Name: Naumannella halotolerans WS 4616
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 12674

Type strain:

Species: Naumannella halotolerans

Strain Designation: WS 4616

Culture col. no.: DSM 24323, LMG 26184, JCM 30997

Strain history: LMG 26184 <-- S. Scherer; Tech. Univ. of Munich, Germany <-- G. Rieser; Tech. Univ. of Munich, Germany; WS4616.

NCBI tax ID(s): 993414 (species)

SI-ID 374254

LMG 26184, DSM 24323, JCM 30997

Special Collections

Other strains from Naumannella halotolerans

Section

When using BacDive for research please cite our paper

Naumannella halotolerans WS 4616 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from pharmaceutical clean room.

coccus-shaped
Gram-positive
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Propionibacteriaceae*
	Genus	*Naumannella*
	Species	**Naumannella halotolerans**
	Full Scientific Name (LPSN)	Naumannella halotolerans Rieser et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30487]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %92.506
[Ref.: #125439]	Gram stain	positive Confidence in %96.1

[Ref.: #30487]	Cell width	1.15 µm

[Ref.: #30487]	Cell shape	coccus-shaped

[Ref.: #30487]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %96.488

[Ref.: #30487]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17435]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #17435]

Culture medium growth

[Ref.: #17435]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17435]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17435]	growth	28 °C
[Ref.: #30487]	growth	15-37 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #30487]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30487]	Oxygen tolerance	aerobe
[Ref.: #125438]	Oxygen tolerance	aerobe Confidence in %90.6
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %98.9

[Ref.: #30487]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30487]		NaCl		growth	0-10	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30487]	arabinose ChEBI	+	carbon source
[Ref.: #30487]	esculin ChEBI	+	hydrolysis
[Ref.: #30487]	fructose ChEBI	+	carbon source
[Ref.: #30487]	galactose ChEBI	+	carbon source
[Ref.: #30487]	glucose ChEBI	+	carbon source
[Ref.: #30487]	glycerol ChEBI	+	carbon source
[Ref.: #30487]	L-arabitol ChEBI	+	carbon source
[Ref.: #30487]	maltose ChEBI	+	carbon source
[Ref.: #30487]	mannitol ChEBI	+	carbon source
[Ref.: #30487]	mannose ChEBI	+	carbon source
[Ref.: #30487]	ribitol ChEBI	+	carbon source
[Ref.: #30487]	ribose ChEBI	+	carbon source
[Ref.: #30487]	sorbitol ChEBI	+	carbon source
[Ref.: #30487]	sucrose ChEBI	+	carbon source
[Ref.: #30487]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30487]	catalase	+	1.11.1.6
[Ref.: #30487]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30487]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #17435]	Sample type/isolated from	pharmaceutical clean room
[Ref.: #17435]	Geographic location (country and/or sea, region)	Sachsen-Anhalt
[Ref.: #17435]	Country	Germany
[Ref.: #17435]	Country ISO 3 Code	DEU
[Ref.: #17435]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Pharmaceutical clean room
* marker position based on {}

Isolation sources categories

#Engineered

#Built environment

#Clean room

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR832425 (>99% sequence identity) for Naumannella halotolerans subclade from Microbeatlas

Aquatic Samples	58
Soil Samples	51
Animal Samples	173
Plant Samples	7
Total Samples	289

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

[Ref.: #17435]

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.: #17435]	Naumannella halotolerans partial 16S rRNA gene, type strain WS4616T	FR832425	1407	GenBank ENA	993414 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Naumannella halotolerans DSM 24323	GCA_004364645	contig	GenBank ENA	993414 tax ID
[Ref.: #66792]	Naumannella halotolerans strain DSM 24323	993414.3	wgs	PATRIC	993414 tax ID	*
[Ref.: #66792]	Naumannella halotolerans DSM 24323	2731957515	draft	JGI IMG/M	993414 tax ID	*

[Ref.: #17435]	GC-content	67.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30487]	GC-content	67.7 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Naumannella halotolerans strain DSM 24323 PATRIC: 993414.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	92.506	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	98.155	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	90.6	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	77.927	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.5	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	96.488	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Naumannella halotolerans DSM 24323 NCBI: GCA_004364645
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	62.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	75
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	96.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.9

Availability in culture collections External links

[Ref.: #17435]

Culture collection no.

DSM 24323, LMG 26184, JCM 30997

[Ref.: #81885]

SI-ID 374254

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Naumannella cuiyingiana sp. nov., isolated from a ca. 1500-year-old mural painting, and emended description of the genus Naumannella.	Tian T, Wu F, Ma Y, Xiang T, Ma W, Hu W, Wu G, An L, Wang W, Feng H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001964	2017	*
Phylogeny	Naumannella huperziae sp. nov., an endophytic actinobacterium isolated from Huperzia serrata (Thunb.).	Sun Y, Chen HH, Sun HM, Ai MJ, Su J, Yu LY, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001882	2017	*
Phylogeny	Naumannella halotolerans gen. nov., sp. nov., a Gram-positive coccus of the family Propionibacteriaceae isolated from a pharmaceutical clean room and from food.	Rieser G, Scherer S, Wenning M	Int J Syst Evol Microbiol	10.1099/ijs.0.037218-0	2012	*

References

#17435

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24323

#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 )

#30487

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 #26820 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#81885

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-ID374254.1 )

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#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 .

#26820

IJSEM 3042 2012 ( DOI 10.1099/ijs.0.037218-0 , PubMed 22307502 )

* These data were automatically processed and therefore are not curated

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Naumannella halotolerans strain DSM 24323

Naumannella halotolerans DSM 24323

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