Archive BacDiveID:10.13145/bacdive503.20230509.8.1

Strain identifier

BacDive ID: 503

Type strain:

Species: Leptolinea tardivitalis

Strain Designation: YMTK-2

Strain history: T. Yamada YMTK-2.

NCBI tax ID(s): 229920 (species)

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

General

@ref: 6508

BacDive-ID: 503

DSM-Number: 16556

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

description: Leptolinea tardivitalis YMTK-2 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sludge in a mesophilic UASB reactor.

NCBI tax id

NCBI tax id: 229920
Matching level: species

strain history

@ref	history
6508	<- T. Yamada, Nagaoka Univ. Technology, Japan; YMTK-2 <- T. Yamada {2001}
67770	T. Yamada YMTK-2.

doi: 10.13145/bacdive503.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/chloroflexota
domain: Bacteria
phylum: Chloroflexota
class: Anaerolineae
order: Anaerolineales
family: Anaerolineaceae
genus: Leptolinea
species: Leptolinea tardivitalis
full scientific name: Leptolinea tardivitalis Yamada et al. 2006

@ref: 6508

domain: Bacteria

phylum: Chloroflexi

class: Anaerolineae

order: Anaerolineales

family: Anaerolineaceae

genus: Leptolinea

species: Leptolinea tardivitalis

full scientific name: Leptolinea tardivitalis Yamada et al. 2006 emend. Nouioui et al. 2018

strain designation: YMTK-2

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
23356	negative	>100 µm	<0.2 µm	filament-shaped	no
69480	negative					99.756

colony morphology

@ref: 6508
incubation period: 8-14 days

Culture and growth conditions

culture medium

@ref: 6508
name: ANAEROLINEA MEDIUM (DSMZ Medium 1004)
growth: yes
link: https://mediadive.dsmz.de/medium/1004
composition: Name: ANAEROLINEA MEDIUM (DSMZ Medium 1004; with strain-specific modifications) Composition: NaHCO3 2.49252 g/l NH4Cl 0.538385 g/l Na2S x 9 H2O 0.249252 g/l L-Cysteine HCl x H2O 0.249252 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l KH2PO4 0.139581 g/l Yeast extract 0.0997009 g/l Na2-EDTA x 2 H2O 0.00518445 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
6508	positive	growth	37	mesophilic
23356	positive	maximum	50	thermophilic
23356	positive	minimum	25	mesophilic
23356	positive	optimum	37	mesophilic
67770	positive	growth	37	mesophilic

culture pH

@ref	ability	type	pH
23356	positive	minimum	6.0
23356	positive	maximum	7.2
23356	positive	optimum	7.0

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6508	anaerobe
23356	anaerobe
69480	anaerobe	99.503

spore formation

@ref	spore formation	confidence
23356	no
69481	no	100
69480	no	99.978

metabolite utilization

@ref: 23356
metabolite: yeast extract
utilization activity: +
kind of utilization tested: required for growth

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
6508	sludge in a mesophilic UASB reactor	Niigata, Nagaoka	Japan	JPN	Asia
23356	sludge in a mesophilic UASB reactor, in an artificial wastewater composed peptone, sucrose, propionate and acetate
67770	Granular sludge collected from a UASB reactor operated under a mesophilic condition (37C)

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Wastewater
#Environmental	#Terrestrial	#Mud (Sludge)

taxonmaps

@ref: 69479
File name: preview.99_5276.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_512;96_2562;97_3131;98_3933;99_5276&stattab=map
Last taxonomy: Leptolinea tardivitalis subclade
16S sequence: AB109438
Sequence Identity:
Total samples: 1360
soil counts: 375
aquatic counts: 836
animal counts: 53
plant counts: 96

Safety information

risk assessment

@ref: 6508
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6508
description: Leptolinea tardivitalis gene for 16S rRNA, partial sequence
accession: AB109438
length: 1426
database: ena
NCBI tax ID: 229920

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Leptolinea tardivitalis strain YMTK-2	229920.8	wgs	patric	229920
66792	Leptolinea tardivitalis strain YMTK-2	229920.7	wgs	patric	229920
67770	Leptolinea tardivitalis YMTK-2	GCA_001050275	contig	ncbi	229920
67770	Leptolinea tardivitalis YMTK-2	GCA_001306095	contig	ncbi	229920

GC content

@ref	GC-content	method
6508	48.2
23356	59.5	high performance liquid chromatography (HPLC)
67770	46.8	genome sequence analysis
67770	48.2	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	53.97	yes
gram-positive	no	94.869	yes
anaerobic	yes	95.502	yes
aerobic	no	95.908	yes
halophile	no	95.324	no
spore-forming	no	83.437	no
glucose-util	yes	79.603	no
flagellated	no	91.38	yes
thermophile	yes	77.293	no
glucose-ferment	no	64.78	no

External links

@ref: 6508

culture collection no.: DSM 16556, JCM 12579

straininfo link

@ref: 70182
straininfo: 297253

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	16738111	Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi.	Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64169-0	2006	Chloroflexi/*classification/genetics/growth & development/isolation & purification, Culture Media, Microscopy, Phase-Contrast, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics	Cultivation
Phylogeny	24215824	Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment.	Imachi H, Sakai S, Lipp JS, Miyazaki M, Saito Y, Yamanaka Y, Hinrichs KU, Inagaki F, Takai K	Int J Syst Evol Microbiol	10.1099/ijs.0.057547-0	2013	Bacterial Typing Techniques, Base Composition, Chloroflexi/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Japan, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Water Microbiology	Genetics
Genetics	26383658	Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Described as Members of the Class Anaerolineae (Chloroflexi).	Matsuura N, Tourlousse DM, Ohashi A, Hugenholtz P, Sekiguchi Y	Genome Announc	10.1128/genomeA.00975-15	2015
Genetics	26586893	Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae.	Ward LM, Hemp J, Pace LA, Fischer WW	Genome Announc	10.1128/genomeA.01356-15	2015

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
6508	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16556)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16556
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
23356	Takeshi Yamada, Yuji Sekiguchi, Satoshi Hanada, Hiroyuki Imachi, Akiyoshi Ohashi, Hideki Harada, Yoichi Kamagata		10.1099/ijs.0.64169-0	Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi	IJSEM 56: 1331-1340 2006	16738111
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)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
70182	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID297253.1	StrainInfo: A central database for resolving microbial strain identifiers