jwokaty
commented
1 year ago The 'yes'/'no' comes from how the data is presented in the API, so I think it means 'yes' it is produced or 'no' it isn't produced. Maybe the 'no' values aren't so helpful. But I can alter the script that gets the BacDive data so that it produces data that makes more sense or uses ontology terms where possible. This is what I get for this strain via the API:
{
"count": 1,
"next": null,
"previous": null,
"results": {
"15070": {
"General": {
"@ref": 9412,
"BacDive-ID": 15070,
"DSM-Number": 40258,
"keywords": [
"antibiotic compound production",
"mesophilic",
"Bacteria",
"16S sequence",
"genome sequence"
],
"description": "Streptomyces catenulae 6563 is a mesophilic bacterium that produces antibiotic compounds.",
"NCBI tax id": {
"NCBI tax id": 66875,
"Matching level": "species"
},
"strain history": [
"<- E.B. Shirling, ISP <- J. Routien, 6563",
"KCC S-0353 <-- IFO 12848 <-- SAJ <-- ISP 5258 <-- Chas. Pfizer & Co.; 6563."
],
"doi": "10.13145/bacdive15070.20220920.7"
},
"Name and taxonomic classification": {
"LPSN": {
"@ref": 20215,
"description": "domain/bacteria",
"keyword": "phylum/actinomycetota",
"domain": "Bacteria",
"phylum": "Actinomycetota",
"class": "Actinomycetes",
"order": "Streptomycetales",
"family": "Streptomycetaceae",
"genus": "Streptomyces",
"species": "Streptomyces catenulae",
"full scientific name": "Streptomyces catenulae Davisson and Finlay 1961 (Approved Lists 1980)"
},
"@ref": 9412,
"domain": "Bacteria",
"phylum": "Actinobacteria",
"class": "Actinobacteria",
"order": "Actinomycetales",
"family": "Streptomycetaceae",
"genus": "Streptomyces",
"species": "Streptomyces catenulae",
"full scientific name": "Streptomyces catenulae Davisson and Finlay 1961 emend. Nouioui et al. 2018",
"strain designation": "6563",
"type strain": "yes"
},
"Morphology": {
"multimedia": {
"@ref": 9412,
"multimedia content": "https://www.dsmz.de/microorganisms/photos/DSM_40258.jpg",
"caption": "Medium 65 28\u00b0C",
"intellectual property rights": "\u00a9 Leibniz-Institut DSMZ"
}
},
"Culture and growth conditions": {
"culture medium": {
"@ref": 9412,
"name": "GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)",
"growth": "yes",
"link": "https://bacmedia.dsmz.de/medium/65",
"composition": "Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)\nComposition:\nAgar 12.0 g/l\nMalt extract 10.0 g/l\nYeast extract 4.0 g/l\nGlucose 4.0 g/l\nCaCO3 2.0 g/l\nDistilled water"
},
"culture temp": [
{
"@ref": 18571,
"growth": "positive",
"type": "optimum",
"temperature": "28",
"range": "mesophilic"
},
{
"@ref": 9412,
"growth": "positive",
"type": "growth",
"temperature": "28",
"range": "mesophilic"
},
{
"@ref": 67770,
"growth": "positive",
"type": "growth",
"temperature": "28",
"range": "mesophilic"
}
]
},
"Physiology and metabolism": {
"tolerance": {
"@ref": 18571,
"compound": "Lysozyme",
"percentage": "1"
},
"compound production": [
{
"@ref": 9412,
"compound": "pepsinostreptin"
},
{
"@ref": 9412,
"compound": "catenulin"
},
{
"@ref": 9412,
"compound": "paramomycin"
},
{
"@ref": 20216,
"compound": "Neomycin E"
},
{
"@ref": 20216,
"compound": "Neomycin F"
},
{
"@ref": 20216,
"compound": "pepsinostreptin complex"
}
],
"halophily": {
"@ref": 18571,
"salt": "NaCl",
"growth": "positive",
"tested relation": "maximum",
"concentration": "5 %"
},
"observation": {
"@ref": 67770,
"observation": "quinones: MK-9(H6), MK-9(H4)"
},
"metabolite utilization": [
{
"@ref": 18571,
"Chebi-ID": 17234,
"metabolite": "glucose",
"utilization activity": "+"
},
{
"@ref": 18571,
"Chebi-ID": 22599,
"metabolite": "arabinose",
"utilization activity": "-"
},
{
"@ref": 18571,
"Chebi-ID": 17992,
"metabolite": "sucrose",
"utilization activity": "-"
},
{
"@ref": 18571,
"Chebi-ID": 18222,
"metabolite": "xylose",
"utilization activity": "-"
},
{
"@ref": 18571,
"Chebi-ID": 17268,
"metabolite": "myo-inositol",
"utilization activity": "-"
},
{
"@ref": 18571,
"Chebi-ID": 29864,
"metabolite": "mannitol",
"utilization activity": "-"
},
{
"@ref": 18571,
"Chebi-ID": 28757,
"metabolite": "fructose",
"utilization activity": "+/-"
},
{
"@ref": 18571,
"Chebi-ID": 26546,
"metabolite": "rhamnose",
"utilization activity": "-"
},
{
"@ref": 18571,
"Chebi-ID": 16634,
"metabolite": "raffinose",
"utilization activity": "-"
},
{
"@ref": 18571,
"Chebi-ID": 62968,
"metabolite": "cellulose",
"utilization activity": "-"
},
{
"@ref": 68368,
"Chebi-ID": 5291,
"metabolite": "gelatin",
"utilization activity": "+",
"kind of utilization tested": "hydrolysis"
},
{
"@ref": 68368,
"Chebi-ID": 27897,
"metabolite": "tryptophan",
"utilization activity": "-",
"kind of utilization tested": "energy source"
},
{
"@ref": 68368,
"Chebi-ID": 16199,
"metabolite": "urea",
"utilization activity": "+",
"kind of utilization tested": "hydrolysis"
},
{
"@ref": 68368,
"Chebi-ID": 16947,
"metabolite": "citrate",
"utilization activity": "-",
"kind of utilization tested": "assimilation"
},
{
"@ref": 68368,
"Chebi-ID": 18257,
"metabolite": "ornithine",
"utilization activity": "-",
"kind of utilization tested": "degradation"
},
{
"@ref": 68368,
"Chebi-ID": 25094,
"metabolite": "lysine",
"utilization activity": "-",
"kind of utilization tested": "degradation"
},
{
"@ref": 68368,
"Chebi-ID": 29016,
"metabolite": "arginine",
"utilization activity": "-",
"kind of utilization tested": "hydrolysis"
}
],
"metabolite production": [
{
"@ref": 68368,
"Chebi-ID": 15688,
"metabolite": "acetoin",
"production": "yes"
},
{
"@ref": 68368,
"Chebi-ID": 35581,
"metabolite": "indole",
"production": "no"
},
{
"@ref": 68368,
"Chebi-ID": 16136,
"metabolite": "hydrogen sulfide",
"production": "no"
},
{
"@ref": 67770,
"Chebi-ID": 7934,
"metabolite": "paromomycin",
"production": "yes"
}
],
"metabolite tests": [
{
"@ref": 68368,
"Chebi-ID": 15688,
"metabolite": "acetoin",
"voges-proskauer-test": "+"
},
{
"@ref": 68368,
"Chebi-ID": 35581,
"metabolite": "indole",
"indole test": "-"
}
],
"enzymes": [
{
"@ref": 68368,
"value": "gelatinase",
"activity": "+"
},
{
"@ref": 68368,
"value": "tryptophan deaminase",
"activity": "+",
"ec": "4.1.99.1"
},
{
"@ref": 68368,
"value": "urease",
"activity": "+",
"ec": "3.5.1.5"
},
{
"@ref": 68368,
"value": "ornithine decarboxylase",
"activity": "-",
"ec": "4.1.1.17"
},
{
"@ref": 68368,
"value": "lysine decarboxylase",
"activity": "-",
"ec": "4.1.1.18"
},
{
"@ref": 68368,
"value": "arginine dihydrolase",
"activity": "-",
"ec": "3.5.3.6"
},
{
"@ref": 68368,
"value": "beta-galactosidase",
"activity": "-",
"ec": "3.2.1.23"
}
],
"API 20E": {
"@ref": 18571,
"ONPG": "-",
"ADH Arg": "-",
"LDC Lys": "-",
"ODC": "-",
"CIT": "-",
"H2S": "-",
"URE": "+",
"TDA Trp": "+",
"IND": "-",
"VP": "+",
"GEL": "+"
}
},
"Isolation, sampling and environmental information": {},
"Safety information": {
"risk assessment": [
{
"@ref": 18571,
"biosafety level": "1",
"biosafety level comment": "German classification"
},
{
"@ref": 9412,
"biosafety level": "1",
"biosafety level comment": "Risk group (German classification)"
}
]
},
"Sequence information": {
"16S sequences": [
{
"@ref": 20218,
"description": "Streptomyces catenulae 16S rRNA gene, type strain DSM 40258T",
"accession": "AJ621613",
"length": 1498,
"database": "ena",
"NCBI tax ID": 66875
},
{
"@ref": 20218,
"description": "Streptomyces catenulae gene for 16S rRNA, partial sequence",
"accession": "AB122748",
"length": 565,
"database": "ena",
"NCBI tax ID": 66875
},
{
"@ref": 20218,
"description": "Streptomyces catenulae strain ISP 5258 16S ribosomal RNA gene, partial sequence",
"accession": "AY999778",
"length": 1497,
"database": "ena",
"NCBI tax ID": 66875
},
{
"@ref": 20218,
"description": "Streptomyces catenulae gene for 16S ribosomal RNA, partial sequence, strain: JCM 4353",
"accession": "D44071",
"length": 121,
"database": "ena",
"NCBI tax ID": 66875
},
{
"@ref": 20218,
"description": "Streptomyces catenulae gene for 16S rRNA, partial sequence, strain: NBRC 12848",
"accession": "AB184191",
"length": 1480,
"database": "ena",
"NCBI tax ID": 66875
}
],
"Genome sequences": {
"@ref": 67770,
"description": "Streptomyces catenulae strain NRRL B-2342, whole genome shotgun sequencing project",
"accession": "JODY00000000",
"database": "ncbi",
"NCBI tax ID": 66875
},
"GC content": {
"@ref": 67770,
"GC-content": "73",
"method": "genome sequence analysis"
}
},
"External links": {
"@ref": 9412,
"culture collection no.": "DSM 40258, ATCC 12476, ATCC 23893, CBS 679.68, IFO 12848, ISP 5258, NBRC 12848, RIA 1183, JCM 4353, BCRC 12092, CGMCC 4.1701, HAMBI 986, IMET 42944, KCTC 9223, NRRL B-2342, VKM Ac-758",
"straininfo link": [
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/165138"
},
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/122455"
},
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/122456"
},
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/230064"
},
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/122458"
},
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/122459"
},
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/334379"
},
{
"@ref": 20218,
"passport": "http://www.straininfo.net/strains/122462"
}
],
"literature": {
"topic": "Phylogeny",
"Pubmed-ID": "35651486",
"title": "Streptomyces benahoarensis sp. nov. Isolated From a Lava Tube of La Palma, Canary Islands, Spain.",
"authors": "Gonzalez-Pimentel JL, Hermosin B, Saiz-Jimenez C, Jurado V",
"journal": "Front Microbiol",
"DOI": "10.3389/fmicb.2022.907816",
"year": 2022
}
},
"Reference": [
{
"@id": 9412,
"authors": "Curators of the DSMZ",
"catalogue": "Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40258)",
"doi/url": "https://www.dsmz.de/collection/catalogue/details/culture/DSM-40258"
},
{
"@id": 18571,
"authors": "Wink, J.",
"title": "Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig",
"doi/url": "http://www.dsmz.de/microorganisms/wink_pdf/DSM40258.pdf"
},
{
"@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": 20216,
"authors": "Curators of the HKI",
"title": "Collection Description Leibniz-Institut f\u00fcr Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Kn\u00f6ll-Institut (HKI)",
"doi/url": "http://www.leibniz-hki.de/de/"
},
{
"@id": 20218,
"authors": "Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.",
"title": "StrainInfo introduces electronic passports for microorganisms.",
"journal": "Syst Appl Microbiol. 37: 42-50 2014",
"doi/url": "10.1016/j.syapm.2013.11.002",
"pubmed": 24321274
},
{
"@id": 67770,
"authors": "Curators of the JCM",
"doi/url": "https://jcm.brc.riken.jp/en/"
},
{
"@id": 68368,
"title": "Automatically annotated from API 20E"
}
]
}
}
}
sdgamboa
In the metabolism production column, there are values of yes and no alongside the metabolites. I thought this meant if the metabolite was produced or not by the bacteria, but I wasn't able to get confirmation from the bacdive website. On the website, I don't see 'yes' or 'no' with the metabolites (metabolism production section). Could @kbeckenrode or @jwokaty confirm the meaning?
An example: https://bacdive.dsmz.de/strain/15070
Created on 2022-12-15 with reprex v2.0.2