Name: Nocardioides pelophilus THG-T63
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158822

Type strain:

Species: Nocardioides pelophilus

Strain Designation: THG-T63

Culture col. no.: KACC 19192, CGMCC 4.7388

NCBI tax ID(s): 2172019 (species)

Section

Nocardioides pelophilus THG-T63 is an aerobe, Gram-positive, motile bacterium that forms circular colonies and was isolated from freshwater mud.

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

Information on morphological and physiological properties Morphology

[Ref.: #65586]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #65586]	Cell length	0.8-1.0 µm

[Ref.: #65586]	Cell width	0.4-0.6 µm

[Ref.: #65586]	Cell shape	rod-shaped

[Ref.: #65586]	Motility	yes

[Ref.: #65586]	Colony size	1-2 mm
[Ref.: #65586]	Colony color	white
[Ref.: #65586]	Colony shape	circular
[Ref.: #65586]	Incubation period	5 days
[Ref.: #65586]	Cultivation medium used	MA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65586]

Culture medium

Marine agar (MA)

[Ref.: #65586]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #65586]			growth	10-40 °C
[Ref.: #65586]			optimum	28-35 °C

[Ref.: #65586]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65586]			optimum	7
[Ref.: #65586]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65586]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.986
[Ref.: #69481]	Ability of spore formation	no Confidence in %95

[Ref.: #65586]

Halophily / tolerance level

slightly halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65586]		NaCl		growth	0-6	%
[Ref.: #65586]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65586]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #65586]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65586]	3-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #65586]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65586]	5-dehydro-D-gluconate ChEBI	+	assimilation
[Ref.: #65586]	adipate ChEBI	-	assimilation
[Ref.: #65586]	casein	+	hydrolysis
[Ref.: #65586]	cellulose ChEBI	+	hydrolysis
[Ref.: #65586]	chitin ChEBI	-	hydrolysis
[Ref.: #65586]	citrate ChEBI	-	assimilation
[Ref.: #65586]	D-glucose ChEBI	+	assimilation
[Ref.: #65586]	D-mannitol ChEBI	-	assimilation
[Ref.: #65586]	D-mannose ChEBI	-	assimilation
[Ref.: #65586]	D-ribose ChEBI	+	assimilation
[Ref.: #65586]	D-sorbitol ChEBI	-	assimilation
[Ref.: #65586]	dna ChEBI	-	hydrolysis
[Ref.: #65586]	gluconate ChEBI	+	assimilation
[Ref.: #65586]	glucose ChEBI	+	builds acid from
[Ref.: #65586]	glycogen ChEBI	+	assimilation
[Ref.: #65586]	itaconate ChEBI	-	assimilation
[Ref.: #65586]	L-alanine ChEBI	+	assimilation
[Ref.: #65586]	L-arabinose ChEBI	-	assimilation
[Ref.: #65586]	L-fucose ChEBI	+	assimilation
[Ref.: #65586]	L-histidine ChEBI	+	assimilation
[Ref.: #65586]	L-proline ChEBI	-	assimilation
[Ref.: #65586]	L-serine ChEBI	-	assimilation
[Ref.: #65586]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #65586]	lactate ChEBI	+	assimilation
[Ref.: #65586]	malate ChEBI	+	assimilation
[Ref.: #65586]	maltose ChEBI	-	assimilation
[Ref.: #65586]	melibiose ChEBI	-	assimilation
[Ref.: #65586]	myo-inositol ChEBI	+	assimilation
[Ref.: #65586]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #65586]	nitrate ChEBI	-	reduction
[Ref.: #65586]	phenylacetate ChEBI	-	assimilation
[Ref.: #65586]	propionate ChEBI	+	assimilation
[Ref.: #65586]	salicin ChEBI	-	assimilation
[Ref.: #65586]	sodium acetate ChEBI	+	assimilation
[Ref.: #65586]	sodium citrate ChEBI	-	assimilation
[Ref.: #65586]	sodium malonate ChEBI	+	assimilation
[Ref.: #65586]	starch ChEBI	+	hydrolysis
[Ref.: #65586]	suberic acid ChEBI	+	assimilation
[Ref.: #65586]	sucrose ChEBI	+	assimilation
[Ref.: #65586]	tween 20 ChEBI	-	hydrolysis
[Ref.: #65586]	tween 80 ChEBI	-	hydrolysis
[Ref.: #65586]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65586]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65586]	acid phosphatase	+	3.1.3.2
[Ref.: #65586]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65586]	alpha-chymotrypsin	+/-	3.4.21.1
[Ref.: #65586]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65586]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65586]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65586]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65586]	arginine dihydrolase	+	3.5.3.6
[Ref.: #65586]	beta-galactosidase	+	3.2.1.23
[Ref.: #65586]	beta-glucosidase	+	3.2.1.21
[Ref.: #65586]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65586]	cystine arylamidase	+	3.4.11.3
[Ref.: #65586]	esterase (C 4)	+
[Ref.: #65586]	esterase Lipase (C 8)	+
[Ref.: #65586]	leucine arylamidase	+	3.4.11.1
[Ref.: #65586]	lipase (C 14)	-
[Ref.: #65586]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65586]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65586]	protease	+
[Ref.: #65586]	trypsin	+	3.4.21.4
[Ref.: #65586]	urease	+	3.5.1.5
[Ref.: #65586]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65586]

Fatty acid	Percentage
C16:0 iso	31.2
C18:1ω9c	20.4
C17:1ω8c	15.6
10-methyl C18:0	10.5
C17:1ω6c	6.5
C16:0	5.3
10-methyl C17:0	2.4
C15:0 iso	1.6
C16:0 2OH	1.6
C16:1ω7c / C15:0 iso 2OH	1.5
C17:0	1.2
C17:0 iso	1.1

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

[Ref.: #65586]	Sample type/isolated from	freshwater mud
[Ref.: #65586]	Sampling date	2015-10-5
[Ref.: #65586]	Geographic location (country and/or sea, region)	Kyung Hee University, Yongin
[Ref.: #65586]	Country	Republic of Korea
[Ref.: #65586]	Country ISO 3 Code	KOR
[Ref.: #65586]	Continent	Asia
[Ref.: #65586]	Geographic location	37.2758°/127.1780°
[Ref.: #65586]	Enrichment culture	MA
[Ref.: #65586]	Enrichment culture duration	7 days
[Ref.: #65586]	Enrichment culture temperature	30 ̊C
[Ref.: #65586]	Isolation/enrichment procedure	1 g of the mud sample was thoroughly suspended in 9 ml 0.85 %(w/v) NaCl solution and mixed in a shaker for 30 min. Aliquots of the serially diluted sample were spread on MA plates
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Mud (Sludge)

What are isolation sources categories?

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.: #65586]	16S rRNA gene sequence	KY287247		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides pelophilus CGMCC 4.7388	GCA_014180685	scaffold	GenBank	2172019 tax ID	*
[Ref.: #66792]	Nocardioides pelophilus strain CGMCC 4.7388	2172019.3	wgs	PATRIC	2172019 tax ID	*
[Ref.: #66792]	Nocardioides pelophilus CGMCC 4.7388	2921387157	draft	JGI IMG/M	2172019 tax ID	*

[Ref.: #65586]

GC-content

74.6 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: Nocardioides pelophilus CGMCC 4.7388 NCBI: GCA_014180685.1
[Ref.: #69481]	spore-forming	no	95	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides pelophilus CGMCC 4.7388 NCBI: GCA_014180685.1
[Ref.: #69480]	motile	no	78.512	no
[Ref.: #69480]	flagellated	no	93.504	no
[Ref.: #69480]	gram-positive	yes	82.704	no
[Ref.: #69480]	anaerobic	no	98.01	yes
[Ref.: #69480]	aerobic	yes	91.36	no
[Ref.: #69480]	halophile	no	96.846	no
[Ref.: #69480]	spore-forming	no	82.015	no
[Ref.: #69480]	glucose-util	yes	86.174	yes
[Ref.: #69480]	thermophile	no	97.474	yes
[Ref.: #69480]	glucose-ferment	no	88.911	no

Availability in culture collections External links

[Ref.: #65586]

Culture collection no.

KACC 19192, CGMCC 4.7388

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides pelophilus sp. nov., isolated from freshwater mud.	Yan ZF, Lin P, Li CT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002776	2018	*
Phylogeny	Nocardioides humilatus sp. nov., isolated from farmland soil in the Republic of Korea.	Lee JM, Jin CZ, Kang MK, Park SH, Park DJ, Kim DG, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004928	2022	*
Phylogeny	Nocardioides stalactiti sp. nov., isolated from a cave stalactite surface.	Zhou XK, Huang Y, Zhang TK, Liu JJ, Liu ZY, Zhu ML, Ma L, Liu T, Wang XJ, Mo MH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004636	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 )

#65586

Zheng-Fei Yan, Pei Lin, Chang-Tian Li, MooChang Kook and Tae-Hoo Yi: Nocardioides pelophilus sp. nov., isolated from freshwater mud. IJSEM 68: 1942 - 1948 2018 ( DOI 10.1099/ijsem.0.002776 , PubMed 29683418 )

#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) .

#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

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Nocardioides pelophilus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Nocardioides pelophilus CGMCC 4.7388

Nocardioides pelophilus CGMCC 4.7388

Change proposal

Change proposal