Archive BacDiveID:10.13145/bacdive3815.20230509.8.1

Strain identifier

BacDive ID: 3815

Type strain:

Species: Runella slithyformis

Strain history: <- NCIMB <- J. M. Larkin, Louisiana State Univ.; LSU4

NCBI tax ID(s): 761193 (strain), 106 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 8198

BacDive-ID: 3815

DSM-Number: 19594

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Runella slithyformis DSM 19594 is a mesophilic bacterium that was isolated from Fresh water lake.

NCBI tax id

NCBI tax id	Matching level
106	species
761193	strain

strain history

@ref: 8198
history: <- NCIMB <- J. M. Larkin, Louisiana State Univ.; LSU4

doi: 10.13145/bacdive3815.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacteroidota
domain: Bacteria
phylum: Bacteroidota
class: Cytophagia
order: Cytophagales
family: Spirosomataceae
genus: Runella
species: Runella slithyformis
full scientific name: Runella slithyformis Larkin and Williams 1978 (Approved Lists 1980)

@ref: 8198

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Runella

species: Runella slithyformis

full scientific name: Runella slithyformis Larkin and Williams 1978 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	no	94.247
69480		99.999	negative

multimedia

@ref: 66793
multimedia content: EM_DSM_19594_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 8198
name: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7)
growth: yes
link: https://mediadive.dsmz.de/medium/7
composition: Name: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7) Composition: Agar 15.0 g/l Yeast extract 1.0 g/l Peptone 1.0 g/l Glucose 1.0 g/l Distilled water

culture temp

@ref: 8198
growth: positive
type: growth
temperature: 28
range: mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.537

Isolation, sampling and environmental information

isolation

@ref: 8198
sample type: Fresh water lake
geographic location: Louisiana, Baton Rouge
country: USA
origin.country: USA
continent: North America

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

taxonmaps

@ref: 69479
File name: preview.99_7156.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_516;96_3355;97_4114;98_5263;99_7156&stattab=map
Last taxonomy: Runella slithyformis subclade
16S sequence: NR_074339
Sequence Identity:
Total samples: 804
soil counts: 40
aquatic counts: 619
animal counts: 124
plant counts: 21

Safety information

risk assessment

@ref: 8198
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 8198
description: Runella slithyformis DSM 19594 16S ribosomal RNA, partial sequence
accession: NR_074339
length: 1493
database: nuccore
NCBI tax ID: 761193

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Runella slithyformis DSM 19594	GCA_000218895	complete	ncbi	761193
66792	Runella slithyformis DSM 19594	761193.13	plasmid	patric	761193
66792	Runella slithyformis DSM 19594	761193.10	plasmid	patric	761193
66792	Runella slithyformis DSM 19594	761193.12	plasmid	patric	761193
66792	Runella slithyformis DSM 19594	761193.11	plasmid	patric	761193
66792	Runella slithyformis DSM 19594	761193.14	plasmid	patric	761193
66792	Runella slithyformis DSM 19594	761193.3	complete	patric	761193
66792	Runella slithyformis LSU4, DSM 19594	2505679030	complete	img	761193

GC content

@ref: 8198
GC-content: 46.6
method: sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	93.869	no
flagellated	no	97.214	no
gram-positive	no	97.663	no
anaerobic	no	98.715	no
aerobic	yes	85.986	no
halophile	no	95.683	no
spore-forming	no	94.943	no
thermophile	no	96.719	yes
glucose-util	yes	86.248	no
glucose-ferment	no	87.531	no

External links

@ref: 8198

culture collection no.: DSM 19594, ATCC 29530, LMG 11500, NCIMB 11436, LSU 4

straininfo link

@ref: 73326
straininfo: 4937

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	17158973	Runella limosa sp. nov., isolated from activated sludge.	Ryu SH, Nguyen TTH, Park W, Kim CJ, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.64460-0	2006	Bacterial Typing Techniques, Cytophagaceae/chemistry/classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phosphorus/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/microbiology	Genetics
Genetics	22768358	Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)).	Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao OD, Goker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K	Stand Genomic Sci	10.4056/sigs.2475579	2012
Phylogeny	27902287	Runella palustris sp. nov., isolated from wetland freshwater.	Kim H, Kang H, Joung Y, Joh K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001692	2017	Bacterial Typing Techniques, Base Composition, Cytophagaceae/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Wetlands	Transcriptome
Phylogeny	30915611	Runella soli sp. nov., isolated from garden soil.	Chhetri G, Kim J, Kim I, Kim MK, Seo T	Antonie Van Leeuwenhoek	10.1007/s10482-019-01257-9	2019	Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytophagaceae/classification/genetics/isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gardens, Glycolipids/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology	Transcriptome
Phylogeny	31120415	Runella aurantiaca sp. nov., isolated from sludge of a manganese mine.	Yang X, Zhou Z, Liao S, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.003435	2019	Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Manganese, Mining, Phospholipids/chemistry, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Soil Microbiology	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
8198	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19594)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-19594
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
73326	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID4937.1	StrainInfo: A central database for resolving microbial strain identifiers