Strain identifier
BacDive ID: 158360
Type strain: 
Species: Petroclostridium xylanilyticum
Strain Designation: SK-Y3
Strain history: <- X. Zhang, Biogas Inst. of Ministry of Agriculture, Chengdu, P.R. China; SK-Y3 <- D. Lirong
NCBI tax ID(s): 1792311 (species)
version 8.1 (current version)
General
@ref: 65036
BacDive-ID: 158360
DSM-Number: 103557
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, thermophilic, Gram-positive, rod-shaped, colony-forming
description: Petroclostridium xylanilyticum SK-Y3 is a spore-forming, thermophilic, Gram-positive bacterium that forms circular colonies and was isolated from oily-sludge treatment plant.
NCBI tax id
- NCBI tax id: 1792311
- Matching level: species
strain history
- @ref: 65036
- history: <- X. Zhang, Biogas Inst. of Ministry of Agriculture, Chengdu, P.R. China; SK-Y3 <- D. Lirong
doi: 10.13145/bacdive158360.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Petroclostridium
- species: Petroclostridium xylanilyticum
- full scientific name: Petroclostridium xylanilyticum Zhang et al. 2018
@ref: 65036
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Oscillospiraceae
genus: Petroclostridium
species: Petroclostridium xylanilyticum
full scientific name: Petroclostridium xylanilyticum Zhang et al. 2018
strain designation: SK-Y3
type strain: yes
Morphology
cell morphology
- @ref: 66689
- gram stain: positive
- cell length: 2.5-8 µm
- cell width: 0.4-0.8 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 66689
- colony size: 0.8-1 mm
- colony color: white
- colony shape: circular
- medium used: agar
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 65036 | ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503) | yes | https://mediadive.dsmz.de/medium/503 | Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: D-Glucose 4.98504 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water |
| 66689 | agar | yes |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 65036 | positive | growth | 50 | thermophilic |
| 66689 | positive | optimum | 50 | thermophilic |
| 66689 | positive | growth | 35-60 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 66689 | positive | optimum | 7.5 | |
| 66689 | positive | growth | 6.5-9 | alkaliphile |
Physiology and metabolism
spore formation
- @ref: 66689
- spore description: Terminally located, ellipsoidal endospores
- type of spore: endospore
- spore formation: yes
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 66689 | NaCl | positive | growth | 0-4 %(w/v) |
| 66689 | NaCl | positive | optimum | 0 %(w/v) |
observation
- @ref: 66689
- observation: The main degradation product of xylan is xylose with trace amount of acetate, isovalerate and lactate. Acetate and H2 are the main degradation products of glucose, arabinose and raffinose. Propionate and butyrate are concomitantly generated when the carbon sources are amended to fructose, galactose and mannose.
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 66689 | 18222 | xylose | - | assimilation |
| 66689 | 29864 | mannitol | - | assimilation |
| 66689 | crystalline cellulose | - | assimilation | |
| 66689 | 16634 | raffinose | + | assimilation |
| 66689 | 17057 | cellobiose | + | assimilation |
| 66689 | 17234 | glucose | + | assimilation |
| 66689 | 17268 | myo-inositol | + | assimilation |
| 66689 | 17306 | maltose | + | assimilation |
| 66689 | 17716 | lactose | + | assimilation |
| 66689 | 17992 | sucrose | + | assimilation |
| 66689 | 22599 | arabinose | + | assimilation |
| 66689 | 26546 | rhamnose | + | assimilation |
| 66689 | 28260 | galactose | + | assimilation |
| 66689 | 28757 | fructose | + | assimilation |
| 66689 | 33942 | ribose | + | assimilation |
| 66689 | 37166 | xylan | + | assimilation |
| 66689 | 37684 | mannose | + | assimilation |
| 66689 | yeast extract | + | assimilation |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 65036 | oily-sludge treatment plant | Shengli oilfield | China | CHN | Asia | 37.9 | 118.55 | |||||
| 66689 | oily sludge of oilfield | Shengli oilfield | China | CHN | Asia | 37.9 | 118.55 | basal mineral medium | (per litre distilled water) 0.5 g NaCl, 0.5 g MgCl2 x 6H2O, 0.1 g CaCl2 x 2H2O, 0.1 g NH4Cl, 0.2 g KH2PO4, 0.5 g KCl, 1 mg resazurin and 0.5 g cysteine hydrochloride. The medium was boiled and cooled under a 99.999 % N2 flow, and dispensed into vials or tubes with butyl rubber stoppers. The culture was reduced by addition of 0.3 g Na2S x 9H2O l-1, and the pH was adjusted to 7.0 with NaHCO3 solutions prior to incubation. | 3-5 months | 55 | The initial culture was diluted 10-fold into 4.5 ml medium supplemented with agar and glucose (both 20 g l-1) and incubated for 3-5 months at 55°C. |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Oil (Fuel) |
| #Engineered | #Industrial | #Plant (Factory) |
| #Engineered | #Waste | #Sewage sludge |
taxonmaps
- @ref: 69479
- File name: preview.99_83676.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3162;96_34989;97_44396;98_58073;99_83676&stattab=map
- Last taxonomy: Petroclostridium xylanilyticum subclade
- 16S sequence: KT630605
- Sequence Identity:
- Total samples: 781
- soil counts: 85
- aquatic counts: 201
- animal counts: 434
- plant counts: 61
Sequence information
16S sequences
- @ref: 65036
- description: Clostridium sp. SK-Y3 16S ribosomal RNA gene, partial sequence
- accession: KT630605
- length: 1480
- database: ena
- NCBI tax ID: 1792311
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Petroclostridium xylanilyticum SK-Y3 | GCA_002252565 | contig | ncbi | 1792311 |
| 66792 | Petroclostridium xylanilyticum SK-Y3 | 2831404242 | draft | img | 1792311 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 65036 | 37.2 | |
| 66689 | 37.2 | genome sequence analysis |
| 66689 | 37.1 | high performance liquid chromatography (HPLC) |
External links
@ref: 65036
culture collection no.: DSM 103557, ACCC 19952
straininfo link
- @ref: 111165
- straininfo: 403924
literature
- topic: Phylogeny
- Pubmed-ID: 30124399
- title: Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov.
- authors: Zhang X, Tu B, Dai LR, Lawson PA, Zheng ZZ, Liu LY, Deng Y, Zhang H, Cheng L
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002966
- year: 2018
- mesh: Bacterial Typing Techniques, Base Composition, China, Clostridiales/*classification/genetics/isolation & purification, Clostridium/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Xylans/metabolism
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | 10.1099/ijsem.0.004332 | |||
| 65036 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103557 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103557) | |||
| 66689 | Xue Zhang, Bo Tu, Li-rong Dai, Paul A. Lawson, Zhen-zhen Zheng, Lai-Yan Liu, Yu Deng, Hui Zhang, Lei Cheng | Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov. | 10.1099/ijsem.0.002966 | IJSEM 68: 3197-3211 2018 | 30124399 | |
| 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) | https://diaspora-project.de/progress.html#genomes | |||
| 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 | https://microbeatlas.org/ | |||
| 111165 | 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 | 10.60712/SI-ID403924.1 |