Name: Phyllobacterium myrsinacearum DSM 5893
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11875

Type strain:

Species: Phyllobacterium myrsinacearum

Culture col. no.: DSM 5893, ATCC 43591, LMG 1t1, NCIMB 12128, JCM 20934, CCUG 34964, CIP 108235, HAMBI 1991, HAMBI 2264, IAM 13587, LMG 1.1, NBRC 100017

Strain history: CIP <- 2004, CCUG <- 1995, LMG, Phyllobacterium rubiacearum <- 1973, D. Knösel

NCBI tax ID(s): 28101 (species)

SI-ID 127101

LMG 1, CCUG 34964, NCIB 12128, ATCC43591, DSM 5893, IAM13587, NCIMB 12128, CECT 4452, NBRC 100017, ATCC BAA-446, CIP 108235, HAMBI 1991, HAMBI 2264, KACC 10501, CFBP 5555, NCIB 121284, JCM 20934, NCPPB 4123

Special Collections

Other strains from Phyllobacterium myrsinacearum

Section

Phyllobacterium myrsinacearum DSM 5893 is an obligate aerobe, Gram-negative bacterium of the family Phyllobacteriaceae.

Gram-negative
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Phyllobacteriaceae*
	Genus	*Phyllobacterium*
	Species	**Phyllobacterium myrsinacearum**
	Full Scientific Name (LPSN)	Phyllobacterium myrsinacearum (ex Knösel 1962) Knösel 1984

Synonym

Phyllobacterium rubiacearum

Information on morphological and physiological properties Morphology

[Ref.: #121213]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98

[Ref.: #121213]	Cell shape	rod-shaped

[Ref.: #121213]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2351]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #2351]

Culture medium growth

[Ref.: #2351]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2351]

Culture medium composition

expand / minimize

[Ref.: #36708]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #36708]

Culture medium growth

[Ref.: #36708]

Culture medium composition

expand / minimize

[Ref.: #121213]

Culture medium

CIP Medium 72

[Ref.: #121213]

Culture medium growth

[Ref.: #121213]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121213]

Culture medium

CIP Medium 328

[Ref.: #121213]

Culture medium growth

[Ref.: #121213]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #2351]		growth	26 °C
[Ref.: #36708]		growth	25 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #121213]		growth	25-30 °C
[Ref.: #121213]	no	growth	10 °C
[Ref.: #121213]	no	growth	37 °C
[Ref.: #121213]	no	growth	41 °C
[Ref.: #121213]	no	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121213]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #121213]	NaCl		growth	0-2	%
[Ref.: #121213]	NaCl	no	growth	4	%
[Ref.: #121213]	NaCl	no	growth	6	%
[Ref.: #121213]	NaCl	no	growth	8	%
[Ref.: #121213]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121213]	citrate ChEBI	+	carbon source
[Ref.: #121213]	esculin ChEBI	+	hydrolysis
[Ref.: #121213]	hippurate ChEBI	+	hydrolysis
[Ref.: #121213]	nitrate ChEBI	-	reduction
[Ref.: #121213]	nitrate ChEBI	-	respiration
[Ref.: #121213]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #121213]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #121213]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #121213]		acetoin ChEBI	-
[Ref.: #121213]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121213]	alcohol dehydrogenase	-	1.1.1.1
[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.: #121213]	amylase	-
[Ref.: #121213]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121213]	caseinase	-	3.4.21.50
[Ref.: #121213]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #121213]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121213]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #121213]	gelatinase	-
[Ref.: #121213]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121213]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121213]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121213]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121213]	oxidase	+
[Ref.: #121213]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #121213]	tryptophan deaminase	-
[Ref.: #121213]	tween esterase	-
[Ref.: #121213]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #121213]	2662	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.: #121213]	11011	-	+	+	+	-	+	-	-	+	+	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #67770]	Sample type/isolated from	Leaf nodule

[Ref.: #121213]	Sample type/isolated from	Plant, Leaf nodule, Pavetta zimmermanniana
[Ref.: #121213]	Geographic location (country and/or sea, region)	Stuttgart Hohenheim
[Ref.: #121213]	Country	Germany
[Ref.: #121213]	Country ISO 3 Code	DEU
[Ref.: #121213]	Continent	Europe

[Ref.: #36708]	Geographic location (country and/or sea, region)	Stuttgart-Hohenheim
[Ref.: #36708]	Country	Germany
[Ref.: #36708]	Country ISO 3 Code	DEU
[Ref.: #36708]	Continent	Europe
* marker position based on {}

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

[Ref.: #2351]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121213]	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.: #67770]	Phyllobacterium myrsinacearum gene for 16S rRNA, strain: IAM 13587	D12790	1430	GenBank ENA	28101 tax ID
[Ref.: #124043]	Phyllobacterium myrsinacearum gene for 16S rRNA, partial sequence, strain: NBRC 100017.	AB681130	1410	GenBank ENA	28101 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phyllobacterium myrsinacearum DSM 5893	GCA_004216655	scaffold	GenBank ENA	28101 tax ID
[Ref.: #66792]	Phyllobacterium myrsinacearum strain DSM 5893	28101.7	wgs	PATRIC	28101 tax ID	*
[Ref.: #66792]	Phyllobacterium rubiacearum DSM 5893	2799112214	draft	JGI IMG/M	28101 tax ID	*

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: Phyllobacterium myrsinacearum DSM 5893 NCBI: GCA_004216655.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phyllobacterium myrsinacearum strain DSM 5893 PATRIC: 28101.7
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.295	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.895	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.338	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.75	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	51.528	no

Availability in culture collections External links

[Ref.: #2351]

Culture collection no.

DSM 5893, ATCC 43591, LMG 1t1, NCIMB 12128, JCM 20934, CCUG 34964, CIP 108235, HAMBI 1991, HAMBI 2264, IAM 13587, LMG 1.1, NBRC 100017

[Ref.: #81092]

SI-ID 127101

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend.	Mergaert J, Cnockaert MC, Swings J	Int J Syst Evol Microbiol	10.1099/00207713-52-5-1821	2002	*
	Third Generation Genome Sequencing Reveals That Endobacteria in Nematophagous Fungi Esteya vermicola Contain Multiple Genes Encoding for Nematicidal Proteins.	Wang R, Dong L, Chen Y, Wang S, Qu L	Front Microbiol	10.3389/fmicb.2022.842684	2022	*

References

#2351

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5893

#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 )

#36708 ; 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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#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 )

#81092

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-ID127101.1 )

#121213 Collection of Institut Pasteur ; Curators of the CIP; CIP 108235

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Phyllobacterium myrsinacearum DSM 5893

Phyllobacterium myrsinacearum strain DSM 5893

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