Name: Anaerocolumna xylanovorans HESP1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2797

Type strain:

Species: Anaerocolumna xylanovorans

Strain Designation: HESP1

Culture col. no.: DSM 12503, JCM 31057

Strain history: DSM 12503 <-- J. L. Garcia; HESP1.

NCBI tax ID(s): 1121345 (strain), 100134 (species)

SI-ID 49306

DSM 12503

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Anaerocolumna xylanovorans HESP1 is an anaerobe, mesophilic bacterium that was isolated from anaerobic digester fed with olive mill wastewater.

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Anaerocolumna*
	Species	**Anaerocolumna xylanovorans**
	Full Scientific Name (LPSN)	Anaerocolumna xylanovorans (Mechichi et al. 2000) Ueki et al. 2016

Synonym

Clostridium xylanovorans

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4749]

Culture medium

ANAEROCOLUMNA MEDIUM (DSMZ Medium 860)

[Ref.: #4749]

Culture medium growth

[Ref.: #4749]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4749]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4749]			growth	35 °C
[Ref.: #67770]			growth	35 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4749]	Oxygen tolerance	anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %97.8

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	metabolism of amino sugars and derivatives	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin E metabolism	100	4 of 4
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[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]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #4749]	Sample type/isolated from	anaerobic digester fed with olive mill wastewater
[Ref.: #4749]	Geographic location (country and/or sea, region)	Sfax
[Ref.: #4749]	Country	Tunisia
[Ref.: #4749]	Country ISO 3 Code	TUN
[Ref.: #4749]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	Methanogenic digester
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Industrial	-
#Engineered	#Waste	#Industrial wastewater
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

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

[Ref.: #4749]

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.: #4749]	Clostridium xylanovorans 16S ribosomal RNA gene, partial sequence	AF116920	1533	GenBank ENA	100134 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Anaerocolumna xylanovorans DSM 12503	GCA_900143645	scaffold	GenBank ENA	1121345 tax ID
[Ref.: #66792]	Anaerocolumna cellulosilytica strain SN021	433286.4	complete	PATRIC	433286 tax ID	*
[Ref.: #66792]	Anaerocolumna xylanovorans DSM 12503	1121345.3	wgs	PATRIC	1121345 tax ID	*
[Ref.: #66792]	Anaerocolumna xylanovorans DSM 12503	2582580727	draft	JGI IMG/M	1121345 tax ID	*

[Ref.: #4749]	GC-content	40.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	40 mol%	high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Anaerocolumna cellulosilytica strain SN021 PATRIC: 433286.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	72.605	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	85.785	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	81.373	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	91.112	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.624	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	79.099	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Anaerocolumna xylanovorans DSM 12503 NCBI: GCA_900143645
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	97.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	85.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	82.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	78.5

Availability in culture collections External links

[Ref.: #4749]

Culture collection no.

DSM 12503, JCM 31057

[Ref.: #72323]

SI-ID 49306

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Descriptions of Anaerotaenia torta gen. nov., sp. nov. and Anaerocolumna cellulosilytica gen. nov., sp. nov. isolated from a methanogenic reactor of cattle waste and reclassification of Clostridium aminovalericum, Clostridium jejuense and Clostridium xylanovorans as Anaerocolumna species.	Ueki A, Ohtaki Y, Kaku N, Ueki K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001123	2016	*
Phylogeny	Characterization of a new xylanolytic bacterium, Clostridium xylanovorans sp. nov.	Mechichi T, Labat M, Garcia JL, Thomas P, Patel BK	Syst Appl Microbiol	10.1016/S0723-2020(99)80044-7	1999	*

References

#4749

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12503

#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 )

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#72323

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-ID49306.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Search for species Anaerocolumna xylanovorans in external resources:
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Anaerocolumna cellulosilytica strain SN021

Anaerocolumna xylanovorans DSM 12503

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