Serratia rubidaea 864 is a facultative anaerobe, Gram-negative, motile animal pathogen of the family Yersiniaceae.
Gram-negative motile rod-shaped facultative anaerobe animal pathogen genome sequence 16S sequence Bacteria| @ref 20215 |
|
|
| Domain Bacteria |
| Phylum Pseudomonadota |
| Class Gammaproteobacteria |
| Order Enterobacterales |
| Family Yersiniaceae |
| Genus Serratia |
| Species Serratia rubidaea |
| Full scientific name Serratia rubidaea (Stapp 1940) Ewing et al. 1973 (Approved Lists 1980) |
| Synonyms (2) |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 1693 | NUTRIENT AGAR (DSMZ Medium 1) | Medium recipe at MediaDive | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water | ||
| 39850 | MEDIUM 72- for trypto casein soja agar | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |||
| 122283 | CIP Medium 72 | Medium recipe at CIP |
| @ref | Spore formation | Confidence | |
|---|---|---|---|
| 125439 | 98.535 |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 68368 | 27613 ChEBI | amygdalin | + | fermentation | from API 20E |
| 68371 | 18305 ChEBI | arbutin | + | builds acid from | from API 50CH acid |
| 68368 | 29016 ChEBI | arginine | - | hydrolysis | from API 20E |
| 68371 | 17057 ChEBI | cellobiose | + | builds acid from | from API 50CH acid |
| 122283 | 16947 ChEBI | citrate | + | carbon source | |
| 68368 | 16947 ChEBI | citrate | + | assimilation | from API 20E |
| 68371 | 17108 ChEBI | D-arabinose | - | builds acid from | from API 50CH acid |
| 68371 | 18333 ChEBI | D-arabitol | + | builds acid from | from API 50CH acid |
| 68371 | 15824 ChEBI | D-fructose | + | builds acid from | from API 50CH acid |
| 68371 | 28847 ChEBI | D-fucose | - | builds acid from | from API 50CH acid |
| 68371 | 12936 ChEBI | D-galactose | + | builds acid from | from API 50CH acid |
| 68371 | 17634 ChEBI | D-glucose | + | builds acid from | from API 50CH acid |
| 68368 | 17634 ChEBI | D-glucose | + | fermentation | from API 20E |
| 68371 | 62318 ChEBI | D-lyxose | - | builds acid from | from API 50CH acid |
| 68371 | 16899 ChEBI | D-mannitol | + | builds acid from | from API 50CH acid |
| 68368 | 16899 ChEBI | D-mannitol | + | fermentation | from API 20E |
| 68371 | 16024 ChEBI | D-mannose | + | builds acid from | from API 50CH acid |
| 68371 | 16988 ChEBI | D-ribose | + | builds acid from | from API 50CH acid |
| 68371 | 17924 ChEBI | D-sorbitol | - | builds acid from | from API 50CH acid |
| 68371 | 16443 ChEBI | D-tagatose | - | builds acid from | from API 50CH acid |
| 68371 | 65327 ChEBI | D-xylose | + | builds acid from | from API 50CH acid |
| 68371 | 4853 ChEBI | esculin | + | builds acid from | from API 50CH acid |
| 68371 | 16813 ChEBI | galactitol | - | builds acid from | from API 50CH acid |
| 68368 | 5291 ChEBI | gelatin | + | hydrolysis | from API 20E |
| 68371 | 28066 ChEBI | gentiobiose | + | builds acid from | from API 50CH acid |
| 68371 | 24265 ChEBI | gluconate | + | builds acid from | from API 50CH acid |
| 122283 | 17234 ChEBI | glucose | + | fermentation | |
| 122283 | 17234 ChEBI | glucose | + | degradation | |
| 68371 | 17754 ChEBI | glycerol | + | builds acid from | from API 50CH acid |
| 68371 | 28087 ChEBI | glycogen | + | builds acid from | from API 50CH acid |
| 68371 | 15443 ChEBI | inulin | - | builds acid from | from API 50CH acid |
| 68371 | 30849 ChEBI | L-arabinose | + | builds acid from | from API 50CH acid |
| 68368 | 30849 ChEBI | L-arabinose | + | fermentation | from API 20E |
| 68371 | 18403 ChEBI | L-arabitol | - | builds acid from | from API 50CH acid |
| 68371 | 18287 ChEBI | L-fucose | - | builds acid from | from API 50CH acid |
| 68371 | 62345 ChEBI | L-rhamnose | - | builds acid from | from API 50CH acid |
| 68368 | 62345 ChEBI | L-rhamnose | + | fermentation | from API 20E |
| 68371 | 17266 ChEBI | L-sorbose | - | builds acid from | from API 50CH acid |
| 68371 | 65328 ChEBI | L-xylose | - | builds acid from | from API 50CH acid |
| 122283 | 17716 ChEBI | lactose | - | fermentation | |
| 68371 | 17716 ChEBI | lactose | + | builds acid from | from API 50CH acid |
| 68368 | 25094 ChEBI | lysine | - | degradation | from API 20E |
| 122283 | 15792 ChEBI | malonate | + | assimilation | |
| 68371 | 17306 ChEBI | maltose | + | builds acid from | from API 50CH acid |
| 122283 | 29864 ChEBI | mannitol | + | fermentation | |
| 68371 | 6731 ChEBI | melezitose | + | builds acid from | from API 50CH acid |
| 68371 | 28053 ChEBI | melibiose | + | builds acid from | from API 50CH acid |
| 68368 | 28053 ChEBI | melibiose | + | fermentation | from API 20E |
| 68371 | 320061 ChEBI | methyl alpha-D-glucopyranoside | + | builds acid from | from API 50CH acid |
| 68371 | 43943 ChEBI | methyl alpha-D-mannoside | - | builds acid from | from API 50CH acid |
| 68371 | 74863 ChEBI | methyl beta-D-xylopyranoside | - | builds acid from | from API 50CH acid |
| 68371 | 17268 ChEBI | myo-inositol | + | builds acid from | from API 50CH acid |
| 68368 | 17268 ChEBI | myo-inositol | + | fermentation | from API 20E |
| 68371 | 59640 ChEBI | N-acetylglucosamine | + | builds acid from | from API 50CH acid |
| 122283 | 17632 ChEBI | nitrate | + | reduction | |
| 122283 | 16301 ChEBI | nitrite | - | reduction | |
| 68368 | 18257 ChEBI | ornithine | - | degradation | from API 20E |
| 68371 | 0 ChEBI | Potassium 2-ketogluconate | + | builds acid from | from API 50CH acid |
| 68371 | 0 ChEBI | Potassium 5-ketogluconate | - | builds acid from | from API 50CH acid |
| 68371 | 16634 ChEBI | raffinose | + | builds acid from | from API 50CH acid |
| 68371 | 15963 ChEBI | ribitol | + | builds acid from | from API 50CH acid |
| 68371 | 17814 ChEBI | salicin | + | builds acid from | from API 50CH acid |
| 122283 | 132112 ChEBI | sodium thiosulfate | - | builds gas from | |
| 68371 | 28017 ChEBI | starch | - | builds acid from | from API 50CH acid |
| 68371 | 17992 ChEBI | sucrose | + | builds acid from | from API 50CH acid |
| 68368 | 17992 ChEBI | sucrose | + | fermentation | from API 20E |
| 68371 | 27082 ChEBI | trehalose | + | builds acid from | from API 50CH acid |
| 68368 | 27897 ChEBI | tryptophan | - | energy source | from API 20E |
| 68371 | 32528 ChEBI | turanose | + | builds acid from | from API 50CH acid |
| 68368 | 16199 ChEBI | urea | - | hydrolysis | from API 20E |
| 68371 | 17151 ChEBI | xylitol | - | builds acid from | from API 50CH acid |
| @ref | Metabolite | Is sensitive | Is resistant | |
|---|---|---|---|---|
| 122283 | 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate) |
| @ref | Value | Activity | Ec | |
|---|---|---|---|---|
| 68382 | acid phosphatase | + | 3.1.3.2 | from API zym |
| 122283 | alcohol dehydrogenase | - | 1.1.1.1 | |
| 68382 | alkaline phosphatase | + | 3.1.3.1 | from API zym |
| 68382 | alpha-chymotrypsin | - | 3.4.21.1 | from API zym |
| 68382 | alpha-fucosidase | - | 3.2.1.51 | from API zym |
| 68382 | alpha-galactosidase | - | 3.2.1.22 | from API zym |
| 68382 | alpha-glucosidase | + | 3.2.1.20 | from API zym |
| 68382 | alpha-mannosidase | - | 3.2.1.24 | from API zym |
| 68368 | arginine dihydrolase | - | 3.5.3.6 | from API 20E |
| 68382 | beta-galactosidase | + | 3.2.1.23 | from API zym |
| 122283 | beta-galactosidase | + | 3.2.1.23 | |
| 68368 | beta-galactosidase | + | 3.2.1.23 | from API 20E |
| 68382 | beta-glucosidase | + | 3.2.1.21 | from API zym |
| 68382 | beta-glucuronidase | - | 3.2.1.31 | from API zym |
| 122283 | catalase | + | 1.11.1.6 | |
| 68382 | cystine arylamidase | - | 3.4.11.3 | from API zym |
| 68368 | cytochrome oxidase | - | 1.9.3.1 | from API 20E |
| 68382 | esterase (C 4) | + | from API zym | |
| 68382 | esterase lipase (C 8) | + | from API zym | |
| 122283 | gelatinase | - | ||
| 68368 | gelatinase | + | from API 20E | |
| 68382 | leucine arylamidase | + | 3.4.11.1 | from API zym |
| 68382 | lipase (C 14) | + | from API zym | |
| 122283 | lysine decarboxylase | + | 4.1.1.18 | |
| 68368 | lysine decarboxylase | - | 4.1.1.18 | from API 20E |
| 68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 | from API zym |
| 68382 | naphthol-AS-BI-phosphohydrolase | + | from API zym | |
| 122283 | ornithine decarboxylase | - | 4.1.1.17 | |
| 68368 | ornithine decarboxylase | - | 4.1.1.17 | from API 20E |
| 122283 | oxidase | - | ||
| 122283 | phenylalanine ammonia-lyase | - | 4.3.1.24 | |
| 68382 | trypsin | + | 3.4.21.4 | from API zym |
| 122283 | tryptophan deaminase | - | ||
| 68368 | tryptophan deaminase | - | 4.1.99.1 | from API 20E |
| 122283 | urease | - | 3.5.1.5 | |
| 68368 | urease | - | 3.5.1.5 | from API 20E |
| 68382 | valine arylamidase | + | from API zym |
| @ref | ONPG | ADH (Arg) | LDC (Lys) | ODC | CIT | H2S productionH2S | URE | TDA (Trp) | IND | Acetoin production (Voges Proskauer test)VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX | Nitrite productionNO2 | Reduction to N2N2 | MotilityMOB | Growth on MacConkey mediumMAC | OF-O | OF-F | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1693 | + | - | - | - | + | - | - | - | - | + | + | + | + | + | + | + | + | + | + | + | - | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | |
| 1693 | + | - | - | - | + | - | - | - | - | + | + | + | + | + | - | + | + | + | + | + | - | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. |
| @ref | ControlQ | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 122283 | not determinedn.d. | + | +/- | - | + | + | + | - | + | - | + | + | + | + | - | - | - | + | + | - | - | + | + | +/- | + | + | + | + | + | + | + | + | + | - | + | + | - | + | - | + | + | - | - | - | - | + | - | + | + | - |
Global distribution of 16S sequence AJ233436 (>99% sequence identity) for Serratia from Microbeatlas ![]()
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 124043 | ASM1602673v1 assembly for Serratia rubidaea FDAARGOS_926 | complete | 61652 | 99.21 | ||||
| 67770 | ASM159867v1 assembly for Serratia rubidaea NBRC 103169 | contig | 1218096 | 73.28 | ||||
| 124043 | 28771_E01 assembly for Serratia rubidaea NCTC12971 | complete | 61652 | 56.36 | ||||
| 67770 | ASM130467v1 assembly for Serratia rubidaea CIP 103234 | contig | 61652 | 19.84 |
| @ref | Description | Accession | Length | Database | NCBI tax ID | |
|---|---|---|---|---|---|---|
| 20218 | Serratia rubidaea 16S rRNA gene (strain DSM 4480) | AJ233436 | 1509 | 61652 | ||
| 20218 | Serratia rubidaea gene for 16S ribosomal RNA, partial sequence | AB004751 | 1442 | 61652 | ||
| 20218 | Serratia rubidaea gene for 16S rRNA, partial sequence, strain: NBRC 103169 | AB681976 | 1467 | 61652 | ||
| 124043 | Serratia rubidaea strain NBRC 103169 16S ribosomal RNA gene, partial sequence. | OP564974 | 1245 | 61652 |
| @ref | GC-content (mol%) | Method | |
|---|---|---|---|
| 67770 | 53.6 | thermal denaturation, midpoint method (Tm) |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125439 | oxygen_tolerance | BacteriaNetⓘ | aerobe | 92.66 | no |
| 125439 | gram_stain | BacteriaNetⓘ | negative | 97.46 | no |
| 125439 | motility | BacteriaNetⓘ | yes | 80.66 | no |
| 125439 | spore_formation | BacteriaNetⓘ | no | 98.54 | no |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positiveⓘ | no | 99.00 | no |
| 125438 | anaerobic | anaerobicⓘ | no | 97.79 | yes |
| 125438 | spore-forming | spore-formingⓘ | no | 89.87 | no |
| 125438 | aerobic | aerobicⓘ | no | 65.96 | yes |
| 125438 | thermophilic | thermophileⓘ | no | 99.47 | yes |
| 125438 | flagellated | motile2+ⓘ | yes | 79.71 | no |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Phylogeny | Phylogenetic insights and antimicrobial biosynthetic potential of Serratia sp. XAFb12 and Pseudomonas sp. XAFb13 from Xylopia aethiopica. | Ezeobiora CE, Igbokwe NH, Amin DH, Okpalanwa CF, Stephen CM, Mendie UE. | Braz J Microbiol | 10.1007/s42770-023-01213-w | 2024 | |
| Phylogeny | Simultaneous Rapid Detection and Serotyping of Cronobacter sakazakii Serotypes O1, O2, and O3 by Using Specific Monoclonal Antibodies. | Scharinger EJ, Dietrich R, Kleinsteuber I, Martlbauer E, Schauer K. | Appl Environ Microbiol | 10.1128/aem.04016-15 | 2016 | |
| Influence of outer membrane permeabilization on intrinsic resistance to the hydrophobic biocide triclosan in opportunistic Serratia species. | Kavya B, King B, Rigsbee AS, Yang JG, Sprinkles W, Patel VM, McDonald AA, Amburn SK, Champlin FR. | Heliyon | 10.1016/j.heliyon.2023.e15385 | 2023 | ||
| Enzymology | Use of quantitative real-time PCR for direct detection of serratia marcescens in marine and other aquatic environments. | Joyner J, Wanless D, Sinigalliano CD, Lipp EK. | Appl Environ Microbiol | 10.1128/aem.02755-13 | 2014 | |
| Enzymology | Molecular method for detection of total coliforms in drinking water samples. | Maheux AF, Boudreau DK, Bisson MA, Dion-Dupont V, Bouchard S, Nkuranga M, Bergeron MG, Rodriguez MJ. | Appl Environ Microbiol | 10.1128/aem.00546-14 | 2014 | |
| Direct Colony Thin-Layer Chromatography and Rapid Characterization of Serratia marcescens Mutants Defective in Production of Wetting Agents. | Matsuyama T, Sogawa M, Yano I. | Appl Environ Microbiol | 10.1128/aem.53.5.1186-1188.1987 | 1987 | ||
| Surface-active novel glycolipid and linked 3-hydroxy fatty acids produced by Serratia rubidaea. | Matsuyama T, Kaneda K, Ishizuka I, Toida T, Yano I. | J Bacteriol | 10.1128/jb.172.6.3015-3022.1990 | 1990 | ||
| Enzymology | Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples. | Maheux AF, Bissonnette L, Boissinot M, Bernier JL, Huppe V, Picard FJ, Berube E, Bergeron MG. | Appl Environ Microbiol | 10.1128/aem.02337-10 | 2011 | |
| Enzymology | Description and evaluation of the semiautomated 4-hour ATB 32E method for identification of members of the family Enterobacteriaceae. | Freney J, Herve C, Desmonceaux M, Allard F, Boeufgras JM, Monget D, Fleurette J. | J Clin Microbiol | 10.1128/jcm.29.1.138-141.1991 | 1991 | |
| Phylogeny | Evaluation of tyrosine medium for the identification of Enterobacteriaceae. | Sheth NK, Kurup VP. | J Clin Microbiol | 10.1128/jcm.1.5.483-485.1975 | 1975 | |
| Compilation of small ribosomal subunit RNA structures. | Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R. | Nucleic Acids Res | 10.1093/nar/21.13.3025 | 1993 | ||
| Enzymology | Kinetic properties of Serratia marcescens adenosine 5'-diphosphate glucose pyrophosphorylase. | Preiss J, Crawford K, Downey J, Lammel C, Greenberg E. | J Bacteriol | 10.1128/jb.127.1.193-203.1976 | 1976 | |
| Metabolism | Characterization of an acetan-like heteropolysaccharide produced by Kozakia baliensis NBRC 16680. | Brandt JU, Jakob F, Wefers D, Bunzel M, Vogel RF. | Int J Biol Macromol | 10.1016/j.ijbiomac.2017.08.022 | 2018 | |
| Metabolism | Characterization of growth and exopolysaccharide production of selected acetic acid bacteria in buckwheat sourdoughs. | Ua-Arak T, Jakob F, Vogel RF. | Int J Food Microbiol | 10.1016/j.ijfoodmicro.2016.04.009 | 2016 | |
| Metabolism | Environmentally triggered genomic plasticity and capsular polysaccharide formation are involved in increased ethanol and acetic acid tolerance in Kozakia baliensis NBRC 16680. | Brandt JU, Born FL, Jakob F, Vogel RF. | BMC Microbiol | 10.1186/s12866-017-1070-y | 2017 | |
| Metabolism | Chromosome-Encoded Broad-Spectrum Ambler Class A beta-Lactamase RUB-1 from Serratia rubidaea. | Bonnin RA, Didi J, Ergani A, Lima S, Naas T | Antimicrob Agents Chemother | 10.1128/AAC.01908-16 | 2017 | |
| Genetics | Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen. | Bonnin RA, Girlich D, Imanci D, Dortet L, Naas T | Genome Announc | 10.1128/genomeA.01340-15 | 2015 | |
| Phylogeny | Isolation and characterization of a chromium-resistant bacterium Serratia sp. Cr-10 from a chromate-contaminated site. | Zhang K, Li F | Appl Microbiol Biotechnol | 10.1007/s00253-011-3120-y | 2011 | |
| Phylogeny | Streptomyces capitiformicae sp. nov., a novel actinomycete producing angucyclinone antibiotics isolated from the head of Camponotus japonicus Mayr. | Jiang S, Piao C, Yu Y, Cao P, Li C, Yang F, Li M, Xiang W, Liu C. | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002468 | 2018 |
| #1693 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4480 |
| #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 ) |
| #39850 | ; Curators of the CIP; |
| #67770 | Japan Collection of Microorganism (JCM) ; Curators of the JCM; |
| #68368 | Automatically annotated from API 20E . |
| #68371 | Automatically annotated from API 50CH acid . |
| #68382 | Automatically annotated from API zym . |
| #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 . |
| #122283 | Collection of Institut Pasteur ; Curators of the CIP; CIP 103234 |
| #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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