Archive BacDiveID:10.13145/bacdive505.20230509.8.1

Strain identifier

BacDive ID: 505

Type strain:

Species: Bellilinea caldifistulae

Strain Designation: GOMI-1

Strain history: T. Yamada GOMI-1.

NCBI tax ID(s): 360411 (species)

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

General

@ref: 7213

BacDive-ID: 505

DSM-Number: 17877

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative

description: Bellilinea caldifistulae GOMI-1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from thermophilic digester sludge.

NCBI tax id

NCBI tax id: 360411
Matching level: species

strain history

@ref	history
7213	<- T. Yamada, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan; GOMI-1 <- T. Yamada {2003}
67770	T. Yamada GOMI-1.

doi: 10.13145/bacdive505.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/chloroflexota
domain: Bacteria
phylum: Chloroflexota
class: Anaerolineae
order: Anaerolineales
family: Anaerolineaceae
genus: Bellilinea
species: Bellilinea caldifistulae
full scientific name: Bellilinea caldifistulae Yamada et al. 2007

@ref: 7213

domain: Bacteria

phylum: Chloroflexi

class: Anaerolineae

order: Anaerolineales

family: Anaerolineaceae

genus: Bellilinea

species: Bellilinea caldifistulae

full scientific name: Bellilinea caldifistulae Yamada et al. 2007 emend. Nouioui et al. 2018

strain designation: GOMI-1

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.806

pigmentation

@ref: 32190
production: no

Culture and growth conditions

culture medium

@ref: 7213
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
7213	positive	growth	55	thermophilic
32190	positive	growth	45-65	thermophilic
32190	positive	optimum	55	thermophilic
67770	positive	growth	55	thermophilic

culture pH

@ref	ability	type	pH
32190	positive	growth	6-7.5
32190	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
7213	anaerobe
32190	anaerobe
69480	anaerobe	93.253

spore formation

@ref	spore formation	confidence
32190	no
69481	no	100
69480	no	99.3

halophily

@ref	salt	growth	tested relation	concentration
32190	NaCl	positive	growth	0-0.5 %
32190	NaCl	positive	optimum	0.25 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
32190	22599	arabinose	+	carbon source
32190	28757	fructose	+	carbon source
32190	28260	galactose	+	carbon source
32190	17234	glucose	+	carbon source
32190	37684	mannose	+	carbon source
32190	16634	raffinose	+	carbon source
32190	33942	ribose	+	carbon source
32190	17992	sucrose	+	carbon source
32190	18222	xylose	+	carbon source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
7213	thermophilic digester sludge	Niigata, Nagaoka	Japan	JPN	Asia
67770	Thermophilic sludge digested sewage sludge and domestic garbage

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_5852.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_512;96_2807;97_3447;98_4353;99_5852&stattab=map
Last taxonomy: Bellilinea caldifistulae subclade
16S sequence: AB243672
Sequence Identity:
Total samples: 849
soil counts: 126
aquatic counts: 631
animal counts: 65
plant counts: 27

Safety information

risk assessment

@ref: 7213
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7213
description: Bellilinea caldifistulae gene for 16S rRNA, partial sequence
accession: AB243672
length: 1425
database: ena
NCBI tax ID: 360411

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Bellilinea caldifistulae strain GOMI-1	360411.11	wgs	patric	360411
66792	Bellilinea caldifistulae strain GOMI-1	360411.10	wgs	patric	360411
67770	Bellilinea caldifistulae GOMI-1	GCA_001050215	scaffold	ncbi	360411
67770	Bellilinea caldifistulae GOMI-1	GCA_001306055	contig	ncbi	360411

GC content

@ref	GC-content	method
7213	54.7
67770	54.7	high performance liquid chromatography (HPLC)
67770	52.8	genome sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
gram-positive	no	93.996	no
anaerobic	yes	91.27	yes
halophile	no	93.14	no
spore-forming	no	88.977	yes
glucose-util	yes	86.546	yes
motile	yes	55.157	no
flagellated	no	86.732	no
aerobic	no	93.668	yes
thermophile	yes	99.245	no
glucose-ferment	no	77.497	no

External links

@ref: 7213

culture collection no.: DSM 17877, JCM 13669

straininfo link

@ref: 70184
straininfo: 310966

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	17911301	Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia.	Yamada T, Imachi H, Ohashi A, Harada H, Hanada S, Kamagata Y, Sekiguchi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65098-0	2007	Anaerobiosis/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism/physiology, Chloroflexi/classification/cytology/isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion/physiology, Molecular Sequence Data, Phylogeny, Proteins/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/microbiology, Soil Microbiology, Temperature	Metabolism
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

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
7213	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17877)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17877
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
32190	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28432	28776041
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		33211880	Nucleic Acids Res. 49: D498-D508 2020
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
70184	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID310966.1	StrainInfo: A central database for resolving microbial strain identifiers