Cite this strain

Methylomonas koyamae (JCM 16701, NBRC 105905, NCIMB 14606)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133754

Type strain

Strain Designation Fw12E-Y

Culture col. no. JCM 16701 NBRC 105905 NCIMB 14606 Fw12E-Y

NCBI tax ID(s) 1294261 702114

Special Collections JCM Literature strains

Links

Name and taxonomic classification

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

Gram-negative motile rod-shaped genome sequence 16S sequence Bacteria

SI-ID 380525

LMG 26899, JCM 16701, NBRC 105905, NCIMB 14606

Last LPSN update 2024-12-09 10:49:18

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Methylococcales

Family Methylococcaceae

Genus Methylomonas

Species Methylomonas koyamae

Full scientific name Methylomonas koyamae Ogiso et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell shape
30405	negative	rod-shaped
125438	negative
125439	negative

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30405	positive	growth	10-40
30405	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
30405	positive	optimum	6.5
30405	positive	growth	5.5-7

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30405	NaCl	positive	growth	0-0.5 %
30405	NaCl	positive	optimum	0.10 %

Observation

67770

Observationquinones: MQ-8

Spore formation

@ref	Spore formation	Confidence
125439		98.6

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	92.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type
30405	freshwater (river, lake, pond)
67770	Floodwater of a rice paddy field

Taxonmaps

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

Safety information

Sequence information

GC content

@ref	GC-content (mol%)
30405	57.1
67770	57.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30405	Methylomonas koyamae gene for 16S rRNA, partial sequence	AB538964	1458		1294261

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Methylomonas koyamae Fw12E-Y	GCA_019669905	complete		702114
66792	Methylomonas koyamae JCM 16701	1294261.13	wgs	PATRIC	1294261
66792	Methylomonas koyamae strain Fw12E-Y	702114.23	wgs	PATRIC	702114
66792	Methylomonas koyamae JCM 16701	2728369704	draft	JGI IMG/M	1294261
67770	Methylomonas koyamae JCM 16701	GCA_001312005	contig		1294261

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Methylomonas koyamae Fw12E-Y
NCBI: GCA_019669905

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	92.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	motility	BacteriaNetⓘ	yes	82.20	no
125439	spore_formation	BacteriaNetⓘ	no	98.60	no

Predictions from Diaspora project based on:
Methylomonas koyamae Fw12E-Y
NCBI: GCA_019669905.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	85.05	no
125438	aerobic	aerobicⓘ	yes	67.48	no
125438	spore-forming	spore-formingⓘ	no	87.76	no
125438	thermophilic	thermophileⓘ	no	95.08	no
125438	flagellated	motile2+ⓘ	yes	67.04	no

External links

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

Straininfo Link

@ref	Straininfo	Culture collections
91585	380525	LMG 26899, JCM 16701, NBRC 105905, NCIMB 14606

Culture collection no.

Culture collection no.
JCM 16701
NBRC 105905
NCIMB 14606
Fw12E-Y

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 .
#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 )
#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 .

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