk HP, Goker M, Brinkhoff T.	Stand Genomic Sci	10.4056/sigs.4448212	2013
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	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	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 )
#27812	IJSEM 1293 2006 ( DOI 10.1099/ijs.0.63724-0 , PubMed 16738106 )
#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
#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 .
#120118	Collection of Institut Pasteur ; Curators of the CIP; CIP 109289
#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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Phaeobacter inhibens (DSM 16374, CIP 109289, LMG 22475)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000473105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

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