Archive BacDiveID:10.13145/bacdive24240.20230509.8.1

Strain identifier

BacDive ID: 24240

Type strain:

Species: Gordonia jinhuaensis

Strain history: W.-J. Li ZYR 51.

NCBI tax ID(s): 1517702 (species)

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

General

@ref: 20593

BacDive-ID: 24240

DSM-Number: 46760

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

description: Gordonia jinhuaensis DSM 46760 is a mesophilic bacterium that was isolated from pharmaceutical wastewater.

NCBI tax id

NCBI tax id: 1517702
Matching level: species

strain history

@ref	history
20593	<- W.-J. Li, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; ZYR 51 <- L.-X. Ding, Yunnan University, China
67770	W.-J. Li ZYR 51.

doi: 10.13145/bacdive24240.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Mycobacteriales
family: Gordoniaceae
genus: Gordonia
species: Gordonia jinhuaensis
full scientific name: Gordonia jinhuaensis Li et al. 2014

@ref: 20593

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia jinhuaensis

full scientific name: Gordonia jinhuaensis Li et al. 2014

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	no	97.404
69480		100	positive

Culture and growth conditions

culture medium

@ref: 20593
name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
growth: yes
link: https://mediadive.dsmz.de/medium/535
composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
20593	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	99
69480	no	99.99

observation

@ref: 67770
observation: quinones: MK-9(H₂)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
20593	pharmaceutical wastewater	Zhejiang Province, Jinhua City (E119.64°, N 29.12°)	China	CHN	Asia	29.12	119.64
67770	Pharmaceutical wastewater	Jinhua City, Zhejiang Province, eastern China	China	CHN	Asia

isolation source categories

Cat1: #Engineered
Cat2: #Waste
Cat3: #Industrial wastewater

Safety information

risk assessment

@ref: 20593
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20593
description: Gordonia jinhuaensis strain ZYR 51 16S ribosomal RNA gene, partial sequence
accession: KJ700483
length: 1524
database: ena
NCBI tax ID: 1517702

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Gordonia jinhuaensis CGMCC 1.12827	GCA_014639795	contig	ncbi	1517702
66792	Gordonia jinhuaensis strain CGMCC 1.12827	1517702.3	wgs	patric	1517702

GC content

@ref: 20593
GC-content: 67.7
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	99	no
motile	no	96.078	no
gram-positive	yes	91.263	no
anaerobic	no	99.411	no
aerobic	yes	86.254	no
halophile	no	85.441	no
spore-forming	no	88.389	no
glucose-util	yes	89.702	no
flagellated	no	98.888	no
thermophile	no	98.257	yes
glucose-ferment	no	89.22	no

External links

@ref: 20593

culture collection no.: DSM 46760, CGMCC 1.12827, NBRC 110001, NRRL B-59111, ZYR 51, JCM 30100

straininfo link

@ref: 88183
straininfo: 401216

literature

topic: Phylogeny
Pubmed-ID: 24912980
title: Gordonia jinhuaensis sp. nov., a novel actinobacterium, isolated from a VBNC (viable but non-culturable) state in pharmaceutical wastewater.
authors: Li SH, Jin Y, Cheng J, Park DJ, Kim CJ, Hozzein WN, Wadaan MA, Shu WS, Ding LX, Li WJ
journal: Antonie Van Leeuwenhoek
DOI: 10.1007/s10482-014-0207-3
year: 2014
mesh: Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid, Fatty Acids/analysis, Hydrogen-Ion Concentration, Industrial Waste, Microscopy, Electron, Scanning, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysis, Waste Water/*microbiology
topic2: Genetics

Reference

@id	authors	title	doi/url	catalogue
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
20593	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-46760	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46760)
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
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
88183	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-ID401216.1