Name: Herbinix luporum SD1D
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132646

Type strain:

Species: Herbinix luporum

Strain Designation: SD1D

Culture col. no.: DSM 100831, CECT 8959

Strain history: <- D. Köck, TU Munich, Freising-Weihenstephan, Germany; SD1D <- D. Köck {2014}

NCBI tax ID(s): 1679721 (species)

SI-ID 402175

DSM 100831

Section

Herbinix luporum SD1D is an anaerobe, thermophilic, Gram-positive bacterium that forms circular colonies and was isolated from thermophilic biogas plant.

colony-forming
Gram-positive
anaerobe
thermophilic
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	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Herbinix*
	Species	**Herbinix luporum**
	Full Scientific Name (LPSN)	Herbinix luporum Koeck et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24929]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #24929]	Cell length	2.0-6.0 µm

[Ref.: #24929]	Cell width	0.5 µm

[Ref.: #24929]	Motility	no

[Ref.: #24929]	Colony size	2-5 mm
[Ref.: #24929]	Colony color	cream
[Ref.: #24929]	Colony shape	circular
[Ref.: #24929]	Cultivation medium used	solid GS2

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24929]

Culture medium

solid GS2

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Culture medium growth

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Culture medium

CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #24435]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24435]	growth	55 °C
[Ref.: #24929]	growth	40-65 °C
[Ref.: #24929]	optimum	55 °C

[Ref.: #24435]	Temperature range	thermophilic
[Ref.: #24929]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #24929]			optimum	7
[Ref.: #24929]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24929]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #24929]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	yes Confidence in %95.96

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24929]		NaCl		growth	0-4	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24929]	arabinose ChEBI	+	carbon source
[Ref.: #24929]	cellobiose ChEBI	+	carbon source
[Ref.: #24929]	cellulose ChEBI	+	carbon source
[Ref.: #24929]	citrate ChEBI	-	degradation
[Ref.: #24929]	fructose ChEBI	-	carbon source
[Ref.: #24929]	galactitol ChEBI	-	fermentation
[Ref.: #24929]	galactose ChEBI	+	carbon source
[Ref.: #24929]	glucose ChEBI	+	carbon source
[Ref.: #24929]	inulin ChEBI	-	carbon source
[Ref.: #24929]	lactose ChEBI	-	carbon source
[Ref.: #24929]	lactose ChEBI	-	fermentation
[Ref.: #24929]	mannose ChEBI	+	carbon source
[Ref.: #24929]	pectin ChEBI	-	carbon source
[Ref.: #24929]	sorbitol ChEBI	-	carbon source
[Ref.: #24929]	starch ChEBI	+	carbon source
[Ref.: #24929]	sucrose ChEBI	-	carbon source
[Ref.: #24929]	sulfate ChEBI	-	reduction
[Ref.: #24929]	tryptophan ChEBI	-	energy source
[Ref.: #24929]	urea ChEBI	-	degradation
[Ref.: #24929]	xylan ChEBI	-	carbon source
[Ref.: #24929]	xylose ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #24929]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #24929]		indole ChEBI	-

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #24929]		catalase	-	1.11.1.6
[Ref.: #24929]		tryptophan deaminase	-	4.1.99.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	purine metabolism	59.57	56 of 94
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	50	14 of 28
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	alanine metabolism	48.28	14 of 29
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[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]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	25	2 of 8
		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.: #24435]	Sample type/isolated from	thermophilic biogas plant
[Ref.: #24435]	Geographic location (country and/or sea, region)	Viersen (Mackenstein 3)
[Ref.: #24435]	Country	Germany
[Ref.: #24435]	Country ISO 3 Code	DEU
[Ref.: #24435]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Industrial	#Plant (Factory)
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

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

[Ref.: #24435]

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.: #24435]	Herbinix sp. SD1D partial 16S rRNA gene, isolate SD1D	LN626359	1354	ENA	1679721 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Herbinix luporum SD1D	GCA_900070325	complete	GenBank	1679721 tax ID	*
[Ref.: #66792]	Herbinix luporum SD1D	2757320858	complete	JGI IMG/M	1679721 tax ID	*

[Ref.: #24929]	GC-content	35.1 mol%	genome sequence analysis
[Ref.: #24435]	GC-content	35.1 mol%	sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Herbinix luporum SD1D NCBI: GCA_900070325.1
[Ref.: #69481]	spore-forming	yes	57	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Herbinix luporum SD1D NCBI: GCA_900070325.1
[Ref.: #69480]	flagellated	no	77.517	yes
[Ref.: #69480]	gram-positive	yes	88.378	yes
[Ref.: #69480]	anaerobic	yes	98.815	no
[Ref.: #69480]	aerobic	no	98.148	yes
[Ref.: #69480]	halophile	no	91.283	no
[Ref.: #69480]	spore-forming	yes	78.337	yes
[Ref.: #69480]	glucose-ferment	yes	71.079	no
[Ref.: #69480]	thermophile	yes	91.658	yes
[Ref.: #69480]	glucose-util	yes	86.965	no
[Ref.: #69480]	motile	yes	69.608	yes

Availability in culture collections External links

[Ref.: #24435]

Culture collection no.

DSM 100831, CECT 8959

[Ref.: #90959]

SI-ID 402175

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.	Koeck DE, Hahnke S, Zverlov VV	Int J Syst Evol Microbiol	10.1099/ijsem.0.001324	2016	*

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 )

#24435

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100831

#24929

D. E. H. Koeck, Sarah,Zverlov, Vladimir V.: Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor. IJSEM 66: 4132 - 4137 2016 ( DOI 10.1099/ijsem.0.001324 , PubMed 27453473 )

#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 )

#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 )

#90959

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-ID402175.1 )

* These data were automatically processed and therefore are not curated

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