Name: Knoellia remsis 3-M5-R-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134268

Type strain:

Species: Knoellia remsis

Strain Designation: 3-M5-R-4

Culture col. no.: ATCC BAA-1496, CIP 109413, JCM 15662, KCTC 39578, NCIMB 14307

Strain history: CIP <- 2006, K. Venkateswaran, Jet Propulsion Lab., Pasadena, California, USA: strain 3-M5-R-4

NCBI tax ID(s): 407159 (species)

SI-ID 323271

ATCC BAA-1496, CIP 109413, JCM 15662

Other strains from Knoellia remsis

K. remsis 3-M5-R-7, CIP 109414

Section

Knoellia remsis 3-M5-R-4 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from Regenerative Enclosed Life Support Module Simulator air.

coccus-shaped
Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Intrasporangiaceae*
	Genus	*Knoellia*
	Species	**Knoellia remsis**
	Full Scientific Name (LPSN)	Knoellia remsis (Osman et al. 2007) Nouioui et al. 2018

Synonym

Tetrasphaera remsis

Information on morphological and physiological properties Morphology

[Ref.: #32213]	Gram stain	positive
[Ref.: #122153]	Gram stain	positive

[Ref.: #32213]	Cell shape	coccus-shaped
[Ref.: #122153]	Cell shape	coccus-shaped

[Ref.: #32213]	Motility	no
[Ref.: #122153]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #40039]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #40039]

Culture medium growth

[Ref.: #40039]

Culture medium composition

expand / minimize

[Ref.: #122153]

Culture medium

CIP Medium 566

[Ref.: #122153]

Culture medium growth

[Ref.: #122153]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #32213]	growth	15-45 °C
[Ref.: #32213]	optimum	25 °C
[Ref.: #40039]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #32213]	Temperature range	mesophilic
[Ref.: #40039]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32213]			optimum	7
[Ref.: #32213]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32213]	Oxygen tolerance	aerobe
[Ref.: #122153]	Oxygen tolerance	obligate aerobe

[Ref.: #32213]

Ability of spore formation

[Ref.: #32213]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32213]	acetate ChEBI	+	carbon source
[Ref.: #32213]	cellobiose ChEBI	+	carbon source
[Ref.: #32213]	dextrin ChEBI	+	carbon source
[Ref.: #32213]	esculin ChEBI	+	hydrolysis
[Ref.: #32213]	fructose ChEBI	+	carbon source
[Ref.: #32213]	galactose ChEBI	+	carbon source
[Ref.: #32213]	glucose ChEBI	+	carbon source
[Ref.: #32213]	glycerol ChEBI	+	carbon source
[Ref.: #32213]	malate ChEBI	+	carbon source
[Ref.: #32213]	maltose ChEBI	+	carbon source
[Ref.: #32213]	mannitol ChEBI	+	carbon source
[Ref.: #32213]	mannose ChEBI	+	carbon source
[Ref.: #32213]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #122153]	nitrate ChEBI	-	reduction
[Ref.: #122153]	nitrite ChEBI	-	reduction
[Ref.: #32213]	pyruvate ChEBI	+	carbon source
[Ref.: #32213]	ribose ChEBI	+	carbon source
[Ref.: #32213]	salicin ChEBI	+	carbon source
[Ref.: #32213]	sucrose ChEBI	+	carbon source
[Ref.: #32213]	trehalose ChEBI	+	carbon source
[Ref.: #32213]	tween 80 ChEBI	+	carbon source
[Ref.: #32213]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122153]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[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.: #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.: #32213]	catalase	+	1.11.1.6
[Ref.: #122153]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #32213]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #122153]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #122153]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #122153]	11845	-	+	+	+	-	+	+	-	+	-	+	-	-	+	-	+	+	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[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]	adipate degradation	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	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]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		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.: #67770]	Sample type/isolated from	Regenerative Enclosed Life Support Module Simulator air

[Ref.: #122153]	Sample type/isolated from	Spaceflight center, REMS
[Ref.: #122153]	Geographic location (country and/or sea, region)	Huntsville, Alabama
[Ref.: #122153]	Country	United States of America
[Ref.: #122153]	Country ISO 3 Code	USA
[Ref.: #122153]	Continent	North America
[Ref.: #122153]	Isolation date	2005
* marker position based on {}

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

[Ref.: #122153]

Biosafety level

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.: #32213]	Tetrasphaera remsis strain 3-M5-R-4 16S ribosomal RNA gene, complete sequence	DQ447774	1253	GenBank	407159 tax ID
[Ref.: #67770]	Tetrasphaera remsis gene for 16S ribosomal RNA, partial sequence	AB537173	1463	ENA	407159 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Knoellia remsis ATCC BAA-1496	GCA_003002895	contig	GenBank	407159 tax ID

[Ref.: #32213]	GC-content	69.2 mol%
[Ref.: #67770]	GC-content	69.2 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	70.7 mol%	genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Knoellia remsis ATCC BAA-1496 NCBI: GCA_003002895.1
[Ref.: #69480]	flagellated	no	98.355	no
[Ref.: #69480]	gram-positive	yes	91.82	no
[Ref.: #69480]	anaerobic	no	98.539	yes
[Ref.: #69480]	aerobic	yes	90.45	no
[Ref.: #69480]	halophile	no	96.363	no
[Ref.: #69480]	spore-forming	no	87.415	yes
[Ref.: #69480]	glucose-util	yes	91.264	yes
[Ref.: #69480]	thermophile	no	95.617	no
[Ref.: #69480]	motile	no	97.199	no
[Ref.: #69480]	glucose-ferment	no	86.988	no

Availability in culture collections External links

[Ref.: #32213]

Culture collection no.

ATCC BAA-1496, CIP 109413, JCM 15662, KCTC 39578, NCIMB 14307

[Ref.: #91854]

SI-ID 323271

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Tetrasphaera remsis sp. nov., isolated from the Regenerative Enclosed Life Support Module Simulator (REMS) air system.	Osman S, Moissl C, Hosoya N, Briegel A, Mayilraj S, Satomi M, Venkateswaran K	Int J Syst Evol Microbiol	10.1099/ijs.0.65137-0	2007	*

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 )

#32213

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 #28455 (see below)

#40039 ; Curators of the CIP;

#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;

#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) .

#91854

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-ID323271.1 )

#122153 Collection of Institut Pasteur ; Curators of the CIP; CIP 109413

#28455

IJSEM 2749 2007 ( DOI 10.1099/ijs.0.65137-0 , PubMed 18048719 )

* These data were automatically processed and therefore are not curated

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Knoellia remsis ATCC BAA-1496

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