Anaerocolumna xylanovorans (DSM 12503, JCM 31057, HESP1)

Name: Anaerocolumna xylanovorans (DSM 12503, JCM 31057, HESP1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2797

Type strain

Strain Designation HESP1

Culture col. no. DSM 12503 JCM 31057 HESP1

NCBI tax ID(s) 1121345 100134

Special Collections DSMZ JCM

History <- J. L. Garcia, Université de Provence, Marseille, France; HESP1 <- T. Mechichi {1998} DSM 12503 <-- J. L. Garcia; HESP1.

Links

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

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49306

JCM 31057,DSM 12503

@ref 20215

Last LPSN update 2026-02-09 11:18:21

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Anaerocolumna

Species Anaerocolumna xylanovorans

Full scientific name Anaerocolumna xylanovorans (Mechichi et al. 2000) Ueki et al. 2016

Synonyms (1)

Clostridium xylanovorans

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4749	ANAEROCOLUMNA MEDIUM (DSMZ Medium 860)		Medium recipe at MediaDive	Name: ANAEROCOLUMNA MEDIUM (DSMZ Medium 860) Composition: D-Fructose 3.99202 g/l Na2CO3 1.49701 g/l NH4Cl 0.998004 g/l Yeast extract 0.998004 g/l NaCl 0.598802 g/l L-Cysteine HCl x H2O 0.499002 g/l K2HPO4 0.299401 g/l KH2PO4 0.299401 g/l Na2S x 9 H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l CaCl2 x 2 H2O 0.0998004 g/l KCl 0.0998004 g/l HCl 0.00374251 g/l FeCl2 x 4 H2O 0.00224551 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000284431 g/l MnCl2 x 4 H2O 0.000149701 g/l ZnCl2 0.00010479 g/l Na2MoO4 x 2 H2O 5.38922e-05 g/l NiCl2 x 6 H2O 3.59281e-05 g/l H3BO3 8.98204e-06 g/l CuCl2 x 2 H2O 2.99401e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4749	positive	growth	35
67770	positive	growth	35

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4749	anaerobe
125439	anaerobe	97.8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	enterobactin biosynthesis	100	3 of 3
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	vitamin E metabolism	100	4 of 4
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	degradation of sugar alcohols	87.5	14 of 16
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	valine metabolism	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	pentose phosphate pathway	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	purine metabolism	68.09	64 of 94
66794	methane metabolism	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	oxidative phosphorylation	64.84	59 of 91
66794	citric acid cycle	64.29	9 of 14
66794	heme metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	gluconeogenesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	hydrogen production	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	polyamine pathway	56.52	13 of 23
66794	degradation of sugar acids	56	14 of 25
66794	proline metabolism	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	myo-inositol biosynthesis	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	ribulose monophosphate pathway	50	1 of 2
66794	degradation of pentoses	46.43	13 of 28
66794	urea cycle	46.15	6 of 13
66794	lipid metabolism	45.16	14 of 31
66794	nitrate assimilation	44.44	4 of 9
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	arginine metabolism	41.67	10 of 24
66794	lysine metabolism	40.48	17 of 42
66794	factor 420 biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	glutathione metabolism	35.71	5 of 14
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	allantoin degradation	33.33	3 of 9
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	tyrosine metabolism	28.57	4 of 14
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	sulfopterin metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Industrial	-
#Engineered	#Waste	#Industrial wastewater
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4749	anaerobic digester fed with olive mill wastewater	Sfax	Tunisia	TUN	Africa
67770	Methanogenic digester

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4749	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1421833v1 assembly for Anaerocolumna cellulosilytica SN021	complete	GCA_014218335	433286.4	8064407441	433286	98.34
67770	IMG-taxon 2582580727 annotated assembly for Anaerocolumna xylanovorans DSM 12503	scaffold	GCA_900143645	1121345.3	2582580727	1121345	67.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4749	Clostridium xylanovorans 16S ribosomal RNA gene, partial sequence	AF116920	1533		100134

GC content

@ref	GC-content (mol%)	Method
4749	40.0	high performance liquid chromatography (HPLC)
67770	40	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: Anaerocolumna xylanovorans DSM 12503
NCBI: GCA_900143645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.80	no
125439	gram_stain	BacteriaNetⓘ	variable	85.80	no
125439	motility	BacteriaNetⓘ	yes	82.50	no
125439	spore_formation	BacteriaNetⓘ	yes	78.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Anaerocolumna cellulosilytica strain SN021
PATRIC: 433286.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.61	no
125438	anaerobic	anaerobicⓘ	yes	85.79	yes
125438	spore-forming	spore-formingⓘ	yes	81.37	no
125438	aerobic	aerobicⓘ	no	91.11	no
125438	thermophilic	thermophileⓘ	no	94.62	yes
125438	flagellated	motile2+ⓘ	yes	79.10	no

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;
#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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Anaerocolumna xylanovorans (DSM 12503, JCM 31057, HESP1)

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

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014218335

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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