Archive BacDiveID:10.13145/bacdive2515.20250331.9.3

Strain identifier

BacDive ID: 2515

Type strain:

Species: Tepidimicrobium xylanilyticum

Strain Designation: PML14

Strain history: X. Dong PML14.

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 16781

BacDive-ID: 2515

DSM-Number: 23310

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive, motile, rod-shaped

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

NCBI tax id

NCBI tax id	Matching level
1123352	species
437529	strain

strain history

@ref	history
16781	<- T. Itoh, JCM/RIKEN <- X. Dong, Chinese Acad. Sci. (CAS), Beijing; PML14
67770	X. Dong PML14.

doi: 10.13145/bacdive2515.20250331.9.3

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Tissierellales
family: Tissierellaceae
genus: Tepidimicrobium
species: Tepidimicrobium xylanilyticum
full scientific name: Tepidimicrobium xylanilyticum Niu et al. 2009

@ref: 16781

domain: Bacteria

phylum: Firmicutes

class: Tissierellia

order: Clostridiales

family: Tissierellaceae

genus: Tepidimicrobium

species: Tepidimicrobium xylanilyticum

full scientific name: Tepidimicrobium xylanilyticum Niu et al. 2009

strain designation: PML14

type strain: yes

Morphology

cell morphology

@ref: 29056
gram stain: positive
cell length: 7 µm
cell width: 0.45 µm
cell shape: rod-shaped
motility: yes

Culture and growth conditions

culture medium

@ref: 16781
name: TEPIDIMICROBIUM MEDIUM (DSMZ Medium 1237)
growth: yes
link: https://mediadive.dsmz.de/medium/1237
composition: 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
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	growth	5.8-9.3	alkaliphile
29056	positive	optimum	8.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
16781	anaerobe
29056	anaerobe
125438	anaerobe	93.963
125439	anaerobe	99.9

spore formation

@ref: 29056
spore formation: yes

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	cellobiose	+	carbon source
29056	17234	glucose	+	carbon source
29056	15428	glycine	+	carbon source
29056	15361	pyruvate	+	carbon source
29056	17822	serine	+	carbon source
29056	26986	threonine	+	carbon source
29056	18222	xylose	+	carbon source

metabolite production

@ref: 29056
Chebi-ID: 16136
metabolite: hydrogen sulfide
production: yes

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	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

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_16820.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_207;96_8631;97_10379;98_12729;99_16820&stattab=map
Last taxonomy: Tepidimicrobium xylanilyticum subclade
16S sequence: EF522948
Sequence Identity:
Total samples: 2092
soil counts: 1129
aquatic counts: 415
animal counts: 252
plant counts: 296

Safety information

risk assessment

@ref: 16781
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16781
description: Clostridium sp. PML14 16S ribosomal RNA gene, partial sequence
accession: EF522948
length: 1528
database: nuccore
NCBI tax ID: 437529

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Tepidimicrobium xylanilyticum strain DSM 23310	1123352.3	wgs	patric	1123352
66792	Tepidimicrobium xylanilyticum DSM 23310	2599185171	draft	img	1123352
67770	Tepidimicrobium xylanilyticum DSM 23310	GCA_900106765	scaffold	ncbi	1123352

GC content

@ref	GC-content	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

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	yes	60.309	no
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	93.963	no
125438	spore-forming	spore-forming	Ability to form endo- or exospores	yes	57.562	no
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	93.958	no
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	no	53.021	yes
125438	motile2+	flagellated	Ability to perform flagellated movement	yes	72.735	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	yes	86.2
125439	BacteriaNet	motility	Ability to perform movement	yes	79.1
125439	BacteriaNet	gram_stain	Reaction to gram-staining	variable	71.4
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	anaerobe	99.9

External links

@ref: 16781

culture collection no.: DSM 23310, CGMCC 1.5080, JCM 15035

straininfo link

@ref: 72050
straininfo: 396842

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19625437	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	Anaerobiosis, Bacteria/classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Xylose/metabolism	Metabolism
Phylogeny	23710623	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	Animals, Bacteria, Anaerobic/classification/enzymology/genetics/isolation & purification, Bacterial Proteins/chemistry/genetics/metabolism, Chickens, Enzyme Stability, Feathers/metabolism, Gram-Positive Bacteria/classification/genetics/isolation & purification/metabolism, Hot Temperature, Keratins/metabolism, Molecular Sequence Data, Peptide Hydrolases/chemistry/genetics/metabolism, Phylogeny, Soil Microbiology	Enzymology

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
16781	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23310)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23310
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29056	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25486	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates		33211880	Nucleic Acids Res. 49: D498-D508 2020
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
72050	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID396842.1	StrainInfo: A central database for resolving microbial strain identifiers
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann		10.1101/2024.08.12.607695	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy		https://github.com/GenomeNet/deepG	deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1