Archive BacDiveID:10.13145/bacdive140789.20230509.8.1

Strain identifier

BacDive ID: 140789

Type strain:

Species: Paludihabitans psychrotolerans

Strain Designation: NC1253

Strain history: <- Yumei Dai, Chengdu Institute of Biology, Chinese Academy of Sciences

NCBI tax ID(s): 2038680 (species)

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

General

@ref: 64911

BacDive-ID: 140789

DSM-Number: 104738

keywords: 16S sequence, Bacteria, anaerobe, spore-forming, Gram-positive, rod-shaped

description: Paludihabitans psychrotolerans NC1253 is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from Zoige wetland soil.

NCBI tax id

NCBI tax id: 2038680
Matching level: species

strain history

@ref	history
64911	<- Y. Dai; Chinese Academy of Sciences, Chengdu, ; NC1253
67771	<- Yumei Dai, Chengdu Institute of Biology, Chinese Academy of Sciences

doi: 10.13145/bacdive140789.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Oscillospiraceae
genus: Paludihabitans
species: Paludihabitans psychrotolerans
full scientific name: Paludihabitans psychrotolerans (Li et al. 2017) Deshmukh and Oren 2023
synonyms
- @ref: 20215
- synonym: Paludicola psychrotolerans

@ref: 64911

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Oscillospiraceae

genus: Paludicola

species: Paludicola psychrotolerans

full scientific name: Paludicola psychrotolerans Li et al. 2017

strain designation: NC1253

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape
43567	positive	1-3 µm	0.3 µm	rod-shaped
67771				rod-shaped
67771	positive

colony morphology

@ref: 43567
colony color: White
medium used: MS agar

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
43567	MS agar	yes
64911	MINERAL SALT MEDIUM WITH COLLOIDAL CHITIN (DSMZ Medium 1681)	yes	https://mediadive.dsmz.de/medium/1681	Name: Mineral salt medium with colloidal chitin (DSMZ Medium 1681) Composition: Polypeptone 10.0 g/l Colloidal chitin 5.0 g/l NaHCO3 3.52 g/l Yeast extract 1.0 g/l KH2PO4 0.4 g/l K2HPO4 0.4 g/l NH4Cl 0.25 g/l MgCl2 x 6 H2O 0.2 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l Sodium resazurin 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l H3BO3 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l Riboflavin 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Thiamine HCl 5e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
43567	positive	growth	4-35
43567	positive	optimum	25-30	mesophilic
64911	positive	growth	28	mesophilic
67771	positive	growth	25-30	mesophilic

culture pH

@ref	ability	type	pH	PH range
43567	positive	growth	6-8.5	alkaliphile
43567	positive	optimum	7.5-8

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
43567	anaerobe
67771	anaerobe

spore formation

@ref	type of spore	spore formation
43567	endospore	yes
67771	spore	yes

halophily

@ref	salt	growth	tested relation	concentration
43567	NaCl	positive	growth	0-2 %(w/v)
43567	NaCl	positive	optimum	0-0.5 %(w/v)

metabolite utilization

@ref	metabolite	utilization activity	kind of utilization tested	Chebi-ID
43567	6-O-alpha-D-glucopyranosyl-D-gluconic acid	-	growth
43567	casein hydrolysate	-	growth
43567	cellobiose	-	growth	17057
43567	D-fucose	-	growth	28847
43567	D-galacturonic acid	-	growth	18024
43567	D-mannose	-	growth	16024
43567	glucose	-	growth	17234
43567	L-fucose	-	growth	18287
43567	L-rhamnose	-	growth	62345
43567	maltodextrin	-	growth	25140
43567	N-acetylglucosamine	-	growth	506227
43567	pyruvate	-	growth	15361
43567	chitin	+	carbon source	17029

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
43567	Zoige wetland soil	Qinghai-Tibetan Plateau	China	CHN	Asia	33.933	102.866
64911	wetland soil	eastern edge of Qinghai-Tibetan Plateau, Zoige Wetland (33° 56' N, 102° 52' E)	China	CHN	Asia	33.9333	102.867
67771	From soil	Zoige wetland, Chengdu Institute of Biology, Chinese Academy of Sciences(CAS)	China	CHN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Wetland (Swamp)

taxonmaps

@ref: 69479
File name: preview.99_139937.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_154;96_53824;97_69417;98_93043;99_139937&stattab=map
Last taxonomy: Paludicola psychrotolerans subclade
16S sequence: KY777734
Sequence Identity:
Total samples: 2715
soil counts: 139
aquatic counts: 422
animal counts: 2078
plant counts: 76

Safety information

risk assessment

@ref: 64911
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 64911
description: Paludicola psychrotolerans strain NC1253 16S ribosomal RNA gene, partial sequence
accession: KY777734
length: 1490
database: ena
NCBI tax ID: 2038680

GC content

@ref	GC-content	method
64911	35.4	high performance liquid chromatography (HPLC)
67771	35.4

External links

@ref: 64911

culture collection no.: KCTC 15582, DSM 104738

straininfo link

@ref: 96792
straininfo: 405356

literature

topic: Phylogeny
Pubmed-ID: 28901896
title: Paludicola psychrotolerans gen. nov., sp. nov., a novel psychrotolerant chitinolytic anaerobe of the family Ruminococcaceae.
authors: Li Y, Zhang LL, Liu L, Tian YQ, Liu XF, Li WJ, Dai YM
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijsem.0.002260
year: 2017
mesh: Bacterial Typing Techniques, Base Composition, China, Chitin/metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Wetlands
topic2: Transcriptome

Reference

@id	authors	title	doi/url	journal	pubmed	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
43567	Yan Li, Ling-Li Zhang, Lan Liu, Yong-Qiang Tian, Xiao-Feng Liu, Wen-Jun Li, Yu-Mei Dai	Paludicola psychrotolerans gen. nov., sp. nov., a novel psychrotolerant chitinolytic anaerobe of the family Ruminococcaceae	10.1099/ijsem.0.002260	IJSEM 67: 4100-4103 2017	28901896
64911	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-104738			Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104738)
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
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/
96792	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-ID405356.1

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

colony morphology

Culture and growth conditions

culture medium

culture temp

culture pH

Physiology and metabolism

oxygen tolerance

spore formation

halophily

metabolite utilization

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

GC content

External links

straininfo link

literature

Reference