Detail View for BacDive IDs
Description
This view contains detailed information on the strain associated with the requested BacDive ID. All other endpoints contain links pointing to this view.
/v2/fetch/{bacdive_id}?predictions={predictions}
{bacdive_id}- the number for the BacDive ID or IDs separated by semicolon. Limit of 100 IDs per call{predictions}- optional parameter. If set to 1 the prediction data generated with AI will be shown. If unset or set to 0, predictions will be excluded from the data.
Examples
/v2/fetch/24493;24494
/v2/fetch/24493;24494?predictions=1
Result description
count- the number of retrieved entries (strains) for the given genus namenext- URL to the next page, if available, otherwisenullprevious- URL to the previous page, if available, otherwisenull-
results- list of retrieved entries (strains) for the given genus name, paginated with 100 entries per page.- You can find detailed information of the content delivered from the API per strain here
GET /v2/fetch/24493{
"count": 1,
"next": null,
"previous": null,
"results": {
"24493": {
"General": {
"@ref": 20729,
"BacDive-ID": 24493,
"DSM-Number": 26640,
"keywords": [
"genome sequence",
"16S sequence",
"Bacteria",
"Gram-negative",
"motile",
"rod-shaped"
],
"description": "Phaeobacter gallaeciensis BS 107 is a Gram-negative, motile, rod-shaped bacterium that was isolated from seawater from larval cultures of scallop, Pecten maximus.",
"NCBI tax id": [
{
"NCBI tax id": 1423144,
"Matching level": "strain"
},
{
"NCBI tax id": 60890,
"Matching level": "species"
}
],
"strain history": [
{
"@ref": 20729,
"history": "<- T. Brinkhoff, Univ. Oldenburg, Germany <- CIP <- C. Ruiz-Ponte; BS 107"
},
{
"@ref": 67770,
"history": "IAM 14812 <-- CIP 105210 <-- C. Ruiz-Ponte BS107."
},
{
"@ref": 119508,
"history": "CIP <- 1997, C. Ruiz-Ponte, IFREMER, Brest, France: strain BS 107"
}
],
"doi": "10.13145/bacdive24493.20251217.10"
},
"Name and taxonomic classification": {
"LPSN": {
"@ref": 20215,
"description": "domain/bacteria",
"keyword": "phylum/pseudomonadota",
"domain": "Bacteria",
"phylum": "Pseudomonadota",
"class": "Alphaproteobacteria",
"order": "Rhodobacterales",
"family": "Roseobacteraceae",
"genus": "Phaeobacter",
"species": "Phaeobacter gallaeciensis",
"full scientific name": "Phaeobacter gallaeciensis (Ruiz-Ponte et al. 1998) Martens et al. 2006",
"synonyms": {
"@ref": 20215,
"synonym": "Roseobacter gallaeciensis"
}
},
"@ref": 20729,
"domain": "Bacteria",
"phylum": "Proteobacteria",
"class": "Alphaproteobacteria",
"order": "Rhodobacterales",
"family": "Rhodobacteraceae",
"genus": "Phaeobacter",
"species": "Phaeobacter gallaeciensis",
"full scientific name": "Phaeobacter gallaeciensis (Ruiz-Ponte et al. 1998) Martens et al. 2006",
"strain designation": "BS 107",
"type strain": "yes"
},
"Morphology": {
"cell morphology": {
"@ref": 119508,
"gram stain": "negative",
"cell shape": "rod-shaped",
"motility": "yes"
},
"colony morphology": {
"@ref": 20729,
"incubation period": "1-2 days"
}
},
"Culture and growth conditions": {
"culture medium": [
{
"@ref": 20729,
"name": "BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)",
"growth": "yes",
"link": "https://mediadive.dsmz.de/medium/514",
"composition": "Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)\nComposition:\nNaCl 19.45 g/l\nMgCl2 5.9 g/l\nBacto peptone 5.0 g/l\nNa2SO4 3.24 g/l\nCaCl2 1.8 g/l\nYeast extract 1.0 g/l\nKCl 0.55 g/l\nNaHCO3 0.16 g/l\nFe(III) citrate 0.1 g/l\nKBr 0.08 g/l\nSrCl2 0.034 g/l\nH3BO3 0.022 g/l\nNa2HPO4 0.008 g/l\nNa-silicate 0.004 g/l\nNaF 0.0024 g/l\n(NH4)NO3 0.0016 g/l\nDistilled water"
},
{
"@ref": 41627,
"name": "Marine agar (MA)",
"growth": "yes",
"composition": "Distilled water make up to (1000.000 ml);Marine agar (55.100 g)"
},
{
"@ref": 119508,
"name": "CIP Medium 13",
"growth": "yes",
"link": "https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13"
}
],
"culture temp": [
{
"@ref": 20729,
"growth": "positive",
"type": "growth",
"temperature": "25"
},
{
"@ref": 41627,
"growth": "positive",
"type": "growth",
"temperature": "22"
},
{
"@ref": 67770,
"growth": "positive",
"type": "growth",
"temperature": "25"
},
{
"@ref": 119508,
"growth": "positive",
"type": "growth",
"temperature": "5-30"
},
{
"@ref": 119508,
"growth": "negative",
"type": "growth",
"temperature": "37"
},
{
"@ref": 119508,
"growth": "negative",
"type": "growth",
"temperature": "41"
},
{
"@ref": 119508,
"growth": "negative",
"type": "growth",
"temperature": "45"
}
]
},
"Physiology and metabolism": {
"metabolite utilization": [
{
"@ref": 119508,
"Chebi-ID": 606565,
"metabolite": "hippurate",
"utilization activity": "-",
"kind of utilization tested": "hydrolysis"
},
{
"@ref": 119508,
"Chebi-ID": 17632,
"metabolite": "nitrate",
"utilization activity": "-",
"kind of utilization tested": "builds gas from"
},
{
"@ref": 119508,
"Chebi-ID": 17632,
"metabolite": "nitrate",
"utilization activity": "+",
"kind of utilization tested": "reduction"
},
{
"@ref": 119508,
"Chebi-ID": 16301,
"metabolite": "nitrite",
"utilization activity": "-",
"kind of utilization tested": "builds gas from"
},
{
"@ref": 119508,
"Chebi-ID": 16301,
"metabolite": "nitrite",
"utilization activity": "-",
"kind of utilization tested": "reduction"
},
{
"@ref": 68369,
"Chebi-ID": 27689,
"metabolite": "decanoate",
"utilization activity": "-",
"kind of utilization tested": "assimilation"
},
{
"@ref": 68369,
"Chebi-ID": 5291,
"metabolite": "gelatin",
"utilization activity": "-",
"kind of utilization tested": "hydrolysis"
},
{
"@ref": 68369,
"Chebi-ID": 4853,
"metabolite": "esculin",
"utilization activity": "-",
"kind of utilization tested": "hydrolysis"
},
{
"@ref": 68369,
"Chebi-ID": 16199,
"metabolite": "urea",
"utilization activity": "-",
"kind of utilization tested": "hydrolysis"
},
{
"@ref": 68369,
"Chebi-ID": 29016,
"metabolite": "arginine",
"utilization activity": "-",
"kind of utilization tested": "hydrolysis"
},
{
"@ref": 68369,
"Chebi-ID": 17634,
"metabolite": "D-glucose",
"utilization activity": "-",
"kind of utilization tested": "fermentation"
},
{
"@ref": 68369,
"Chebi-ID": 27897,
"metabolite": "tryptophan",
"utilization activity": "-",
"kind of utilization tested": "energy source"
},
{
"@ref": 68369,
"Chebi-ID": 17632,
"metabolite": "nitrate",
"utilization activity": "-",
"kind of utilization tested": "reduction"
}
],
"antibiotic resistance": {
"@ref": 119508,
"metabolite": "0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)",
"is sensitive": "no",
"is resistant": "yes"
},
"metabolite production": [
{
"@ref": 68369,
"Chebi-ID": 35581,
"metabolite": "indole",
"production": "no"
},
{
"@ref": 119508,
"Chebi-ID": 35581,
"metabolite": "indole",
"production": "no"
}
],
"metabolite tests": {
"@ref": 68369,
"Chebi-ID": 35581,
"metabolite": "indole",
"indole test": "-"
},
"enzymes": [
{
"@ref": 20729,
"value": "catalase",
"activity": "+",
"ec": "1.11.1.6"
},
{
"@ref": 20729,
"value": "cytochrome-c oxidase",
"activity": "+",
"ec": "1.9.3.1"
},
{
"@ref": 68382,
"value": "alkaline phosphatase",
"activity": "+",
"ec": "3.1.3.1"
},
{
"@ref": 68382,
"value": "esterase (C 4)",
"activity": "+"
},
{
"@ref": 68382,
"value": "esterase lipase (C 8)",
"activity": "+"
},
{
"@ref": 68382,
"value": "lipase (C 14)",
"activity": "-"
},
{
"@ref": 68382,
"value": "leucine arylamidase",
"activity": "+",
"ec": "3.4.11.1"
},
{
"@ref": 68382,
"value": "valine arylamidase",
"activity": "-"
},
{
"@ref": 68382,
"value": "cystine arylamidase",
"activity": "-",
"ec": "3.4.11.3"
},
{
"@ref": 68382,
"value": "trypsin",
"activity": "-",
"ec": "3.4.21.4"
},
{
"@ref": 68382,
"value": "alpha-chymotrypsin",
"activity": "-",
"ec": "3.4.21.1"
},
{
"@ref": 68382,
"value": "acid phosphatase",
"activity": "+",
"ec": "3.1.3.2"
},
{
"@ref": 68382,
"value": "naphthol-AS-BI-phosphohydrolase",
"activity": "+"
},
{
"@ref": 68382,
"value": "alpha-galactosidase",
"activity": "-",
"ec": "3.2.1.22"
},
{
"@ref": 68382,
"value": "beta-galactosidase",
"activity": "-",
"ec": "3.2.1.23"
},
{
"@ref": 68382,
"value": "beta-glucuronidase",
"activity": "-",
"ec": "3.2.1.31"
},
{
"@ref": 68382,
"value": "alpha-glucosidase",
"activity": "-",
"ec": "3.2.1.20"
},
{
"@ref": 68382,
"value": "beta-glucosidase",
"activity": "-",
"ec": "3.2.1.21"
},
{
"@ref": 68382,
"value": "N-acetyl-beta-glucosaminidase",
"activity": "-",
"ec": "3.2.1.52"
},
{
"@ref": 68382,
"value": "alpha-mannosidase",
"activity": "-",
"ec": "3.2.1.24"
},
{
"@ref": 68382,
"value": "alpha-fucosidase",
"activity": "-",
"ec": "3.2.1.51"
},
{
"@ref": 119508,
"value": "oxidase",
"activity": "+"
},
{
"@ref": 119508,
"value": "beta-galactosidase",
"activity": "+",
"ec": "3.2.1.23"
},
{
"@ref": 119508,
"value": "gelatinase",
"activity": "+/-"
},
{
"@ref": 119508,
"value": "amylase",
"activity": "+"
},
{
"@ref": 119508,
"value": "caseinase",
"activity": "-",
"ec": "3.4.21.50"
},
{
"@ref": 119508,
"value": "catalase",
"activity": "+",
"ec": "1.11.1.6"
},
{
"@ref": 119508,
"value": "gamma-glutamyltransferase",
"activity": "+",
"ec": "2.3.2.2"
},
{
"@ref": 119508,
"value": "lecithinase",
"activity": "-"
},
{
"@ref": 119508,
"value": "lipase",
"activity": "-"
},
{
"@ref": 119508,
"value": "tryptophan deaminase",
"activity": "-"
},
{
"@ref": 119508,
"value": "urease",
"activity": "-",
"ec": "3.5.1.5"
},
{
"@ref": 68369,
"value": "gelatinase",
"activity": "-"
},
{
"@ref": 68369,
"value": "beta-glucosidase",
"activity": "-",
"ec": "3.2.1.21"
},
{
"@ref": 68369,
"value": "urease",
"activity": "-",
"ec": "3.5.1.5"
},
{
"@ref": 68369,
"value": "arginine dihydrolase",
"activity": "-",
"ec": "3.5.3.6"
}
],
"API zym": {
"@ref": 119508,
"Control": "-",
"Alkaline phosphatase": "+",
"Esterase": "+",
"Esterase Lipase": "+",
"Lipase": "-",
"Leucine arylamidase": "+",
"Valine arylamidase": "-",
"Cystine arylamidase": "-",
"Trypsin": "-",
"alpha- Chymotrypsin": "-",
"Acid phosphatase": "+",
"Naphthol-AS-BI-phosphohydrolase": "+",
"alpha- Galactosidase": "-",
"beta- Galactosidase": "-",
"beta- Glucuronidase": "-",
"alpha- Glucosidase": "-",
"beta- Glucosidase": "-",
"N-acetyl-beta- glucosaminidase": "-",
"alpha- Mannosidase": "-",
"alpha- Fucosidase": "-"
},
"API 20NE": [
{
"@ref": 20729,
"NO3": "-",
"TRP": "-",
"GLU_ Ferm": "-",
"ADH Arg": "-",
"URE": "-",
"ESC": "-",
"GEL": "-",
"PNPG": "+",
"GLU_ Assim": "-",
"ARA": "-",
"MNE": "-",
"MAN": "+/-",
"NAG": "+/-",
"MAL": "+/-",
"GNT": "-",
"CAP": "-",
"ADI": "-",
"MLT": "+/-",
"CIT": "-",
"PAC": "-"
},
{
"@ref": 20729,
"NO3": "-",
"TRP": "-",
"GLU_ Ferm": "-",
"ADH Arg": "-",
"URE": "-",
"ESC": "-",
"GEL": "-",
"PNPG": "+/-",
"GLU_ Assim": "+",
"ARA": "+",
"MNE": "+",
"MAN": "+",
"NAG": "+",
"MAL": "+",
"GNT": "+",
"CAP": "-",
"ADI": "+",
"MLT": "+",
"CIT": "+",
"PAC": "+/-"
}
],
"API biotype100": {
"@ref": 119508,
"GLU": "-",
"FRU": "-",
"GAL": "-",
"TRE": "-",
"MNE": "-",
"SBE": "-",
"MEL": "-",
"SAC": "-",
"RAF": "-",
"MTE": "-",
"MAL": "-",
"LAC": "-",
"LTE": "-",
"MbGa": "-",
"MaGa": "-",
"CEL": "-",
"GEN": "-",
"MbGu": "-",
"ESC": "-",
"RIB": "-",
"ARA": "-",
"XYL": "-",
"PLE": "-",
"RHA": "-",
"FUC": "-",
"MLZ": "-",
"DARL": "-",
"LARL": "-",
"XLT": "-",
"DUL": "-",
"TAG": "-",
"GLY": "-",
"INO": "-",
"MAN": "-",
"MTL": "-",
"TUR": "-",
"SOR": "-",
"ADO": "-",
"HBG": "-",
"LYX": "-",
"ERY": "-",
"MDG": "-",
"3MDG": "-",
"SAT": "-",
"MUC": "-",
"LTAT": "-",
"DTAT": "-",
"MTAT": "-",
"DMLT": "-",
"LMLT": "-",
"CATE": "-",
"TATE": "-",
"TTE": "-",
"CIT": "-",
"GRT": "-",
"GAT": "-",
"2KG": "-",
"5KG": "-",
"TRY": "-",
"NAG": "-",
"GNT": "-",
"PAC": "-",
"PAT": "-",
"pOBE": "-",
"QAT": "-",
"GTE": "-",
"mOBE": "-",
"BAT": "-",
"PPAT": "-",
"CMT": "-",
"TGE": "-",
"BET": "-",
"PCE": "-",
"ABT": "-",
"HIN": "-",
"LAT": "-",
"CAP": "-",
"CYT": "-",
"HIS": "-",
"SUC": "-",
"FUM": "-",
"GRE": "-",
"GYT": "-",
"AVT": "-",
"ETN": "-",
"TTN": "-",
"GLN": "-",
"ITA": "-",
"3OBU": "-",
"APT": "-",
"GTT": "-",
"PRO": "-",
"DALA": "-",
"LALA": "-",
"SER": "-",
"MNT": "-",
"PROP": "-",
"TYR": "-",
"2KT": "-"
}
},
"Isolation, sampling and environmental information": {
"isolation": [
{
"@ref": 20729,
"sample type": "seawater from larval cultures of scallop, Pecten maximus",
"geographic location": "Galicia",
"country": "Spain",
"origin.country": "ESP",
"continent": "Europe"
},
{
"@ref": 67770,
"sample type": "Seawater from larval cultures of the scallop, Pecten maximus",
"host species": "Pecten maximus",
"geographic location": "Instituto Oceanografico, A Coru\u00f1a",
"country": "Spain",
"origin.country": "ESP",
"continent": "Europe"
},
{
"@ref": 119508,
"sample type": "Animal, Scallop Pecten maximus, larva",
"geographic location": "Galicia",
"country": "Spain",
"origin.country": "ESP",
"continent": "Europe",
"isolation date": "1994"
}
],
"isolation source categories": [
{
"Cat1": "#Environmental",
"Cat2": "#Aquatic",
"Cat3": "#Marine"
},
{
"Cat1": "#Host",
"Cat2": "#Invertebrates (Other)",
"Cat3": "#Mollusca"
}
],
"taxonmaps": {
"@ref": 69479,
"File name": "preview.99_1899.png",
"url": "https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_566;98_1495;99_1899&stattab=map",
"Last taxonomy": "Phaeobacter",
"16S sequence": "Y13244",
"Sequence Identity": null,
"Total samples": 7469,
"soil counts": 318,
"aquatic counts": 6774,
"animal counts": 295,
"plant counts": 82
}
},
"Interaction and safety": {
"risk assessment": [
{
"@ref": 20729,
"biosafety level": "1",
"biosafety level comment": "Risk group (German classification)"
},
{
"@ref": 119508,
"biosafety level": "1",
"biosafety level comment": "Risk group (French classification)"
}
]
},
"Sequence information": {
"Genome sequences": [
{
"@ref": 66792,
"description": "ASM51138v1 assembly for Phaeobacter gallaeciensis DSM 26640",
"assembly level": "complete",
"INSDC accession": "GCA_000511385",
"BV-BRC accession": "1423144.3",
"IMG accession": "2558309061",
"NCBI tax ID": 1423144,
"score": 95.9
},
{
"@ref": 67770,
"description": "ASM81962v1 assembly for Phaeobacter gallaeciensis DSM 26640",
"assembly level": "contig",
"INSDC accession": "GCA_000819625",
"BV-BRC accession": "1423144.14",
"IMG accession": "2545555837",
"NCBI tax ID": 1423144,
"score": 68.42
}
],
"16S sequences": [
{
"@ref": 20729,
"description": "Phaeobacter gallaeciensis strain CIP 105210 16S ribosomal RNA gene, partial sequence",
"accession": "KC176239",
"length": 1380,
"database": "nuccore",
"NCBI tax ID": 1423144
},
{
"@ref": 67770,
"description": "Roseobacter gallaeciensis 16S rRNA gene",
"accession": "Y13244",
"length": 1382,
"database": "nuccore",
"NCBI tax ID": 1423144
}
]
},
"Genome-based predictions": {},
"Literature": {
"@ref": 20729,
"culture collection no.": "DSM 26640, CIP 105210, IAM 14812, JCM 21319, ATCC 700781, IFO 16654, NBRC 16654",
"straininfo link": {
"@ref": 126262,
"straininfo": 44134
},
"literature": [
{
"topic": "Phylogeny",
"Pubmed-ID": "9731295",
"title": "Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus.",
"authors": "Ruiz-Ponte C, Cilia V, Lambert C, Nicolas JL",
"journal": "Int J Syst Bacteriol",
"DOI": "10.1099/00207713-48-2-537",
"year": 1998,
"mesh": "Animals, Base Composition, Base Sequence, DNA, Bacterial, Gram-Negative Aerobic Rods and Cocci/*classification/metabolism/physiology, Microbial Sensitivity Tests, Molecular Sequence Data, Mollusca/*microbiology, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial, RNA, Ribosomal",
"topic2": "Genetics"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "16738106",
"title": "Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera.",
"authors": "Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T",
"journal": "Int J Syst Evol Microbiol",
"DOI": "10.1099/ijs.0.63724-0",
"year": 2006,
"mesh": "Chromosomes, Bacterial, DNA, Bacterial/genetics, Fatty Acids/analysis, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Roseobacter/*classification/drug effects/growth & development/isolation & purification/ultrastructure",
"topic2": "Genetics"
},
{
"topic": "Metabolism",
"Pubmed-ID": "20601479",
"title": "Expression of tropodithietic acid biosynthesis is controlled by a novel autoinducer.",
"authors": "Geng H, Belas R.",
"journal": "J Bacteriol",
"DOI": "10.1128/jb.00410-10",
"year": 2010,
"mesh": "Pfiesteria piscicida, Rhodobacteraceae, analogs & derivatives, metabolism, Symbiosis, Gene Expression Regulation, Bacterial"
},
{
"Pubmed-ID": "21097494",
"title": "Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales.",
"authors": "Petersen J, Brinkmann H, Berger M, Brinkhoff T, Pauker O, Pradella S.",
"journal": "Mol Biol Evol",
"DOI": "10.1093/molbev/msq310",
"year": 2011,
"mesh": "genetics, genetics, DNA, Bacterial, Plasmids"
},
{
"topic": "Metabolism",
"Pubmed-ID": "21430694",
"title": "The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis.",
"authors": "Seyedsayamdost MR, Case RJ, Kolter R, Clardy J.",
"journal": "Nat Chem",
"DOI": "10.1038/nchem.1002",
"year": 2011,
"mesh": "metabolism, metabolism, metabolism, physiology, metabolism"
},
{
"topic": "Metabolism",
"Pubmed-ID": "21928816",
"title": "Roseobacticides: small molecule modulators of an algal-bacterial symbiosis.",
"authors": "Seyedsayamdost MR, Carr G, Kolter R, Clardy J.",
"journal": "J Am Chem Soc",
"DOI": "10.1021/ja207172s",
"year": 2011,
"mesh": "metabolism, metabolism, Symbiosis"
},
{
"topic": "Metabolism",
"Pubmed-ID": "22037399",
"title": "Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.",
"authors": "Haft DH, Payne SH, Selengut JD.",
"journal": "J Bacteriol",
"DOI": "10.1128/jb.06026-11",
"year": 2012,
"mesh": "metabolism, metabolism, metabolism, metabolism, physiology"
},
{
"topic": "Genetics",
"Pubmed-ID": "22336032",
"title": "High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade.",
"authors": "Christie-Oleza JA, Miotello G, Armengaud J.",
"journal": "BMC Genomics",
"DOI": "10.1186/1471-2164-13-73",
"year": 2012,
"mesh": "genetics, Proteomics, Genomics, genetics"
},
{
"topic": "Metabolism",
"Pubmed-ID": "22563425",
"title": "The Ruegeria pomeroyi acuI gene has a role in DMSP catabolism and resembles yhdH of E. coli and other bacteria in conferring resistance to acrylate.",
"authors": "Todd JD, Curson AR, Sullivan MJ, Kirkwood M, Johnston AW.",
"journal": "PLoS One",
"DOI": "10.1371/journal.pone.0035947",
"year": 2012,
"mesh": "metabolism, enzymology, pharmacology, metabolism, metabolism, metabolism, metabolism",
"topic2": "Enzymology"
},
{
"Pubmed-ID": "23161030",
"title": "A novel inducer of Roseobacter motility is also a disruptor of algal symbiosis.",
"authors": "Sule P, Belas R.",
"journal": "J Bacteriol",
"DOI": "10.1128/jb.01777-12",
"year": 2013,
"mesh": "physiology, physiology, physiology"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "24187021",
"title": "Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395.",
"authors": "Buddruhs N, Pradella S, Goker M, Pauker O, Pukall R, Sproer C, Schumann P, Petersen J, Brinkhoff T",
"journal": "Int J Syst Evol Microbiol",
"DOI": "10.1099/ijs.0.053900-0",
"year": 2013,
"mesh": "Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Electrophoresis, Gel, Pulsed-Field, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Hybridization, *Phylogeny, Plasmids/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/growth & development, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization",
"topic2": "Enzymology"
},
{
"Pubmed-ID": "24586966",
"title": "Assessing the exoproteome of marine bacteria, lesson from a RTX-toxin abundantly secreted by Phaeobacter strain DSM 17395.",
"authors": "Durighello E, Christie-Oleza JA, Armengaud J.",
"journal": "PLoS One",
"DOI": "10.1371/journal.pone.0089691",
"year": 2014,
"mesh": "genetics"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "25027448",
"title": "Seohaeicola nanhaiensis sp. nov., a moderately halophilic bacterium isolated from the benthic sediment of South China Sea.",
"authors": "Xie BS, Lv XL, Cai M, Tang YQ, Wang YN, Cui HL, Liu XY, Tan Y, Wu XL",
"journal": "Curr Microbiol",
"DOI": "10.1007/s00284-014-0658-9",
"year": 2014,
"mesh": "Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature",
"topic2": "Genetics"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "25180090",
"title": "Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.",
"authors": "Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC",
"journal": "Int J Syst Evol Microbiol",
"DOI": "10.1099/ijs.0.066142-0",
"year": 2014,
"mesh": "Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry",
"topic2": "Genetics"
},
{
"topic": "Genetics",
"Pubmed-ID": "25197473",
"title": "Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).",
"authors": "Frank O, Pradella S, Rohde M, Scheuner C, Klenk HP, Goker M, Petersen J",
"journal": "Stand Genomic Sci",
"DOI": "10.4056/sigs.5179110",
"year": 2014
},
{
"topic": "Phylogeny",
"Pubmed-ID": "25355001",
"title": "Phaeobacter marinintestinus sp. nov., isolated from the intestine of a sea cucumber (Apostichopus japonicus).",
"authors": "Lee MH, Song EJ, Seo MJ, Hyun DW, Bae JW, Lee SY, Roh SW, Nam YD.",
"journal": "Antonie Van Leeuwenhoek",
"DOI": "10.1007/s10482-014-0318-x",
"year": 2015,
"mesh": "microbiology, classification, isolation & purification",
"topic2": "Enzymology"
},
{
"topic": "Metabolism",
"Pubmed-ID": "25355937",
"title": "A solo luxI-type gene directs acylhomoserine lactone synthesis and contributes to motility control in the marine sponge symbiont Ruegeria sp. KLH11.",
"authors": "Zan J, Choi O, Meharena H, Uhlson CL, Churchill MEA, Hill RT, Fuqua C.",
"journal": "Microbiology (Reading)",
"DOI": "10.1099/mic.0.083956-0",
"year": 2015,
"mesh": "microbiology, genetics, metabolism, genetics, genetics, Symbiosis, metabolism"
},
{
"topic": "Genetics",
"Pubmed-ID": "25755651",
"title": "Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes.",
"authors": "Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV.",
"journal": "Front Microbiol",
"DOI": "10.3389/fmicb.2015.00123",
"year": 2015,
"mesh": "Symbiosis, Genomics, Cephalopoda, Alphaproteobacteria, Euprymna Scolopes, Roseobacter Clade"
},
{
"Pubmed-ID": "25779873",
"title": "Thermodynamic matchers for the construction of the cuckoo RNA family.",
"authors": "Reinkensmeier J, Giegerich R.",
"journal": "RNA Biol",
"DOI": "10.1080/15476286.2015.1017206",
"year": 2015,
"mesh": "Small RNA, Alphaproteobacteria, Homology Search, Structural Rna, Rbs, Ribosome Binding Site, Cin, Conserved Intergenic Neighborhood, Cm, Covariance Model, Hmm, Hidden Markov Model, Mfe, Minimum Free Energy, Og, Orthologous Group Of Genes, Rfm, Rna Family Model, Tdm, Thermodynamic Matcher, Asd, Anti Shine-dalgarno, Cuckoo Rna, Drna-seq, Differential Rna Sequencing, Family Model, Srna, Small Non-coding Rna, Thermodynamic Matcher, genetics, genetics, chemistry, Algorithms, chemistry"
},
{
"Pubmed-ID": "25867634",
"title": "A small volume bioassay to assess bacterial/phytoplankton co-culture using WATER-Pulse-Amplitude-Modulated (WATER-PAM) fluorometry.",
"authors": "Bramucci AR, Labeeuw L, Mayers TJ, Saby JA, Case RJ.",
"journal": "J Vis Exp",
"DOI": "10.3791/52455",
"year": 2015,
"mesh": "cytology, methods, methods, cytology"
},
{
"topic": "Metabolism",
"Pubmed-ID": "26058574",
"title": "Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade.",
"authors": "Lidbury I, Kimberley G, Scanlan DJ, Murrell JC, Chen Y.",
"journal": "Environ Microbiol",
"DOI": "10.1111/1462-2920.12943",
"year": 2015,
"mesh": "genetics, metabolism, metabolism"
},
{
"topic": "Metabolism",
"Pubmed-ID": "27092515",
"title": "Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes.",
"authors": "Amoutzias GD, Chaliotis A, Mossialos D.",
"journal": "Mar Drugs",
"DOI": "10.3390/md14040080",
"year": 2016,
"mesh": "Evolution, Nonribosomal peptide synthetase, Bioactive compounds, Metagenomics, Bioprospecting, Polyketide Synthase, Genome Mining, Marine Microbiomes, metabolism, metabolism, biosynthesis, physiology",
"topic2": "Genetics"
},
{
"Pubmed-ID": "27379036",
"title": "A Bacterial Pathogen Displaying Temperature-Enhanced Virulence of the Microalga Emiliania huxleyi.",
"authors": "Mayers TJ, Bramucci AR, Yakimovich KM, Case RJ.",
"journal": "Front Microbiol",
"DOI": "10.3389/fmicb.2016.00892",
"year": 2016,
"mesh": "Climate change, Phytoplankton, Emiliania huxleyi, Roseobacter, Ocean Warming, Marine Pathogen, Ruegeria, Temperature-enhanced Virulence"
},
{
"topic": "Metabolism",
"Pubmed-ID": "27834614",
"title": "Conserved small mRNA with an unique, extended Shine-Dalgarno sequence.",
"authors": "Hahn J, Thalmann S, Migur A, von Boeselager RF, Kubatova N, Kubareva E, Schwalbe H, Evguenieva-Hackenberg E.",
"journal": "RNA Biol",
"DOI": "10.1080/15476286.2016.1256534",
"year": 2017,
"mesh": "genetics, genetics, metabolism, metabolism"
},
{
"Pubmed-ID": "27895629",
"title": "Genome-Wide Discovery of Putative sRNAs in Paracoccus denitrificans Expressed under Nitrous Oxide Emitting Conditions.",
"authors": "Gaimster H, Chalklen L, Alston M, Munnoch JT, Richardson DJ, Gates AJ, Rowley G.",
"journal": "Front Microbiol",
"DOI": "10.3389/fmicb.2016.01806",
"year": 2016,
"mesh": "Soil, Denitrification, Regulation, Nitrous oxide, sRNA, Nosz"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "28699865",
"title": "Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour.",
"authors": "Breider S, Freese HM, Sproer C, Simon M, Overmann J, Brinkhoff T",
"journal": "Int J Syst Evol Microbiol",
"DOI": "10.1099/ijsem.0.001879",
"year": 2017,
"mesh": "Anti-Bacterial Agents/biosynthesis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Heterotrophic Processes, North Sea, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry",
"topic2": "Transcriptome"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "28809139",
"title": "Paraphaeobacter pallidus gen. nov., sp. nov., isolated from seawater.",
"authors": "Cai X, Wang Y, Yang X, Liu J, Wu Y, Zhang XH",
"journal": "Int J Syst Evol Microbiol",
"DOI": "10.1099/ijsem.0.001935",
"year": 2017,
"mesh": "Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA",
"topic2": "Transcriptome"
},
{
"Pubmed-ID": "28912769",
"title": "Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton.",
"authors": "Freese HM, Methner A, Overmann J",
"journal": "Front Microbiol",
"DOI": "10.3389/fmicb.2017.01659",
"year": 2017
},
{
"topic": "Metabolism",
"Pubmed-ID": "29192774",
"title": "Nitrogen-Containing Volatiles from Marine Salinispora pacifica and Roseobacter-Group Bacteria.",
"authors": "Harig T, Schlawis C, Ziesche L, Pohlner M, Engelen B, Schulz S.",
"journal": "J Nat Prod",
"DOI": "10.1021/acs.jnatprod.7b00789",
"year": 2017,
"mesh": "metabolism, metabolism, metabolism, metabolism"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "29458459",
"title": "Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill.",
"authors": "Klotz F, Brinkhoff T, Freese HM, Wietz M, Teske A, Simon M, Giebel HA.",
"journal": "Int J Syst Evol Microbiol",
"DOI": "10.1099/ijsem.0.002573",
"year": 2018,
"mesh": "Oil spill, Roseobacter, Deepwater Horizon, Rhodobacteraceae, Oil Degradation, classification, microbiology, Phylogeny, Petroleum Pollution"
},
{
"topic": "Phylogeny",
"Pubmed-ID": "31913437",
"title": "Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench.",
"authors": "Ding W, Liu P, Xu Y, Fang J, Cao J",
"journal": "FEMS Microbiol Lett",
"DOI": "10.1093/femsle/fnaa004",
"year": 2019,
"mesh": "Base Composition, China, Chromosomes, Bacterial, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Phospholipids/analysis, *Phylogeny, Plasmids/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature",
"topic2": "Transcriptome"
},
{
"Pubmed-ID": "32896070",
"title": "Quorum sensing regulates 'swim-or-stick' lifestyle in the phycosphere.",
"authors": "Fei C, Ochsenkuhn MA, Shibl AA, Isaac A, Wang C, Amin SA.",
"journal": "Environ Microbiol",
"DOI": "10.1111/1462-2920.15228",
"year": 2020,
"mesh": "microbiology, microbiology, Bacterial Adhesion, Locomotion, physiology"
},
{
"Pubmed-ID": "33178167",
"title": "Evaluation of the Production of Dissolved Organic Matter by Three Marine Bacterial Strains.",
"authors": "Goto S, Tada Y, Suzuki K, Yamashita Y.",
"journal": "Front Microbiol",
"DOI": "10.3389/fmicb.2020.584419",
"year": 2020,
"mesh": "DOC, Vibrio splendidus, Alteromonas Macleodii, Fluorescent Dom, Microbial Carbon Pump, Phaeobacter Gallaeciensis"
},
{
"Pubmed-ID": "34341505",
"title": "Bacterial controlled mitigation of dysbiosis in a seaweed disease.",
"authors": "Li J, Majzoub ME, Marzinelli EM, Dai Z, Thomas T, Egan S.",
"journal": "ISME J",
"DOI": "10.1038/s41396-021-01070-1",
"year": 2022,
"mesh": "Seaweed, Rhodobacteraceae, Rhodophyta"
},
{
"Pubmed-ID": "35049126",
"title": "Fluid dynamics and cell-bound Psl polysaccharide allows microplastic capture, aggregation and subsequent sedimentation by Pseudomonas aeruginosa in water.",
"authors": "Romero M, Carabelli A, R Swift M, I Smith M.",
"journal": "Environ Microbiol",
"DOI": "10.1111/1462-2920.15916",
"year": 2022,
"mesh": "Water Pollutants, Chemical, Microplastics"
},
{
"Pubmed-ID": "35532230",
"title": "Draft Genome Sequence of Nereida sp. Strain MMG025, Isolated from Giant Kelp.",
"authors": "Alker AT, Hern NA, Ali MA, Baez MI, Baswell BC, Baxter BI, Blitz A, Calimlim TM, Chevalier CA, Eguia CA, Esparza T, Fuller AE, Gwynn CJ, Hedin AL, Johnson RA, Kaur M, Laxina RT, Lee K, Maguire PN, Martelino IF, Melendez JA, Navarro JJ, Navarro JN, Osborn JM, Padilla MR, Peralta ND, Pureza JLR, Rojas JJ, Romo TR, Sakha M, Salcedo GJ, Sims KA, Trieu TH, Niesman IR, Shikuma NJ.",
"journal": "Microbiol Resour Announc",
"DOI": "10.1128/mra.00122-22",
"year": 2022
},
{
"topic": "Genetics",
"Pubmed-ID": "35730934",
"title": "Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.",
"authors": "Morris MM, Kimbrel JA, Geng H, Tran-Gyamfi MB, Yu ET, Sale KL, Lane TW, Mayali X.",
"journal": "mSphere",
"DOI": "10.1128/msphere.00231-22",
"year": 2022,
"mesh": "Community Assembly, Rhodobacteraceae, Algal-bacterial Interactions, Metagenome-assembled Genomes, Microchloropsis, Biofuels, Microbiota"
},
{
"Pubmed-ID": "36914732",
"title": "Vitamin B12 is not shared by all marine prototrophic bacteria with their environment.",
"authors": "Sultana S, Bruns S, Wilkes H, Simon M, Wienhausen G.",
"journal": "ISME J",
"DOI": "10.1038/s41396-023-01391-3",
"year": 2023,
"mesh": "Diatoms, Vitamin B 12"
},
{
"Pubmed-ID": "38718218",
"title": "Modular Low-Copy-Number Plasmid Vectors for Rhodobacterales with Extended Host Range in Alphaproteobacteria.",
"authors": "Korner D, Schafer NM, Lagares A, Birmes L, Oehlmann NN, Addison H, Pohl S, Thanbichler M, Rebelein JG, Petersen J, Becker A.",
"journal": "ACS Synth Biol",
"DOI": "10.1021/acssynbio.4c00062",
"year": 2024,
"mesh": "Rhodobacterales, Repabc, Rhodospirillales, Hyphomicrobiales, Caulobacterales, Low-copy-number Plasmid Vectors, Alphaproteobacteria, Genetic Vectors, Plasmids"
}
]
},
"Reference": [
{
"@id": 20215,
"authors": "Parte, A.C., Sard\u00e0 Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and G\u00f6ker, M.",
"title": "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ",
"doi/url": "10.1099/ijsem.0.004332"
},
{
"@id": 20729,
"authors": "Curators of the DSMZ",
"catalogue": "Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26640)",
"doi/url": "https://www.dsmz.de/collection/catalogue/details/culture/DSM-26640"
},
{
"@id": 41627,
"authors": "Curators of the CIP",
"doi/url": "https://brclims.pasteur.fr/brcWeb/souche/detail/1/17205\r"
},
{
"@id": 66792,
"authors": "Julia Koblitz, Joaquim Sard\u00e0, Lorenz Christian Reimer, Boyke Bunk, J\u00f6rg Overmann",
"title": "Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)",
"doi/url": "https://diaspora-project.de/progress.html#genomes"
},
{
"@id": 66794,
"authors": "Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg",
"title": "BRENDA, the ELIXIR core data resource in 2021: new developments and updates",
"journal": "Nucleic Acids Res. 49: D498-D508 2020",
"doi/url": "10.1093/nar/gkaa1025",
"pubmed": 33211880
},
{
"@id": 67770,
"authors": "Curators of the JCM",
"doi/url": "https://jcm.brc.riken.jp/en/"
},
{
"@id": 68369,
"title": "Automatically annotated from API 20NE"
},
{
"@id": 68382,
"title": "Automatically annotated from API zym"
},
{
"@id": 69479,
"authors": "Jo\u00e3o F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas N\u00e4pflin and Christian von Mering. University of Zurich.",
"title": "MicrobeAtlas 1.0 beta",
"doi/url": "https://microbeatlas.org/"
},
{
"@id": 119508,
"authors": "Curators of the CIP",
"catalogue": "Collection of Institut Pasteur (CIP 105210)",
"doi/url": "https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105210"
},
{
"@id": 125438,
"authors": "Julia Koblitz, Lorenz Christian Reimer, R\u00fcdiger Pukall, J\u00f6rg Overmann",
"title": "Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets",
"doi/url": "10.1101/2024.08.12.607695"
},
{
"@id": 125439,
"authors": "Philipp M\u00fcnch, Ren\u00e9 Mreches, Martin Binder, H\u00fcseyin Anil G\u00fcnd\u00fcz, Xiao-Yin To, Alice McHardy",
"title": "deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1",
"doi/url": "https://github.com/GenomeNet/deepG"
},
{
"@id": 126262,
"authors": "A. Lissin, I. Schober, J. F. Witte, H. L\u00fcken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer",
"title": "StrainInfo\u2014the central database for linked microbial strain identifiers",
"doi/url": "10.1093/database/baaf059"
}
]
}
}
}
License