Limnochorda pilosa (DSM 28787, NBRC 110152, HC45)

Name: Limnochorda pilosa (DSM 28787, NBRC 110152, HC45)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131397

Type strain

Strain Designation HC45

Culture col. no. DSM 28787 NBRC 110152 HC45

NCBI tax ID(s) 1555112

Special Collections DSMZ

Links

Limnochorda pilosa HC45 is an anaerobe, thermophilic prokaryote that was isolated from meromictic lake sediment.

anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 399467

NBRC 110152,DSM 28787

@ref 20215

Last LPSN update 2025-12-16 10:01:14

Domain Bacillati

Phylum Bacillota

Class Limnochordia

Order Limnochordales

Family Limnochordaceae

Genus Limnochorda

Species Limnochorda pilosa

Full scientific name Limnochorda pilosa Watanabe et al. 2015

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22624	DESULFOBACTER CURVATUS MEDIUM (DSMZ Medium 195)		Medium recipe at MediaDive	Name: DESULFOBACTER CURVATUS MEDIUM (DSMZ Medium 195) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-acetate x 3 H2O 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 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 p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 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 (°C)	Range
22624	positive	growth	45	thermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
22624	anaerobe
125439	facultative anaerobe	91.3

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22624	meromictic lake sediment	Hokkaido, Kushiro, Lake Harutori	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22624	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM154401v1 assembly for Limnochorda pilosa HC45	complete	GCA_001544015	1555112.8	2687453276	1555112	97.39

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22624	Limnochorda pilosa gene for 16S rRNA, partial sequence	AB992259	1461		1555112

GC content

@ref	GC-content (mol%)	Method
22624	71	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Limnochorda pilosa HC45
IMG: 2687453276

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	83.60	no
125439	motility	BacteriaNetⓘ	yes	57.90	no
125439	gram_stain	BacteriaNetⓘ	negative	86.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Limnochorda pilosa HC45
NCBI: GCA_001544015.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	69.19	no
125438	anaerobic	anaerobicⓘ	no	68.16	no
125438	aerobic	aerobicⓘ	no	59.21	yes
125438	spore-forming	spore-formingⓘ	yes	62.72	no
125438	thermophilic	thermophileⓘ	yes	53.27	no
125438	flagellated	motile2+ⓘ	yes	57.43	no

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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Limnochorda pilosa (DSM 28787, NBRC 110152, HC45)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001544015

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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