Name: Limnochorda pilosa HC45
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131397

Type strain:

Species: Limnochorda pilosa

Strain Designation: HC45

Culture col. no.: DSM 28787, NBRC 110152

Strain history: <- M. Watanabe, Inst. Low Temperature Sci., Hokkaido Univ., Sapporo, Japan; HC45

NCBI tax ID(s): 1555112 (species)

SI-ID 399467

DSM 28787

Special Collections

DSMZ

Section

Limnochorda pilosa HC45 is an anaerobe bacterium that was isolated from meromictic lake sediment.

anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Limnochordia*
	Order	*Limnochordales*
	Family	*Limnochordaceae*
	Genus	*Limnochorda*
	Species	**Limnochorda pilosa**
	Full Scientific Name (LPSN)	Limnochorda pilosa Watanabe et al. 2015

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22624]

Culture medium

DESULFOBACTER MEDIUM (DSMZ Medium 195)

[Ref.: #22624]

Culture medium growth

[Ref.: #22624]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22624]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22624]			growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #22624]

Oxygen tolerance

anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	benzoyl-CoA degradation	57.14	4 of 7
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	ubiquinone biosynthesis	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #22624]	Sample type/isolated from	meromictic lake sediment
[Ref.: #22624]	Geographic location (country and/or sea, region)	Hokkaido, Kushiro, Lake Harutori
[Ref.: #22624]	Country	Japan
[Ref.: #22624]	Country ISO 3 Code	JPN
[Ref.: #22624]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB992259 (>99% sequence identity) for Limnochorda pilosa subclade from Microbeatlas

Aquatic Samples	134
Soil Samples	70
Animal Samples	390
Plant Samples	36
Total Samples	630

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #22624]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #22624]	Limnochorda pilosa gene for 16S rRNA, partial sequence	AB992259	1461	GenBank ENA	1555112 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Limnochorda pilosa HC45	GCA_001544015	complete	GenBank ENA	1555112 tax ID	*
[Ref.: #66792]	Limnochorda pilosa HC45	2687453276	complete	JGI IMG/M	1555112 tax ID	*

[Ref.: #22624]

GC-content

71 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Limnochorda pilosa HC45 NCBI: GCA_001544015.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	51	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Limnochorda pilosa HC45 NCBI: GCA_001544015.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	69.193	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	68.163	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	59.212	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	62.72	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	53.269	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	57.431	no

Availability in culture collections External links

[Ref.: #22624]

Culture collection no.

DSM 28787, NBRC 110152

[Ref.: #89830]

SI-ID 399467

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Limnochorda pilosa gen. nov., sp. nov., a moderately thermophilic, facultatively anaerobic, pleomorphic bacterium and proposal of Limnochordaceae fam. nov., Limnochordales ord. nov. and Limnochordia classis nov. in the phylum Firmicutes.	Watanabe M, Kojima H, Fukui M	Int J Syst Evol Microbiol	10.1099/ijs.0.000267	2015	*

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#22624

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28787

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#89830

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 . ( DOI 10.60712/SI-ID399467.1 )

* These data were automatically processed and therefore are not curated

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