Name: Methylomonas koyamae Fw12E-Y
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133754

Type strain:

Species: Methylomonas koyamae

Strain Designation: Fw12E-Y

Culture col. no.: JCM 16701, NBRC 105905, NCIMB 14606

Strain history: S. Asakawa Fw12E-Y.

NCBI tax ID(s): 1294261 (strain), 702114 (species)

SI-ID 380525

LMG 26899, JCM 16701, NBRC 105905, NCIMB 14606

Special Collections

Section

Methylomonas koyamae Fw12E-Y is a Gram-negative, motile, rod-shaped bacterium that was isolated from freshwater .

Gram-negative
motile
rod-shaped
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Methylococcales*
	Family	*Methylococcaceae*
	Genus	*Methylomonas*
	Species	**Methylomonas koyamae**
	Full Scientific Name (LPSN)	Methylomonas koyamae Ogiso et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30405]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.5

[Ref.: #30405]	Cell shape	rod-shaped

[Ref.: #30405]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30405]	growth	10-40 °C
[Ref.: #30405]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30405]			optimum	6.5
[Ref.: #30405]			growth	5.5-7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30405]		NaCl		growth	0-0.5	%
[Ref.: #30405]		NaCl		optimum	0.10	%

[Ref.: #67770]

Observation

quinones: MQ-8

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

[Ref.: #30405]	Sample type/isolated from	freshwater (river, lake, pond)

[Ref.: #67770]	Sample type/isolated from	Floodwater of a rice paddy field
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB538964 (>99% sequence identity) for Methylomonas koyamae subclade from Microbeatlas

Aquatic Samples	915
Soil Samples	294
Animal Samples	74
Plant Samples	75
Total Samples	1358

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.: #30405]	Methylomonas koyamae gene for 16S rRNA, partial sequence	AB538964	1458	GenBank ENA	1294261 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Methylomonas koyamae JCM 16701	GCA_001312005	contig	GenBank ENA	1294261 tax ID
[Ref.: #66792]	Methylomonas koyamae Fw12E-Y	GCA_019669905	complete	GenBank ENA	702114 tax ID	*
[Ref.: #66792]	Methylomonas koyamae JCM 16701	1294261.13	wgs	PATRIC	1294261 tax ID	*
[Ref.: #66792]	Methylomonas koyamae strain Fw12E-Y	702114.23	wgs	PATRIC	702114 tax ID	*
[Ref.: #66792]	Methylomonas koyamae JCM 16701	2728369704	draft	JGI IMG/M	1294261 tax ID	*

[Ref.: #30405]	GC-content	57.1 mol%
[Ref.: #67770]	GC-content	57.1 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methylomonas koyamae Fw12E-Y NCBI: GCA_019669905.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methylomonas koyamae Fw12E-Y NCBI: GCA_019669905.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	85.045	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	67.481	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.764	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.082	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	67.038	no

Availability in culture collections External links

[Ref.: #30405]

Culture collection no.

JCM 16701, NBRC 105905, NCIMB 14606

[Ref.: #91585]

SI-ID 380525

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field.	Ogiso T, Ueno C, Dianou D, Huy TV, Katayama A, Kimura M, Asakawa S	Int J Syst Evol Microbiol	10.1099/ijs.0.035261-0	2011	*
Phylogeny	Methylomonas rhizoryzae sp. nov., a type I methanotroph isolated from the rhizosphere soil of rice.	Zhu P, Cheng M, Pei D, Liu Y, Yan X	Antonie Van Leeuwenhoek	10.1007/s10482-020-01487-2	2020	*

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 )

#30405

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 #26742 (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;

#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 )

#91585

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-ID380525.1 )

#26742

IJSEM 1832 2012 ( DOI 10.1099/ijs.0.035261-0 , PubMed 21984674 )

* These data were automatically processed and therefore are not curated

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