Name: Parvularcula lutaonensis CC-MMS-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133452

Type strain:

Species: Parvularcula lutaonensis

Strain Designation: CC-MMS-1

Culture col. no.: BCRC 17814, KCTC 22245

NCBI tax ID(s): 491923 (species)

Special Collections

Section

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Parvularcula lutaonensis CC-MMS-1 is an aerobe, Gram-negative, motile bacterium that was isolated from hot spring.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	"Parvularculales"
	Family	"Parvularculaceae"
	Genus	*Parvularcula*
	Species	**Parvularcula lutaonensis**
	Full Scientific Name (LPSN)	Parvularcula lutaonensis Arun et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29033]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %97
[Ref.: #125438]	Gram stain	negative Confidence in %96.796

[Ref.: #29033]	Cell length	2 µm

[Ref.: #29033]	Cell width	0.55 µm

[Ref.: #29033]	Cell shape	rod-shaped

[Ref.: #29033]	Motility	yes

[Ref.: #29033]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #29033]			growth	25-50 °C
[Ref.: #29033]			optimum	37 °C

	pH	Kind of pH		pH
[Ref.: #29033]			optimum	7
[Ref.: #29033]			growth	07-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29033]

Oxygen tolerance

aerobe

[Ref.: #29033]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.5
[Ref.: #125438]	Ability of spore formation	no Confidence in %90.392

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29033]		NaCl		optimum	3	%

[Ref.: #29033]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29033]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #29033]	cellobiose ChEBI	+	carbon source
[Ref.: #29033]	dextrin ChEBI	+	carbon source
[Ref.: #29033]	esculin ChEBI	+	hydrolysis
[Ref.: #29033]	fructose ChEBI	+	carbon source
[Ref.: #29033]	gluconate ChEBI	+	carbon source
[Ref.: #29033]	glucose ChEBI	+	carbon source
[Ref.: #29033]	glycerol ChEBI	+	carbon source
[Ref.: #29033]	glycogen ChEBI	+	carbon source
[Ref.: #29033]	lactate ChEBI	+	carbon source
[Ref.: #29033]	maltose ChEBI	+	carbon source
[Ref.: #29033]	mannitol ChEBI	+	carbon source
[Ref.: #29033]	mannose ChEBI	+	carbon source
[Ref.: #29033]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #29033]	sorbitol ChEBI	+	carbon source
[Ref.: #29033]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29033]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29033]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29033]	gelatinase	+

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

[Ref.: #29033]	Sample type/isolated from	hot spring
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU346850 (>99% sequence identity) for Parvularcula lutaonensis subclade from Microbeatlas

Aquatic Samples	247
Soil Samples	1
Animal Samples	6
Plant Samples
Total Samples	254

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.: #29033]	Parvularcula lutaonensis strain CC-MMS-1 16S ribosomal RNA gene, partial sequence	EU346850	1402	GenBank ENA	491923 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parvularcula lutaonensis KCTC 22245	GCA_014651915	scaffold	GenBank ENA	491923 tax ID	*
[Ref.: #66792]	Parvularcula lutaonensis strain KCTC 22245	491923.4	wgs	PATRIC	491923 tax ID	*

[Ref.: #29033]

GC-content

59 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: Parvularcula lutaonensis KCTC 22245 NCBI: GCA_014651915.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.796	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	91.259	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	85.304	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.392	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	90.219	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	65.249	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parvularcula lutaonensis KCTC 22245 NCBI: GCA_014651915
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	61.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	78.3

Availability in culture collections External links

[Ref.: #29033]

Culture collection no.

BCRC 17814, KCTC 22245

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parvularcula flava sp. nov., an alphaproteobacterium isolated from surface seawater of the South China Sea.	Zhang XQ, Wu YH, Zhou X, Zhang X, Xu XW, Wu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.001225	2016	*
Phylogeny	Parvularcula oceani [corrected] sp. nov., isolated from deep-sea water of the Southeastern Pacific Ocean.	Li S, Tang K, Liu K, Yu CP, Jiao N	Antonie Van Leeuwenhoek	10.1007/s10482-013-0071-6	2013	*
Phylogeny	Parvularcula dongshanensis sp. nov., isolated from soft coral.	Yu Z, Lai Q, Li G, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.044313-0	2012	*
Phylogeny	Parvularcula lutaonensis sp. nov., a moderately thermotolerant marine bacterium isolated from a coastal hot spring.	Arun AB, Chen WM, Lai WA, Chou JH, Rekha PD, Shen FT, Singh S, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.004481-0	2009	*

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 )

#29033

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 #25463 (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) .

#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 .

#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 .

#25463

IJSEM 998 2009 ( DOI 10.1099/ijs.0.004481-0 , PubMed 19406781 )

* These data were automatically processed and therefore are not curated

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Parvularcula lutaonensis KCTC 22245

Parvularcula lutaonensis KCTC 22245

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