Methylopila capsulata (DSM 6130, VKM B-1606)

Name: Methylopila capsulata (DSM 6130, VKM B-1606)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7222

Type strain

Culture col. no. DSM 6130 VKM B-1606

NCBI tax ID(s) 61654

Special Collections DSMZ

Links

Methylopila capsulata DSM 6130 is a mesophilic prokaryote that was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 44100

ATCC 700716,VKM B-1606,DSM 6130,NCIMB 13895

@ref 20215

Last LPSN update 2025-12-16 09:48:31

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylocystaceae

Genus Methylopila

Species Methylopila capsulata

Full scientific name Methylopila capsulata Doronina et al. 1998

BacDive ID	Other strains from **Methylopila capsulata** (1)	Type strain
7223	M. capsulata R2L2, DSM 16542

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.2
125438	negative	98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2496	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Methanol 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2496	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.7

Spore formation

@ref	Spore formation	Confidence
125439		97.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2496	soil	Uzbekistan, Tashkent	USSR	UZB	Asia

Taxonmaps

69479

Global distribution of 16S sequence AF004844 (>99% sequence identity) for Methylopila from Microbeatlas

Aquatic Samples	89
Soil Samples	79
Animal Samples	81
Plant Samples	25
Total Samples	274

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2496	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1690797v1 assembly for Methylopila capsulata DSM 6130	contig	GCA_016907975	61654.3	2901030786	61654	74.95
124043	ASM2792220v1 assembly for Methylopila capsulata VKM B-1606	contig	GCA_027922205	61654.5	8118446543	61654	73.39

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Methylopila capsulata strain IM1 16S ribosomal RNA gene, partial sequence	AF004844	1331		61654
124043	Methylopila capsulata strain VKM B-1606 16S ribosomal RNA gene, partial sequence.	MT760664	1317		61654

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methylopila capsulata DSM 6130
NCBI: GCA_016907975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.60	no
125439	motility	BacteriaNetⓘ	yes	65.10	no
125439	gram_stain	BacteriaNetⓘ	negative	95.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylopila capsulata strain DSM 6130
PATRIC: 61654.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	95.60	no
125438	spore-forming	spore-formingⓘ	no	88.32	no
125438	aerobic	aerobicⓘ	yes	86.40	no
125438	thermophilic	thermophileⓘ	no	98.77	no
125438	flagellated	motile2+ⓘ	yes	66.59	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Diversity of Methylobacterium species associated with New Zealand native plants.	Jahan R, McDonald IR.	FEMS Microbiol Lett	10.1093/femsle/fnad124	2023
Metabolism	Degradation of simazine by microorganisms isolated from soils of Spanish olive fields.	Santiago-Mora R, Martin-Laurent F, de Prado R, Franco AR.	Pest Manag Sci	10.1002/ps.1097	2005
Metabolism	Isolation and taxonomic affiliation of N-heterocyclic aromatic hydrocarbon-transforming bacteria.	Willumsen PA, Johansen JE, Karlson U, Hansen BM.	Appl Microbiol Biotechnol	10.1007/s00253-004-1799-8	2005
Phylogeny	Methylopila capsulata gen. nov., sp. nov., a novel non-pigmented aerobic facultatively methylotrophic bacterium.	Doronina NV, Trotsenko YA, Krausova VI, Boulygina ES, Tourova TP	Int J Syst Bacteriol	10.1099/00207713-48-4-1313	1998

References

#2496	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6130
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Methylopila capsulata (DSM 6130, VKM B-1606)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016907975

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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