Archive BacDiveID:10.13145/bacdive24739.20230509.8.1

Strain identifier

BacDive ID: 24739

Type strain:

Species: Gracilimonas mengyeensis

Strain history: <- X.-L. Cui, YIM; YIM J14 <- J.-H. Liu and Y.-X. Wang

NCBI tax ID(s): 1302730 (species)

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

General

@ref: 21195

BacDive-ID: 24739

DSM-Number: 21985

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Gracilimonas mengyeensis DSM 21985 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sediment from a salt mine.

NCBI tax id

NCBI tax id: 1302730
Matching level: species

strain history

@ref: 21195
history: <- X.-L. Cui, YIM; YIM J14 <- J.-H. Liu and Y.-X. Wang

doi: 10.13145/bacdive24739.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/balneolota
domain: Bacteria
phylum: Balneolota
class: Balneolia
order: Balneolales
family: Balneolaceae
genus: Gracilimonas
species: Gracilimonas mengyeensis
full scientific name: Gracilimonas mengyeensis Wang et al. 2013

@ref: 21195

domain: Bacteria

phylum: Balneolaeota

class: Balneolia

order: Sphingobacteriales

family: Balneolaceae

genus: Gracilimonas

species: Gracilimonas mengyeensis

full scientific name: Gracilimonas mengyeensis Wang et al. 2013

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31097	negative	7.25 µm	0.4 µm	rod-shaped	no
69480	negative					99.996

pigmentation

@ref: 31097
production: yes

Culture and growth conditions

culture medium

@ref: 21195
name: MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)
growth: yes
link: https://mediadive.dsmz.de/medium/514b
composition: Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
21195	positive	growth	28	mesophilic
31097	positive	growth	20-37
31097	positive	optimum	28	mesophilic

culture pH

@ref	ability	type	pH
31097	positive	growth	6.5-8.0
31097	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref: 31097
oxygen tolerance: facultative anaerobe

spore formation

@ref	spore formation	confidence
31097	no
69481	no	100
69480	no	99.98

halophily

@ref	salt	growth	tested relation	concentration
31097	NaCl	positive	growth	02-15 %
31097	NaCl	positive	optimum	6.5 %

observation

@ref: 31097
observation: aggregates in clumps

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31097	23652	dextrin	+	carbon source
31097	28260	galactose	+	carbon source
31097	17234	glucose	+	carbon source
31097	17754	glycerol	+	carbon source
31097	17716	lactose	+	carbon source
31097	17306	maltose	+	carbon source
31097	30911	sorbitol	+	carbon source
31097	17992	sucrose	+	carbon source
31097	18222	xylose	+	carbon source
31097	4853	esculin	+	hydrolysis
31097	17632	nitrate	+	reduction

enzymes

@ref	value	activity	ec
31097	acid phosphatase	+	3.1.3.2
31097	alkaline phosphatase	+	3.1.3.1
31097	alpha-galactosidase	+	3.2.1.22
31097	catalase	+	1.11.1.6
31097	cytochrome oxidase	+	1.9.3.1
31097	urease	+	3.5.1.5

Isolation, sampling and environmental information

isolation

@ref: 21195
sample type: sediment from a salt mine
geographic location: Yunnan Province, Mengye salt mine (22° 71' N 101° 63' E)
country: China
origin.country: CHN
continent: Asia
latitude: 23.1833
longitude: 102.05

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Condition	#Saline
#Environmental	#Terrestrial	#Sediment
#Environmental	#Terrestrial	#Geologic

taxonmaps

@ref: 69479
File name: preview.99_32096.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_471;96_3029;97_19094;98_23817;99_32096&stattab=map
Last taxonomy: Gracilimonas mengyeensis subclade
16S sequence: KC561141
Sequence Identity:
Total samples: 91
soil counts: 11
aquatic counts: 80

Safety information

risk assessment

@ref: 21195
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 21195
description: Gracilimonas mengyeensis strain YIM J14 16S ribosomal RNA gene, partial sequence
accession: KC561141
length: 1396
database: ena
NCBI tax ID: 1302730

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Gracilimonas mengyeensis DSM 21985	GCA_900182705	contig	ncbi	1302730
66792	Gracilimonas mengyeensis strain DSM 21985	1302730.3	wgs	patric	1302730
66792	Gracilimonas mengyeensis DSM 21985	2724679790	draft	img	1302730

GC content

@ref	GC-content	method
21195	47.2	high performance liquid chromatography (HPLC)
31097	47.2

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	57.471	no
gram-positive	no	97.575	yes
anaerobic	no	98.186	yes
halophile	yes	86.861	yes
spore-forming	no	92.235	yes
thermophile	no	89.867	yes
glucose-util	yes	89.401	yes
aerobic	yes	79.102	no
flagellated	no	85.224	no
glucose-ferment	no	67.011	no

External links

@ref: 21195

culture collection no.: DSM 21985, ACCC 10717, YIM J14

straininfo link

@ref: 88567
straininfo: 406532

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	23710054	Gracilimonas mengyeensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-western China.	Wang YX, Li YP, Liu JH, Xiao W, Lai YH, Li ZY, Ding ZG, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.052043-0	2013	Bacterial Typing Techniques, Bacteroidetes/classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride	Genetics
Phylogeny	28109207	Rhodohalobacter halophilus gen. nov., sp. nov., a moderately halophilic member of the family Balneolaceae.	Xia J, Xie ZH, Dunlap CA, Rooney AP, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001806	2017	Bacterial Typing Techniques, Bacteroidetes/classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology	Transcriptome
Phylogeny	29611802	Gracilimonas amylolytica sp. nov., isolated from deep-sea sediment.	Wu YH, Yan J, Fang C, Huo YY, Ma WL, Zhang DM, Wang CS, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002734	2018	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Gram-Negative Aerobic Rods and Cocci/classification/genetics/isolation & purification, Pacific Ocean, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry	Transcriptome

Reference

@id	authors	title	doi/url	catalogue	ID_cross_reference	pubmed	journal
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	10.1099/ijsem.0.004332
21195	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-21985	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21985)
31097	Barberan A, Caceres Velazquez H, Jones S, Fierer N.	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	10.1128/mSphere.00237-17		27426	28776041
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)	https://diaspora-project.de/progress.html#genomes
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	10.1093/nar/gkaa1025			33211880	Nucleic Acids Res. 49: D498-D508 2020
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	https://microbeatlas.org/
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)	https://diaspora-project.de/progress.html#genomes
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch	Predictions based on the model GenomeNet Sporulation v. 1	10.21203/rs.3.rs-2527258/v1
88567	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	10.60712/SI-ID406532.1