Name: Mycobacterium paragordonae 49061
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134025

Type strain:

Species: Mycobacterium paragordonae

Strain Designation: 49061

Culture col. no.: JCM 18565, KCTC 29126T, KCTC 29126

Strain history: B.-J. Kim; Seoul Natl. Univ. Coll. of Med., South Korea; 49061.

NCBI tax ID(s): 1389713 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Mycobacterium paragordonae 49061 is a mesophilic, rod-shaped bacterium that was isolated from human - mouth.

rod-shaped
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	*Mycobacteriales*
	Family	*Mycobacteriaceae*
	Genus	*Mycobacterium*
	Species	**Mycobacterium paragordonae**
	Full Scientific Name (LPSN)	Mycobacterium paragordonae Kim et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %94.9
[Ref.: #125438]	Gram stain	positive Confidence in %90.161

[Ref.: #31080]	Cell shape	rod-shaped

[Ref.: #31080]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #31080]			growth	25-30 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

aerobe Confidence in %94.5

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31080]		tween 80 ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #31080]	arylsulfatase	+	3.1.6.1
[Ref.: #31080]	catalase	+	1.11.1.6
[Ref.: #31080]	urease	+	3.5.1.5

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

[Ref.: #31080]	Sample type/isolated from	human - mouth

[Ref.: #67770]	Sample type/isolated from	Sputum of a patient with a symptomatic pulmonary infection
[Ref.: #67770]	Geographic location (country and/or sea, region)	Seoul
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Mouth

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.: #31080]	Mycobacterium paragordonae strain 49061 16S ribosomal RNA gene, partial sequence	KC525204	1393	GenBank ENA	1389713 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Mycobacterium paragordonae 49061	GCA_003614435	complete	GenBank ENA	1389713 tax ID	*
[Ref.: #66792]	Mycobacterium paragordonae JCM 18565	GCA_010723415	scaffold	GenBank ENA	1389713 tax ID	*
[Ref.: #66792]	Mycobacterium paragordonae strain JCM 18565	1389713.13	wgs	PATRIC	1389713 tax ID	*
[Ref.: #66792]	Mycobacterium paragordonae 49061	2923207141	complete	JGI IMG/M	1389713 tax ID	*

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: Mycobacterium paragordonae 49061 NCBI: GCA_003614435.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	90.161	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.109	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	73.499	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	60.028	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium paragordonae 49061 IMG: 2923207141
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	54.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	84.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	94.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	94.5

Availability in culture collections External links

[Ref.: #31080]

Culture collection no.

JCM 18565, KCTC 29126T, KCTC 29126

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Mycobacterium paragordonae sp. nov., a slowly growing, scotochromogenic species closely related to Mycobacterium gordonae.	Kim BJ, Hong SH, Kook YH, Kim BJ	Int J Syst Evol Microbiol	10.1099/ijs.0.051540-0	2013	*

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 )

#31080

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 #27409 (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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#27409

IJSEM 39 2014 ( DOI 10.1099/ijs.0.051540-0 , PubMed 24006480 )

* These data were automatically processed and therefore are not curated

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