Archive BacDiveID:10.13145/bacdive504.20230509.8.1

Strain identifier

BacDive ID: 504

Type strain:

Species: Levilinea saccharolytica

Strain Designation: KIBI-1

Strain history: T. Yamada KIBI-1.

NCBI tax ID(s): 229921 (species)

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

General

@ref: 6507

BacDive-ID: 504

DSM-Number: 16555

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

description: Levilinea saccharolytica KIBI-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sludge in a mesophilic UASB reactor.

NCBI tax id

NCBI tax id: 229921
Matching level: species

strain history

@ref	history
6507	<- T. Yamada, Nagaoka Univ. Technology, Japan; KIBI-1 <- T. Yamada {2001}
67770	T. Yamada KIBI-1.

doi: 10.13145/bacdive504.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 6507

domain: Bacteria

phylum: Chloroflexi

class: Anaerolineae

order: Anaerolineales

family: Anaerolineaceae

genus: Levilinea

species: Levilinea saccharolytica

full scientific name: Levilinea saccharolytica Yamada et al. 2006

strain designation: KIBI-1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
23356	negative	>100 µm	0.4-0.5 µm	filament-shaped	no
69480					no	94.169
69480	negative					99.807

colony morphology

@ref: 6507
incubation period: 8-14 days

Culture and growth conditions

culture medium

@ref: 6507
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: Sucrose 7.17846 g/l 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 NaOH 0.000498504 g/l Sodium resazurin 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 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 Calcium D-(+)-pantothenate 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
6507	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
6507	anaerobe
23356	anaerobe
69480	anaerobe	94.234

spore formation

@ref	spore formation	confidence
23356	no
69481	no	99
69480	no	99.948

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
6507	sludge in a mesophilic UASB reactor	Niigata, Nagaoka	Japan	JPN	Asia
23356	sludge in a mesophilic UASB reactor, in sugar-manufacturing wastewater
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_5492.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_512;96_2656;97_3260;98_4100;99_5492&stattab=map
Last taxonomy: Levilinea saccharolytica subclade
16S sequence: AB109439
Sequence Identity:
Total samples: 6532
soil counts: 746
aquatic counts: 5334
animal counts: 302
plant counts: 150

Safety information

risk assessment

@ref: 6507
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6507
description: Levilinea saccharolytica gene for 16S rRNA, partial sequence
accession: AB109439
length: 1424
database: ena
NCBI tax ID: 229921

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Levilinea saccharolytica strain KIBI-1	229921.15	wgs	patric	229921
66792	Levilinea saccharolytica strain KIBI-1	229921.16	wgs	patric	229921
66792	Levilinea saccharolytica DSM 16555	2740892510	draft	img	229921
67770	Levilinea saccharolytica KIBI-1	GCA_001050255	scaffold	ncbi	229921
67770	Levilinea saccharolytica KIBI-1	GCA_001306035	contig	ncbi	229921

GC content

@ref	GC-content	method
6507	59.5
23356	48.2	high performance liquid chromatography (HPLC)
67770	59.5	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	99	no
motile	no	94.275	yes
gram-positive	no	94.891	yes
anaerobic	yes	91.437	yes
aerobic	no	89.881	no
halophile	no	92.055	no
spore-forming	no	93.544	no
glucose-util	yes	80.122	no
flagellated	no	98.164	no
thermophile	yes	65.33	no
glucose-ferment	no	74.707	no

External links

@ref: 6507

culture collection no.: DSM 16555, JCM 12578

straininfo link

@ref: 70183
straininfo: 297234

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	22328612	Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae.	Podosokorskaya OA, Bonch-Osmolovskaya EA, Novikov AA, Kolganova TV, Kublanov IV	Int J Syst Evol Microbiol	10.1099/ijs.0.041012-0	2012	Bacterial Typing Techniques, Base Composition, Cellulose/metabolism, Chloroflexi/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fermentation, Hot Temperature, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, *Water Microbiology	Stress
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	26586894	Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the Chloroflexi Class Anaerolineae.	Hemp J, Ward LM, Pace LA, Fischer WW	Genome Announc	10.1128/genomeA.01357-15	2015

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
6507	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16555)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16555
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
70183	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID297234.1	StrainInfo: A central database for resolving microbial strain identifiers