Name: Nocardioides allogilvus KCTC 49020
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159868

Type strain:

Species: Nocardioides allogilvus

Culture col. no.: KCTC 49020, CGMCC 4.7457, CFH 30205

Strain history: <- Wenjun Li, Sun Sat-Sen Univ.

NCBI tax ID(s): 2072017 (species)

Section

Nocardioides allogilvus KCTC 49020 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from soil collected at a karst cave.

coccus-shaped
colony-forming
Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides allogilvus**
	Full Scientific Name (LPSN)	Nocardioides allogilvus Zhang et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66607]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.719

[Ref.: #66607]	Cell shape	coccus-shaped

[Ref.: #66607]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.089

[Ref.: #66607]	Colony color	pale yellow
[Ref.: #66607]	Colony shape	circular
[Ref.: #66607]	Incubation period	4 days
[Ref.: #66607]	Cultivation medium used	R2A medium

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Czapek's agar

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Culture medium growth

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Culture medium

ISP 2

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Culture medium growth

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Culture medium

ISP 3

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Culture medium growth

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Culture medium

ISP 4

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Gause's synthetic agar

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Culture medium growth

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Culture medium

ISP 5

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Culture medium growth

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Culture medium

potato-dextrose agar

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Culture medium growth

		Temperature
[Ref.: #66607]	optimum	28 °C
[Ref.: #66607]	growth	4-35 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #66607]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66607]			growth	8.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66607]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.684
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66607]		NaCl		growth	0-6	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66607]	3-O-methyl-D-glucose ChEBI	+	carbon source
[Ref.: #66607]	cellobiose ChEBI	+	carbon source
[Ref.: #66607]	cellulose ChEBI	-	hydrolysis
[Ref.: #66607]	D-fucose ChEBI	+	carbon source
[Ref.: #66607]	D-glucarate ChEBI	+	carbon source
[Ref.: #66607]	D-glucuronate ChEBI	+	carbon source
[Ref.: #66607]	D-mannitol ChEBI	+	carbon source
[Ref.: #66607]	gelatin ChEBI	-	hydrolysis
[Ref.: #66607]	glucuronamide ChEBI	+	carbon source
[Ref.: #66607]	inosine ChEBI	+	carbon source
[Ref.: #66607]	L-aspartate ChEBI	+	carbon source
[Ref.: #66607]	L-fucose ChEBI	+	carbon source
[Ref.: #66607]	L-rhamnose ChEBI	+	carbon source
[Ref.: #66607]	L-serine ChEBI	+	carbon source
[Ref.: #66607]	lactose ChEBI	+	carbon source
[Ref.: #66607]	maltose ChEBI	+	carbon source
[Ref.: #66607]	melibiose ChEBI	+	carbon source
[Ref.: #66607]	methyl beta-D-glucopyranoside ChEBI	+	carbon source
[Ref.: #66607]	milk	-	hydrolysis
[Ref.: #66607]	N-acetyl-D-mannosamine ChEBI	+	carbon source
[Ref.: #66607]	N-acetylgalactosamine ChEBI	+	carbon source
[Ref.: #66607]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #66607]	n-acetylneuraminate ChEBI	+	carbon source
[Ref.: #66607]	nalidixic acid ChEBI	+	carbon source
[Ref.: #66607]	nitrate ChEBI	+	reduction
[Ref.: #66607]	pectin ChEBI	+	carbon source
[Ref.: #66607]	quinate ChEBI	+	carbon source
[Ref.: #66607]	raffinose ChEBI	+	carbon source
[Ref.: #66607]	salicin ChEBI	+	carbon source
[Ref.: #66607]	stachyose ChEBI	+	carbon source
[Ref.: #66607]	starch ChEBI	-	hydrolysis
[Ref.: #66607]	sucrose ChEBI	+	carbon source
[Ref.: #66607]	trehalose ChEBI	+	carbon source
[Ref.: #66607]	turanose ChEBI	+	carbon source
[Ref.: #66607]	tween 20 ChEBI	+	hydrolysis
[Ref.: #66607]	tween 40 ChEBI	+	carbon source
[Ref.: #66607]	tween 40 ChEBI	+	hydrolysis
[Ref.: #66607]	tween 60 ChEBI	+	hydrolysis
[Ref.: #66607]	tween 80 ChEBI	-	hydrolysis
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	Metabolite production	Metabolite	Production
[Ref.: #66607]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66607]	acid phosphatase	+	3.1.3.2
[Ref.: #66607]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66607]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66607]	alpha-glucosidase	+	3.2.1.20
[Ref.: #66607]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66607]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #66607]	beta-galactosidase	-	3.2.1.23
[Ref.: #66607]	beta-glucosidase	-	3.2.1.21
[Ref.: #66607]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66607]	catalase	+	1.11.1.6
[Ref.: #66607]	chymotrypsin	-	3.4.4.5
[Ref.: #66607]	cystine arylamidase	+	3.4.11.3
[Ref.: #66607]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66607]	esterase (C 4)	+
[Ref.: #66607]	esterase Lipase (C 8)	+
[Ref.: #66607]	leucine arylamidase	+	3.4.11.1
[Ref.: #66607]	lipase (C 14)	+
[Ref.: #66607]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66607]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66607]	trypsin	-	3.4.21.4
[Ref.: #66607]	urease	-	3.5.1.5
[Ref.: #66607]	valine arylamidase	+
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Fatty acid profile

Metadata FA analysis

Reference

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Fatty acid	Percentage
C16:0 iso	25.4
C14:0 anteiso	22.2
C17:1 w8c	8.4
C18:1 w9c	7.9
C16:1 iso H	7.7
C17:1 iso w9c / C16:0 10-methyl	4
C19:1 w11c / C19:1 w9c	3.9
C16:1 w7c / C16:1 w6c	3.7
C18:1 2OH	2.7
C18:0 iso	2.2
C18:1 iso H	1.7
C16:0	1.6
C20:1 w9c	1.2
C17:0 anteiso	1.1
C19:0 iso	1
C14:0 iso	0.7
C17:1 w6c	0.6
C17:0 iso	0.5
C17:0	0.5
C16:0 anteiso	0.5

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

[Ref.: #66607]	Sample type/isolated from	soil collected at a karst cave
[Ref.: #66607]	Geographic location (country and/or sea, region)	Luoyang County, Henan Province
[Ref.: #66607]	Country	China
[Ref.: #66607]	Country ISO 3 Code	CHN
[Ref.: #66607]	Continent	Asia
[Ref.: #66607]	Geographic location	33.7667°/111.5670°
[Ref.: #66607]	Enrichment culture	ISP 2
[Ref.: #66607]	Enrichment culture composition	supplemented with nystatin (50 mg/l), nalidixic acid (20 mg/l)
[Ref.: #66607]	Enrichment culture duration	14 days
[Ref.: #66607]	Enrichment culture temperature	28 ̊C

[Ref.: #67771]	Sample type/isolated from	From soil of karst cave
[Ref.: #67771]	Geographic location (country and/or sea, region)	Henan province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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Global distribution of 16S sequence MG800321 (>99% sequence identity) for Nocardioides from Microbeatlas

Aquatic Samples	2750
Soil Samples	13298
Animal Samples	3378
Plant Samples	2376
Total Samples	21802

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.: #66607]	Nocardioides sp. CFH 30205 16S ribosomal RNA gene, partial sequence	MG800321	1471	ENA	2072017 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides allogilvus KCTC 49020	GCA_003047285	contig	GenBank	2072017 tax ID	*
[Ref.: #66792]	Nocardioides sp. KCTC 49020	2144186.3	wgs	PATRIC	2072017 tax ID	*
[Ref.: #66792]	Nocardioides allogilvus KCTC 49020	2855286858	draft	JGI IMG/M	2072017 tax ID	*

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GC-content

69.90 mol%

genome sequence analysis

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: Nocardioides sp. KCTC 49020 PATRIC: 2144186.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides sp. KCTC 49020 PATRIC: 2144186.3
[Ref.: #69480]	motile	no	96.299	yes
[Ref.: #69480]	gram-positive	yes	90.173	yes
[Ref.: #69480]	anaerobic	no	98.208	yes
[Ref.: #69480]	aerobic	yes	91.031	yes
[Ref.: #69480]	halophile	no	90.832	no
[Ref.: #69480]	spore-forming	no	84.637	no
[Ref.: #69480]	glucose-util	yes	90.11	no
[Ref.: #69480]	flagellated	no	97.682	yes
[Ref.: #69480]	thermophile	no	97.758	no
[Ref.: #69480]	glucose-ferment	no	90.674	no

Availability in culture collections External links

[Ref.: #66607]

Culture collection no.

KCTC 49020, CGMCC 4.7457, CFH 30205

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave.	Zhang LY, Ming H, Zhao ZL, Ji WL, Salam N, Jiao JY, Fang BZ, Li WJ, Nie GX	Int J Syst Evol Microbiol	10.1099/ijsem.0.002863	2018	*
Phylogeny	Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish).	Hyun DW, Jeong YS, Lee JY, Sung H, Lee SY, Choi JW, Kim HS, Kim PS, Bae JW	J Microbiol	10.1007/s12275-021-1036-5	2021	*

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 )

#66607

Ling-Yu Zhang, Hong Ming, Zhuo-Li Zhao, Wei-Li Ji, Nimaichand Salam, Jian-Yu Jiao, Bao-Zhu Fang, Wen-Jun Li and Guo-Xing Nie: Nocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave. IJSEM 68: 2485 - 2490 2018 ( DOI 10.1099/ijsem.0.002863 , PubMed 29927366 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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Nocardioides sp. KCTC 49020

Nocardioides sp. KCTC 49020

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