Tepidimicrobium xylanilyticum (DSM 23310, CGMCC 1.5080, JCM 15035)

Name: Tepidimicrobium xylanilyticum (DSM 23310, CGMCC 1.5080, JCM 15035)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2515

Type strain

Strain Designation PML14

Culture col. no. DSM 23310 CGMCC 1.5080 JCM 15035 PML14

NCBI tax ID(s) 437529 1123352

Special Collections DSMZ JCM Literature strains

History DSMZ <- T. Itoh, JCM/RIKEN <- X. Dong, Chinese Acad. Sci. (CAS), Beijing; PML14 JCM <-- X. Dong PML14.

Links

Tepidimicrobium xylanilyticum PML14 is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from sludge of a thermophilic anaerobic digester.

spore-forming Gram-positive motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 396842

JCM 15035,DSM 23310

@ref 20215

Last LPSN update 2026-05-29 08:25:29

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Tissierellales

Family Tissierellaceae

Genus Tepidimicrobium

Species Tepidimicrobium xylanilyticum

Full scientific name Tepidimicrobium xylanilyticum Niu et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29056	positive	7 µm	0.45 µm	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16781	TEPIDIMICROBIUM MEDIUM (DSMZ Medium 1237)		Medium recipe at MediaDive	Name: TEPIDIMICROBIUM MEDIUM (DSMZ Medium 1237) Composition: D-Glucose 4.93583 g/l Na2CO3 2.46792 g/l Tryptone 1.97433 g/l Proteose peptone 1.97433 g/l Yeast extract 1.97433 g/l Na2HPO4 1.17473 g/l Na2S x 9 H2O 0.493583 g/l L-Cysteine HCl x H2O 0.493583 g/l KH2PO4 0.483712 g/l NH4Cl 0.29615 g/l MgCl2 x 6 H2O 0.0987167 g/l MgSO4 x 7 H2O 0.029615 g/l Nitrilotriacetic acid 0.0148075 g/l NaCl 0.00987167 g/l MnSO4 x H2O 0.00493583 g/l CoSO4 x 7 H2O 0.0017769 g/l ZnSO4 x 7 H2O 0.0017769 g/l FeCl2 0.00148075 g/l FeSO4 x 7 H2O 0.000987167 g/l CaCl2 x 2 H2O 0.000987167 g/l Sodium resazurin 0.000493583 g/l NiCl2 x 6 H2O 0.00029615 g/l AlK(SO4)2 x 12 H2O 0.000197433 g/l CuSO4 x 5 H2O 9.87167e-05 g/l Pyridoxine hydrochloride 9.87167e-05 g/l H3BO3 9.87167e-05 g/l Na2MoO4 x 2 H2O 9.87167e-05 g/l (DL)-alpha-Lipoic acid 4.93583e-05 g/l Thiamine HCl 4.93583e-05 g/l Riboflavin 4.93583e-05 g/l Nicotinic acid 4.93583e-05 g/l Calcium D-(+)-pantothenate 4.93583e-05 g/l p-Aminobenzoic acid 4.93583e-05 g/l Biotin 1.97433e-05 g/l Folic acid 1.97433e-05 g/l Na2WO4 x 2 H2O 3.94867e-06 g/l Na2SeO3 x 5 H2O 2.9615e-06 g/l Vitamin B12 9.87167e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16781	positive	growth	60
29056	positive	growth	25-67
29056	positive	optimum	60
67770	positive	growth	60

Culture pH

@ref	Ability	Type	PH	PH range
29056	positive	optimum	8.5
29056	positive	growth	5.8-9.3	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16781	anaerobe
29056	anaerobe
125438	anaerobe	93.963
125439	anaerobe	99.672

Spore formation

29056

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29056	NaCl	positive	growth	0-4.5 %
29056	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29056	17057 ChEBI	cellobiose	+	carbon source
29056	17234 ChEBI	glucose	+	carbon source
29056	15428 ChEBI	glycine	+	carbon source
29056	15361 ChEBI	pyruvate	+	carbon source
29056	17822 ChEBI	serine	+	carbon source
29056	26986 ChEBI	threonine	+	carbon source
29056	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29056	16136 ChEBI	hydrogen sulfide

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gluconeogenesis	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	pyrimidine metabolism	88.89	40 of 45
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	vitamin B12 metabolism	85.29	29 of 34
66794	purine metabolism	81.91	77 of 94
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	flavin biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	glutathione metabolism	64.29	9 of 14
66794	oxidative phosphorylation	62.64	57 of 91
66794	urea cycle	61.54	8 of 13
66794	non-pathway related	60.53	23 of 38
66794	propionate fermentation	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	heme metabolism	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	methionine metabolism	53.85	14 of 26
66794	histidine metabolism	51.72	15 of 29
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	lysine metabolism	50	21 of 42
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	isoleucine metabolism	50	4 of 8
66794	glycogen biosynthesis	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	suberin monomers biosynthesis	50	1 of 2
66794	tryptophan metabolism	47.37	18 of 38
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	allantoin degradation	44.44	4 of 9
66794	valine metabolism	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of pentoses	42.86	12 of 28
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	lipid metabolism	41.94	13 of 31
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	glycogen metabolism	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	starch degradation	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	arginine metabolism	37.5	9 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	leucine metabolism	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M biosynthesis	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	vitamin B6 metabolism	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	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
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16781	sludge of a thermophilic anaerobic digester	Beijing	China	CHN	Asia
67770	Sludge of a thermophilic anaerobic digester treating municipal solid and sewage in Beijing		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF522948 (>99% sequence identity) for Tepidimicrobium xylanilyticum subclade from Microbeatlas

Aquatic Samples	415
Soil Samples	1129
Animal Samples	252
Plant Samples	296
Total Samples	2092

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16781	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
67770	IMG-taxon 2599185171 annotated assembly for Tepidimicrobium xylanilyticum DSM 23310	scaffold	GCA_900106765	1123352.3	2599185171	1123352	69.06

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16781	Clostridium sp. PML14 16S ribosomal RNA gene, partial sequence	EF522948	1528		437529

GC content

@ref	GC-content (mol%)	Method
16781	36.2±0.8	thermal denaturation, midpoint method (Tm)
29056	36.2
67770	36.2	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2599185171 annotated assembly for Tepidimicrobium xylanilyticum DSM 23310
NCBI: GCA_900106765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.67	no
125439	gram_stain	BacteriaNetⓘ	variable	52.58	no
125439	motility	BacteriaNetⓘ	yes	72.39	no
125439	spore_formation	BacteriaNetⓘ	yes	81.89	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Tepidimicrobium xylanilyticum strain DSM 23310
PATRIC: 1123352.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	60.31	no
125438	anaerobic	anaerobicⓘ	yes	93.96	no
125438	spore-forming	spore-formingⓘ	yes	57.56	no
125438	aerobic	aerobicⓘ	no	93.96	no
125438	thermophilic	thermophileⓘ	no	53.02	yes
125438	flagellated	motile2+ⓘ	yes	72.74	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity.	Huang Y, Sun Y, Ma S, Chen L, Zhang H, Deng Y	FEMS Microbiol Lett	10.1111/1574-6968.12184	2013
Phylogeny	Tepidimicrobium xylanilyticum sp. nov., an anaerobic xylanolytic bacterium, and emended description of the genus Tepidimicrobium.	Niu L, Song L, Liu X, Dong X	Int J Syst Evol Microbiol	10.1099/ijs.0.005124-0	2009

References

#16781	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23310
#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 )
#25486	IJSEM 2698 2009 ( DOI 10.1099/ijs.0.005124-0 , PubMed 19625437 )
#29056	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25486
#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;
#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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Tepidimicrobium xylanilyticum (DSM 23310, CGMCC 1.5080, JCM 15035)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900106765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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