Name: Tepidimicrobium xylanilyticum PML14
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2515

Type strain:

Species: Tepidimicrobium xylanilyticum

Strain Designation: PML14

Culture col. no.: DSM 23310, CGMCC 1.5080, JCM 15035

Strain history: X. Dong PML14.

NCBI tax ID(s): 437529 (strain), 1123352 (species)

SI-ID 396842

DSM 23310

Special Collections

Section

When using BacDive for research please cite our paper

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

Gram-positive
motile
rod-shaped
spore-forming
anaerobe
thermophilic
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	*Tissierellales*
	Family	*Tissierellaceae*
	Genus	*Tepidimicrobium*
	Species	**Tepidimicrobium xylanilyticum**
	Full Scientific Name (LPSN)	Tepidimicrobium xylanilyticum Niu et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29056]	Gram stain	positive

[Ref.: #29056]	Cell length	7 µm

[Ref.: #29056]	Cell width	0.45 µm

[Ref.: #29056]	Cell shape	rod-shaped

[Ref.: #29056]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16781]

Culture medium

TEPIDIMICROBIUM MEDIUM (DSMZ Medium 1237)

[Ref.: #16781]

Culture medium growth

[Ref.: #16781]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16781]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16781]	growth	60 °C
[Ref.: #29056]	growth	25-67 °C
[Ref.: #29056]	optimum	60 °C
[Ref.: #67770]	growth	60 °C

	pH	Kind of pH		pH
[Ref.: #29056]			optimum	8.5
[Ref.: #29056]			growth	5.8-9.3

Information on physiology and metabolism Physiology and metabolism

[Ref.: #16781]	Oxygen tolerance	anaerobe
[Ref.: #29056]	Oxygen tolerance	anaerobe
[Ref.: #125438]	Oxygen tolerance	anaerobe Confidence in %93.963
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %99.9

[Ref.: #29056]

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29056]		NaCl		growth	0-4.5	%
[Ref.: #29056]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29056]	cellobiose ChEBI	+	carbon source
[Ref.: #29056]	glucose ChEBI	+	carbon source
[Ref.: #29056]	glycine ChEBI	+	carbon source
[Ref.: #29056]	pyruvate ChEBI	+	carbon source
[Ref.: #29056]	serine ChEBI	+	carbon source
[Ref.: #29056]	threonine ChEBI	+	carbon source
[Ref.: #29056]	xylose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #29056]		hydrogen sulfide ChEBI	yes

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[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]	threonine metabolism	90	9 of 10
[Ref.: #66794]	pyrimidine metabolism	88.89	40 of 45
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	valine metabolism	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	leucine metabolism	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	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.: #16781]	Sample type/isolated from	sludge of a thermophilic anaerobic digester
[Ref.: #16781]	Geographic location (country and/or sea, region)	Beijing
[Ref.: #16781]	Country	China
[Ref.: #16781]	Country ISO 3 Code	CHN
[Ref.: #16781]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sludge of a thermophilic anaerobic digester treating municipal solid and sewage in Beijing
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #16781]

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.: #16781]	Clostridium sp. PML14 16S ribosomal RNA gene, partial sequence	EF522948	1528	GenBank ENA	437529 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Tepidimicrobium xylanilyticum DSM 23310	GCA_900106765	scaffold	GenBank ENA	1123352 tax ID
[Ref.: #66792]	Tepidimicrobium xylanilyticum strain DSM 23310	1123352.3	wgs	PATRIC	1123352 tax ID	*
[Ref.: #66792]	Tepidimicrobium xylanilyticum DSM 23310	2599185171	draft	JGI IMG/M	1123352 tax ID	*

[Ref.: #16781]	GC-content	36.2±0.8 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #29056]	GC-content	36.2 mol%
[Ref.: #67770]	GC-content	36.2 mol%	thermal denaturation, midpoint method (Tm)

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: Tepidimicrobium xylanilyticum strain DSM 23310 PATRIC: 1123352.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	60.309	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	93.963	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	57.562	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	93.958	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	53.021	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	72.735	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Tepidimicrobium xylanilyticum DSM 23310 NCBI: GCA_900106765
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	86.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	79.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	71.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	99.9

Availability in culture collections External links

[Ref.: #16781]

Culture collection no.

DSM 23310, CGMCC 1.5080, JCM 15035

[Ref.: #72050]

SI-ID 396842

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 )

#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 (see below)

#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;

#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 .

#72050

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-ID396842.1 )

#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 .

#25486

IJSEM 2698 2009 ( DOI 10.1099/ijs.0.005124-0 , PubMed 19625437 )

* These data were automatically processed and therefore are not curated

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Tepidimicrobium xylanilyticum strain DSM 23310

Tepidimicrobium xylanilyticum DSM 23310

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