Name: Nubsella zeaxanthinifaciens TDMA-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134324

Type strain:

Species: Nubsella zeaxanthinifaciens

Strain Designation: TDMA-5

Culture col. no.: NBRC 102579, CCUG 54348

NCBI tax ID(s): 392412 (species)

SI-ID 343463

CCUG 54348

Section

Nubsella zeaxanthinifaciens TDMA-5 is an aerobe, Gram-negative, motile bacterium that was isolated from freshwater .

Gram-negative
motile
rod-shaped
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	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Nubsella*
	Species	**Nubsella zeaxanthinifaciens**
	Full Scientific Name (LPSN)	Nubsella zeaxanthinifaciens Asker et al. 2008

Synonym

"Pedobacter zeaxanthinifaciens"

Information on morphological and physiological properties Morphology

[Ref.: #32436]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #32436]	Cell length	3 µm

[Ref.: #32436]	Cell width	0.25 µm

[Ref.: #32436]	Cell shape	rod-shaped

[Ref.: #32436]	Motility	yes
[Ref.: #69480]	Motility	no Confidence in %91.448

[Ref.: #32436]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #32436]	growth	18-40 °C
[Ref.: #32436]	optimum	30 °C
[Ref.: #60142]	growth	30 °C

[Ref.: #32436]	Temperature range	mesophilic
[Ref.: #60142]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32436]			optimum	6.5
[Ref.: #32436]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32436]	Oxygen tolerance	aerobe
[Ref.: #60142]	Oxygen tolerance	aerobe

[Ref.: #32436]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32436]	esculin ChEBI	+	hydrolysis
[Ref.: #32436]	glucose ChEBI	+	carbon source
[Ref.: #32436]	malate ChEBI	+	carbon source
[Ref.: #32436]	maltose ChEBI	+	carbon source
[Ref.: #32436]	mannose ChEBI	+	carbon source
[Ref.: #32436]	N-acetylglucosamine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32436]	catalase	+	1.11.1.6
[Ref.: #32436]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32436]	gelatinase	+

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

[Ref.: #32436]	Sample type/isolated from	freshwater (river, lake, pond)

[Ref.: #60142]	Sample type/isolated from	Fresh water
[Ref.: #60142]	Sampling date	2005-09-01
[Ref.: #60142]	Geographic location (country and/or sea, region)	Tottori,Misasa
[Ref.: #60142]	Country	Japan
[Ref.: #60142]	Country ISO 3 Code	JPN
[Ref.: #60142]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB264126 (>99% sequence identity) for Nubsella zeaxanthinifaciens subclade from Microbeatlas

Aquatic Samples	274
Soil Samples	129
Animal Samples	168
Plant Samples	214
Total Samples	785

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.: #32436]	Nubsella zeaxanthinifaciens gene for 16S rRNA, partial sequence	AB264126	1422	GenBank	392412 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nubsella zeaxanthinifaciens TDMA-5	GCA_003313335	scaffold	GenBank	392412 tax ID	*

[Ref.: #32436]

GC-content

38.6 mol%

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: Nubsella zeaxanthinifaciens TDMA-5 NCBI: GCA_003313335.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nubsella zeaxanthinifaciens TDMA-5 NCBI: GCA_003313335.1
[Ref.: #69480]	motile	no	85.673	yes
[Ref.: #69480]	flagellated	no	96.735	no
[Ref.: #69480]	gram-positive	no	97.654	yes
[Ref.: #69480]	anaerobic	no	99.085	no
[Ref.: #69480]	aerobic	yes	92.205	yes
[Ref.: #69480]	halophile	no	96.129	no
[Ref.: #69480]	spore-forming	no	94.503	yes
[Ref.: #69480]	glucose-util	yes	87.01	no
[Ref.: #69480]	thermophile	no	97.371	yes
[Ref.: #69480]	glucose-ferment	no	90.727	no

Availability in culture collections External links

[Ref.: #32436]

Culture collection no.

NBRC 102579, CCUG 54348

[Ref.: #91899]

SI-ID 343463

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.	Kim DU, Kim YJ, Shin DH, Weon HY, Kwon SW, Seong CN, Ka JO	J Microbiol	10.1007/s12275-013-2231-9	2013	*
Phylogeny	Pedobacter chitinilyticus sp. nov., a chitin-degrading bacterium isolated from wheat leaf tissue.	Zhang LL, Gan LZ, Xu ZB, Yang F, Li Y, Fan XL, Liu XF, Tian YQ, Dai YM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003017	2018	*
Phylogeny	Nubsella zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Sphingobacteriaceae isolated from freshwater.	Asker D, Beppu T, Ueda K	Int J Syst Evol Microbiol	10.1099/ijs.0.65493-0	2008	*
Phylogeny	Pedobacter pollutisoli sp. nov., Isolated from Tetrabromobisphenol A-Contaminated Soil.	Mu Y, Ke Z, Feng CX, Wang XW, Wang XW, Wang HM, Chen Q, He J	Curr Microbiol	10.1007/s00284-019-01643-6	2019	*
Phylogeny	Pelobium manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine.	Xia X, Wu S, Han Y, Liao S, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.001451	2016	*
Phylogeny	Pedobacter nanyangensis sp. nov., isolated from herbicide-contaminated soil.	Zhang H, Zhang J, Song M, Cheng MG, Wu YD, Guo SH, Li Q, Hong Q, Huang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.000448	2015	*
Phylogeny	Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil.	Ngo HTT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000055	2015	*
Phylogeny	Pedobacter xixiisoli sp. nov., isolated from bank soil.	Zeng Y, Feng H, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.065946-0	2014	*

References

#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 )

#32436

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 #28658 (see below)

#60142 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54348

#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) .

#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 )

#91899

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-ID343463.1 )

#28658

IJSEM 601 2008 ( DOI 10.1099/ijs.0.65493-0 , PubMed 18319463 )

* These data were automatically processed and therefore are not curated

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