Thermotoga neapolitana NS-E is an anaerobe, hyperthermophilic prokaryote that was isolated from submarine hot spring.
anaerobe hyperthermophilic genome sequence 16S sequence| @ref 20215 |
|
|
| Domain Thermotogati |
| Phylum Thermotogota |
| Class Thermotogae |
| Order Thermotogales |
| Family Thermotogaceae |
| Genus Thermotoga |
| Species Thermotoga neapolitana |
| Full scientific name Thermotoga neapolitana Jannasch et al. 1989 |
| BacDive ID | Other strains from Thermotoga neapolitana (1) | Type strain |
|---|---|---|
| 17062 | T. neapolitana LA4, DSM 5068 |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 1545 | THERMOTOGA TF(C) MEDIUM (DSMZ Medium 613) | Medium recipe at MediaDive | Name: THERMOTOGA TF(C) MEDIUM (DSMZ Medium 613; with strain-specific modifications) Composition: Yeast extract 1.97824 g/l Trypticase peptone 1.97824 g/l K2HPO4 1.58259 g/l MgCl2 x 6 H2O 1.38477 g/l Na2HPO4 x H2O 0.98912 g/l Starch 0.49456 g/l NH4Cl 0.49456 g/l Na2S x 9 H2O 0.296736 g/l L-Cysteine HCl x H2O 0.296736 g/l CaCl2 x 2 H2O 0.0593472 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Biotin 1.97824e-05 g/l Folic acid 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water |
| @ref | Growth | Type | Temperature (°C) | Range | |
|---|---|---|---|---|---|
| 1545 | positive | growth | 85 | hyperthermophilic |
| Cat1 | Cat2 | Cat3 | |
|---|---|---|---|
| #Environmental | #Aquatic | #Marine | |
| #Environmental | #Aquatic | #Thermal spring | |
| #Condition | #Thermophilic (>45°C) | - |
| @ref | Sample type | Geographic location | Country | Country ISO 3 Code | Continent | |
|---|---|---|---|---|---|---|
| 1545 | submarine hot spring | Bay of Naples | Italy | ITA | Europe |
Global distribution of 16S sequence AB039768 (>99% sequence identity) for Thermotoga from Microbeatlas ![]()
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 124043 | ASM4924464v1 assembly for Thermotoga neapolitana DSM 4359 | complete | 309803 | 99.06 | ||||
| 66792 | ASM1894v1 assembly for Thermotoga neapolitana DSM 4359 | complete | 309803 | 98.22 |
| @ref | Description | Accession | Length | Database | NCBI tax ID | |
|---|---|---|---|---|---|---|
| 20218 | Thermotoga neapolitana DSM 4359 gene for 16S rRNA | AB039768 | 1482 | 309803 |
| @ref | GC-content (mol%) | Method | |
|---|---|---|---|
| 1545 | 46 | sequence analysis |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125439 | spore_formation | BacteriaNetⓘ | yes | 55.70 | no |
| 125439 | motility | BacteriaNetⓘ | yes | 52.90 | no |
| 125439 | gram_stain | BacteriaNetⓘ | variable | 75.40 | no |
| 125439 | oxygen_tolerance | BacteriaNetⓘ | anaerobe | 99.10 | no |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positiveⓘ | no | 67.98 | no |
| 125438 | anaerobic | anaerobicⓘ | yes | 90.88 | yes |
| 125438 | aerobic | aerobicⓘ | no | 93.48 | no |
| 125438 | spore-forming | spore-formingⓘ | no | 71.50 | no |
| 125438 | thermophilic | thermophileⓘ | yes | 82.96 | no |
| 125438 | flagellated | motile2+ⓘ | yes | 58.37 | no |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Identification, heterologous expression, and characterisation of beta-1,3-xylanase BcXyn26B from human gut bacterium Bacteroides cellulosilyticus WH2. | Hori S, Okazaki F. | Biotechnol Lett | 10.1007/s10529-024-03547-3 | 2024 | ||
| Characterization of a novel thermophilic beta-glucosidase from Thermotoga sp. and its application in the transformation of notoginsenoside R1. | Zhong P, Xiu Y, Zhou K, Zhao H, Wang N, Zheng F, Yu S. | 3 Biotech | 10.1007/s13205-022-03352-7 | 2022 | ||
| Enzymology | Molecular Characterization of the Iron-Containing Alcohol Dehydrogenase from the Extremely Thermophilic Bacterium Pseudothermotoga hypogea. | Hao L, Ayinla Z, Ma K. | Microorganisms | 10.3390/microorganisms12020311 | 2024 | |
| Enzymatic transformation of ginsenosides Re, Rg1, and Rf to ginsenosides Rg2 and aglycon PPT by using beta-glucosidase from Thermotoga neapolitana | Bi YF, Wang XZ, Jiang S, Liu JS, Zheng MZ, Chen P. | Biotechnol Lett | 2019 | |||
| Characterization and insight mechanism of an acid-adapted beta-Glucosidase from Lactobacillus paracasei and its application in bioconversion of glycosides. | Xie Y, Yan X, Li C, Wang S, Jia L. | Front Bioeng Biotechnol | 10.3389/fbioe.2024.1334695 | 2024 | ||
| Metabolism | A novel bifunctional aldehyde/alcohol dehydrogenase catalyzing reduction of acetyl-CoA to ethanol at temperatures up to 95 °C. | Wang Q, Sha C, Wang H, Ma K, Wiegle J, Abomohra AE, Shao W. | Sci Rep | 10.1038/s41598-020-80159-7 | 2021 | |
| Enzymology | Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium. | Baudrexl M, Schwarz WH, Zverlov VV, Zverlov VV, Liebl W. | Sci Rep | 10.1038/s41598-019-52251-0 | 2019 | |
| Enzymology | Functional Expression and Characterization of Acetyl Xylan Esterases CE Family 7 from Lactobacillus antri and Bacillus halodurans. | Kim MJ, Jang MU, Nam GH, Shin H, Song JR, Kim TJ. | J Microbiol Biotechnol | 10.4014/jmb.2001.01004 | 2020 | |
| Genetics | Determination of GC content of Thermotoga maritima, Thermotoga neapolitana and Thermotoga thermarum strains: A GC dataset for higher level hierarchical classification. | Rekadwad BN, Khobragade CN. | Data Brief | 10.1016/j.dib.2016.05.045 | 2016 | |
| Structural studies of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus. | Sotiropoulou AI, Hatzinikolaou DG, Chrysina ED. | Acta Crystallogr D Struct Biol | 10.1107/s2059798324009252 | 2024 | ||
| Metabolism | Bioaugmentation enhances dark fermentative hydrogen production in cultures exposed to short-term temperature fluctuations. | Okonkwo O, Escudie R, Bernet N, Mangayil R, Lakaniemi AM, Trably E. | Appl Microbiol Biotechnol | 10.1007/s00253-019-10203-8 | 2020 | |
| Enzymology | Identification and Characterization of a Novel Thermostable and Salt-Tolerant beta-1,3 Xylanase from Flammeovirga pacifica Strain WPAGA1. | Yi Z, Cai Z, Zeng B, Zeng R, Zhang G. | Biomolecules | 10.3390/biom10091287 | 2020 | |
| Diversity of Marine 1,3-Xylan-Utilizing Bacteria and Characters of Their Extracellular 1,3-Xylanases. | Sun HN, Yu CM, Fu HH, Wang P, Fang ZG, Zhang YZ, Chen XL, Zhao F. | Front Microbiol | 10.3389/fmicb.2021.721422 | 2021 | ||
| Enzymology | Degradative actions of microbial xylanolytic activities on hemicelluloses from rhizome of Arundo donax. | Lama L, Tramice A, Finore I, Anzelmo G, Calandrelli V, Pagnotta E, Tommonaro G, Poli A, Di Donato P, Nicolaus B, Fagnano M, Mori M, Impagliazzo A, Trincone A. | AMB Express | 10.1186/s13568-014-0055-6 | 2014 | |
| Metabolism | Diversity and versatility of the Thermotoga maritima sugar kinome. | Rodionova IA, Yang C, Li X, Kurnasov OV, Best AA, Osterman AL, Rodionov DA. | J Bacteriol | 10.1128/jb.01136-12 | 2012 | |
| A novel beta-glucosidase from Saccharophagus degradans 2-40T for the efficient hydrolysis of laminarin from brown macroalgae. | Kim DH, Kim DH, Lee SH, Kim KH. | Biotechnol Biofuels | 10.1186/s13068-018-1059-2 | 2018 | ||
| Metabolism | Aerobic Hydrogen Production via Nitrogenase in Azotobacter vinelandii CA6. | Noar J, Loveless T, Navarro-Herrero JL, Olson JW, Bruno-Barcena JM. | Appl Environ Microbiol | 10.1128/aem.00679-15 | 2015 | |
| Enzymology | Kinetics and structural features of dimeric glutamine-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites. | Santos ARS, Gerhardt ECM, Moure VR, Pedrosa FO, Souza EM, Diamanti R, Hogbom M, Huergo LF. | J Biol Chem | 10.1074/jbc.ra118.002241 | 2018 | |
| Construction and transformation of a Thermotoga-E. coli shuttle vector. | Han D, Norris SM, Xu Z. | BMC Biotechnol | 10.1186/1472-6750-12-2 | 2012 | ||
| Enzymology | Expression, purification, crystallization and preliminary X-ray diffraction analysis of Thermotoga neapolitana beta-glucosidase B. | Turner P, Pramhed A, Kanders E, Hedstrom M, Karlsson EN, Logan DT. | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/s1744309107040341 | 2007 | |
| Metabolism | Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana. | Olszewski M, Grot A, Wojciechowski M, Nowak M, Mickiewicz M, Kur J. | BMC Microbiol | 10.1186/1471-2180-10-260 | 2010 | |
| Enzymology | Characterization of the GH13 and GH57 glycogen branching enzymes from Petrotoga mobilis SJ95 and potential role in glycogen biosynthesis. | Zhang X, Leemhuis H, van der Maarel MJEC. | PLoS One | 10.1371/journal.pone.0219844 | 2019 | |
| Metabolism | Natural transformation of Thermotoga sp. strain RQ7. | Han D, Xu H, Puranik R, Xu Z. | BMC Biotechnol | 10.1186/1472-6750-14-39 | 2014 | |
| Metabolism | Fermentative hydrogen production from agroindustrial lignocellulosic substrates. | Reginatto V, Antonio RV. | Braz J Microbiol | 10.1590/s1517-838246220140111 | 2015 | |
| Efficient hydrogen production from the lignocellulosic energy crop Miscanthus by the extreme thermophilic bacteria Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana. | de Vrije T, Bakker RR, Budde MA, Lai MH, Mars AE, Claassen PA. | Biotechnol Biofuels | 10.1186/1754-6834-2-12 | 2009 | ||
| Crystal structure of the N-terminal domain of MinC dimerized via domain swapping. | An JY, Kim TG, Park KR, Lee JG, Youn HS, Lee Y, Kang JY, Kang GB, Eom SH. | J Synchrotron Radiat | 10.1107/s0909049513022760 | 2013 | ||
| Metabolism | A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. | Morton JT, Freed SD, Lee SW, Friedberg I. | BMC Bioinformatics | 10.1186/s12859-015-0792-9 | 2015 | |
| Metabolism | Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria. | Carere CR, Rydzak T, Verbeke TJ, Cicek N, Levin DB, Sparling R. | BMC Microbiol | 10.1186/1471-2180-12-295 | 2012 | |
| Genetics | Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). | Grotzinger SW, Alam I, Ba Alawi W, Bajic VB, Stingl U, Eppinger J. | Front Microbiol | 10.3389/fmicb.2014.00134 | 2014 | |
| Relevance of GC content to the conservation of DNA polymerase III/mismatch repair system in Gram-positive bacteria. | Akashi M, Yoshikawa H. | Front Microbiol | 10.3389/fmicb.2013.00266 | 2013 | ||
| Metabolism | Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production. | Chowdhary N, Selvaraj A, KrishnaKumaar L, Kumar GR. | PLoS One | 10.1371/journal.pone.0133183 | 2015 | |
| Metabolism | Phylogenomically guided identification of industrially relevant GH1 beta-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. | Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. | ACS Chem Biol | 10.1021/cb500244v | 2014 | |
| Genetics | Horizontal gene transfer and genome evolution in Methanosarcina. | Garushyants SK, Kazanov MD, Gelfand MS. | BMC Evol Biol | 10.1186/s12862-015-0393-2 | 2015 | |
| Thiosulfate reduction, an important physiological feature shared by members of the order thermotogales. | Ravot G, Ollivier B, Magot M, Patel B, Crolet J, Fardeau M, Garcia J. | Appl Environ Microbiol | 10.1128/aem.61.5.2053-2055.1995 | 1995 | ||
| Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors. | Tatarinova T, Salih B, Dien Bard J, Cohen I, Bolshoy A. | Biomed Res Int | 10.1155/2015/786861 | 2015 | ||
| Phylogeny | Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. | Boussau B, Gueguen L, Gouy M. | BMC Evol Biol | 10.1186/1471-2148-8-272 | 2008 | |
| Enzymology | Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. | Das D, Moiani D, Axelrod HL, Miller MD, McMullan D, Jin KK, Abdubek P, Astakhova T, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tainer JA, Wilson IA. | J Mol Biol | 10.1016/j.jmb.2010.01.049 | 2010 | |
| Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. | Brochier-Armanet C, Forterre P. | Archaea | 10.1155/2006/582916 | 2007 | ||
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| Methods of combinatorial optimization to reveal factors affecting gene length. | Bolshoy A, Tatarinova T. | Bioinform Biol Insights | 10.4137/bbi.s10525 | 2012 | ||
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| Keratin Degradation by Fervidobacterium pennavorans, a Novel Thermophilic Anaerobic Species of the Order Thermotogales. | Friedrich AB, Antranikian G. | Appl Environ Microbiol | 10.1128/aem.62.8.2875-2882.1996 | 1996 | ||
| Genetics | Information theoretic perspective on genome clustering. | Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S. | Saudi J Biol Sci | 10.1016/j.sjbs.2020.12.039 | 2021 | |
| Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms. | Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G. | Genes (Basel) | 10.3390/genes2040869 | 2011 | ||
| Metabolism | Evolutionary primacy of sodium bioenergetics. | Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV. | Biol Direct | 10.1186/1745-6150-3-13 | 2008 | |
| Metabolism | Introducing capnophilic lactic fermentation in a combined dark-photo fermentation process: a route to unparalleled H2 yields. | Dipasquale L, Adessi A, d'Ippolito G, Rossi F, Fontana A, De Philippis R | Appl Microbiol Biotechnol | 10.1007/s00253-014-6231-4 | 2014 | |
| Enzymology | Cloning and biochemical characterization of a glucosidase from a marine bacterium Aeromonas sp. HC11e-3. | Huang X, Zhao Y, Dai Y, Wu G, Shao Z, Zeng Q, Liu Z | World J Microbiol Biotechnol | 10.1007/s11274-012-1145-8 | 2012 | |
| Metabolism | Enzymatic transformation of ginsenosides Re, Rg1, and Rf to ginsenosides Rg2 and aglycon PPT by using beta-glucosidase from Thermotoga neapolitana. | Bi YF, Wang XZ, Jiang S, Liu JS, Zheng MZ, Chen P | Biotechnol Lett | 10.1007/s10529-019-02665-7 | 2019 | |
| Enzymology | Biochemical characterization of a thermostable beta-1,3-xylanase from the hyperthermophilic eubacterium, Thermotoga neapolitana strain DSM 4359. | Okazaki F, Nakashima N, Ogino C, Tamaru Y, Kondo A | Appl Microbiol Biotechnol | 10.1007/s00253-012-4555-5 | 2012 | |
| Enzymology | Expression, crystallization and preliminary X-ray diffraction studies of thermostable beta-1,3-xylanase from Thermotoga neapolitana strain DSM 4359. | Okazaki F, Ogino C, Kondo A, Mikami B, Kurebayashi Y, Tsuruta H | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S1744309111017222 | 2011 | |
| Enzymology | Purification and biochemical characterization of a native invertase from the hydrogen-producing Thermotoga neapolitana (DSM 4359). | Dipasquale L, Gambacorta A, Siciliano RA, Mazzeo MF, Lama L | Extremophiles | 10.1007/s00792-008-0222-2 | 2009 | |
| Genetics | Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. | DeBoy RT, Mongodin EF, Emerson JB, Nelson KE | J Bacteriol | 10.1128/JB.188.7.2364-2374.2006 | 2006 | |
| Phylogeny | Growth requirements of hyperthermophilic sulfur-dependent heterotrophic archaea isolated from a shallow submarine geothermal system with reference to their essential amino acids. | Hoaki T, Nishijima M, Kato M, Adachi K, Mizobuchi S, Hanzawa N, Maruyama T | Appl Environ Microbiol | 10.1128/aem.60.8.2898-2904.1994 | 1994 |
| #1545 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4359 |
| #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 ) |
| #20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 ) |
| #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) . |
| #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 . |
| #124043 | Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy . |
| #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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