Name: Gemmobacter nectariphilus DSM 15620
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13655

Type strain:

Species: Gemmobacter nectariphilus

Culture col. no.: DSM 15620, JCM 11959, NBRC 100046, AST 4, CGMCC 1.8899, CGMCC 1.8904

Strain history: Y. Tanaka AST4.

NCBI tax ID(s): 1121271 (strain), 220343 (species)

SI-ID 132013

DSM 15620, JCM 11959, NBRC 100046

Section

Gemmobacter nectariphilus DSM 15620 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

Gram-negative
rod-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	*Paracoccaceae*
	Genus	*Gemmobacter*
	Species	**Gemmobacter nectariphilus**
	Full Scientific Name (LPSN)	Gemmobacter nectariphilus (Tanaka et al. 2004) Chen et al. 2013

	Synonym	Wagnerdoeblera nectariphila
	Synonym	Catellibacterium nectariphilum

Information on morphological and physiological properties Morphology

[Ref.: #30689]	Gram stain	negative
[Ref.: #29963]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #30689]	Cell shape	rod-shaped
[Ref.: #29963]	Cell shape	rod-shaped

[Ref.: #30689]	Motility	no
[Ref.: #29963]	Motility	no

[Ref.: #29963]	Cell length	1.65 µm

[Ref.: #29963]	Cell width	0.7 µm

[Ref.: #29963]	Pigment production	no
[Ref.: #30689]	Pigment production	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5913]

Culture medium

NPB MEDIUM (DSMZ Medium 995)

[Ref.: #5913]

Culture medium growth

[Ref.: #5913]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5913]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #5913]	growth	30 °C
[Ref.: #29963]	growth	20-37 °C
[Ref.: #29963]	optimum	30 °C
[Ref.: #30689]	growth	15-40 °C
[Ref.: #30689]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #5913]	Temperature range	mesophilic
[Ref.: #29963]	Temperature range	mesophilic
[Ref.: #30689]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

		pH
[Ref.: #29963]	optimum	7
[Ref.: #30689]	optimum	7.5
[Ref.: #29963]	growth	06-08
[Ref.: #30689]	growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29963]	Oxygen tolerance	aerobe
[Ref.: #30689]	Oxygen tolerance	aerobe

[Ref.: #30689]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %90
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Salt		Salt conc.
[Ref.: #30689]	NaCl	growth	0-2	%
[Ref.: #30689]	NaCl	optimum	1	%
[Ref.: #29963]	NaCl	optimum	<3	%

[Ref.: #29963]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29963]	glutamate ChEBI	+	carbon source
[Ref.: #29963]	glycogen ChEBI	+	carbon source
[Ref.: #29963]	L-alaninamide ChEBI	+	carbon source
[Ref.: #29963]	lactate ChEBI	+	carbon source
[Ref.: #29963]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #29963]	serine ChEBI	+	carbon source
[Ref.: #29963]	succinate ChEBI	+	carbon source
[Ref.: #29963]	tween 80 ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30689]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29963]	catalase	+	1.11.1.6
[Ref.: #29963]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #5913]	Sample type/isolated from	activated sludge
[Ref.: #5913]	Geographic location (country and/or sea, region)	Kawasaki plant of Ajinomoto Co.
[Ref.: #5913]	Country	Japan
[Ref.: #5913]	Country ISO 3 Code	JPN
[Ref.: #5913]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Activated sludge
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB101543 (>99% sequence identity) for Gemmobacter nectariphilus subclade from Microbeatlas

Aquatic Samples	5101
Soil Samples	639
Animal Samples	1734
Plant Samples	351
Total Samples	7825

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

[Ref.: #5913]

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.: #5913]	Catellibacterium nectariphilum gene for 16S ribosomal RNA, partial sequence	AB101543	1386	ENA	1121271 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Gemmobacter nectariphilus DSM 15620	GCA_000429765	scaffold	GenBank	1121271 tax ID
[Ref.: #66792]	Catellibacterium nectariphilum DSM 15620	1121271.3	wgs	PATRIC	1121271 tax ID	*
[Ref.: #66792]	Gemmobacter nectariphilus DSM 15620	2524614723	draft	JGI IMG/M	1121271 tax ID	*

[Ref.: #5913]	GC-content	64.5 mol%
[Ref.: #67770]	GC-content	64.5 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Gemmobacter nectariphilus DSM 15620 DSM 15620 NCBI: GCA_000429765.1
[Ref.: #69481]	spore-forming	no	90	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Catellibacterium nectariphilum DSM 15620 PATRIC: 1121271.3
[Ref.: #69480]	motile	no	68.043	no
[Ref.: #69480]	flagellated	no	92.52	no
[Ref.: #69480]	gram-positive	no	98.217	yes
[Ref.: #69480]	anaerobic	no	98.401	no
[Ref.: #69480]	aerobic	yes	84.759	no
[Ref.: #69480]	halophile	no	65.349	yes
[Ref.: #69480]	spore-forming	no	96.429	no
[Ref.: #69480]	thermophile	no	94.529	yes
[Ref.: #69480]	glucose-util	yes	58.236	no
[Ref.: #69480]	glucose-ferment	no	88.778	no

Availability in culture collections External links

[Ref.: #5913]

Culture collection no.

DSM 15620, JCM 11959, NBRC 100046, AST 4, CGMCC 1.8899, CGMCC 1.8904

[Ref.: #82838]

SI-ID 132013

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gemmobacter straminiformis sp. nov., isolated from an artificial fountain.	Kang JY, Kim MJ, Chun J, Son KP, Jahng KY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002403	2017	*
Phylogeny	Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds.	Liu JJ, Zhang XQ, Chi FT, Pan J, Sun C, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.050955-0	2013	*
Phylogeny	Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis.	Chen WM, Cho NT, Huang WC, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.042051-0	2012	*
Phylogeny	Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004.	Liu Y, Xu CJ, Jiang JT, Liu YH, Song XF, Li H, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.017632-0	2009	*
Phylogeny	Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth.	Tanaka Y, Hanada S, Manome A, Tsuchida T, Kurane R, Nakamura K, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.02750-0	2004	*

References

#5913

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15620

#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 )

#29963

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 #26332 (see below)

#30689

#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;

#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 )

#82838

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-ID132013.1 )

#26332

IJSEM 955 2004 ( DOI 10.1099/ijs.0.02750-0 , PubMed 15143049 )

#27020

IJSEM 470 2013 ( DOI 10.1099/ijs.0.042051-0 , PubMed 22493172 )

* These data were automatically processed and therefore are not curated

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Gemmobacter nectariphilus DSM 15620 DSM 15620

Catellibacterium nectariphilum DSM 15620

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