{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003078","ANALYSIS_ID":"AN005036","VERSION":"1","CREATED_ON":"February 15, 2024, 7:35 am"},

"PROJECT":{"PROJECT_TITLE":"Dynamic exometabolomics reveals metabolic adaptations of Staphylococcus epidermidis to pH-mimicking skin and bloodstream","PROJECT_SUMMARY":"A common human skin coloniser, Staphylococcus epidermidis (SE), is often the cause of infections associated with medical devices. Strains that retain this pathogenic and commensal potential coexist in human skin, belonging to clonal lineages A/C and B, respectively. The pH is an abiotic factor that changes during infection when SE is transferred from host skin to blood. However, pathogenicity mechanisms are poorly understood in this organism and recognizing how it deals with increments of pH, is relevant to design effective prevention and treatment strategies against SE infections. To investigate the metabolic adaptations of A/C and B representative strains to an increase in pH, we mimicked the pH conditions of skin and blood (5.5 and 7.4). Biomass formation, growth media pH and 1H-NMR exometabolomic data were measured until the stationary phase was reached, at the two selected pH values. Higher biomass was reached for both strains when grown at pH 7.4. For all experimental conditions, media pH significantly changed during growth, revealing several pH adaptation mechanisms. SE metabolism relies on saccharides and amino acids uptake, citric acid cycle, mixed acid and alcoholic fermentations at a higher extent in blood than at skin pH. This study highlighted accumulation of extracellular formate by the pathogenic strain at blood pH, consistent with the absence of a formate dehydrogenase gene in this strain. This, most likely constitutes a virulence factor that, together with higher media acidification, impacts on host invasion. This work depicts the relevance of specific metabolic processes in determining SE commensalism and pathogenicity, thus providing helpful information towards new design strategies against SE infections.","INSTITUTE":"ITQB NOVA","LAST_NAME":"Morais","FIRST_NAME":"Elisabete","ADDRESS":"Campus de Campolide, ITQB NOVA, Av. da República, 2780-157 Oeiras","EMAIL":"elisabete.morais@itqb.unl.pt","PHONE":"(+351) 21 446 91 00"},

"STUDY":{"STUDY_TITLE":"Dynamic exometabolomics reveals metabolic adaptations of Staphylococcus epidermidis to pH-mimicking skin and bloodstream","STUDY_SUMMARY":"A common human skin coloniser, Staphylococcus epidermidis (SE), is often the cause of infections associated with medical devices. Strains that retain this pathogenic and commensal potential coexist in human skin, belonging to clonal lineages A/C and B, respectively. The pH is an abiotic factor that changes during infection when SE is transferred from host skin to blood. However, pathogenicity mechanisms are poorly understood in this organism and recognizing how it deals with increments of pH, is relevant to design effective prevention and treatment strategies against SE infections. To investigate the metabolic adaptations of A/C and B representative strains to an increase in pH, we mimicked the pH conditions of skin and blood (5.5 and 7.4). Biomass formation, growth media pH and 1H-NMR exometabolomic data were measured until the stationary phase was reached, at the two selected pH values. Higher biomass was reached for both strains when grown at pH 7.4. For all experimental conditions, media pH significantly changed during growth, revealing several pH adaptation mechanisms. SE metabolism relies on saccharides and amino acids uptake, citric acid cycle, mixed acid and alcoholic fermentations at a higher extent in blood than at skin pH. This study highlighted accumulation of extracellular formate by the pathogenic strain at blood pH, consistent with the absence of a formate dehydrogenase gene in this strain. This, most likely constitutes a virulence factor that, together with higher media acidification, impacts on host invasion. This work depicts the relevance of specific metabolic processes in determining SE commensalism and pathogenicity, thus providing helpful information towards new design strategies against SE infections.","INSTITUTE":"ITQB NOVA","LAST_NAME":"Morais","FIRST_NAME":"Elisabete","ADDRESS":"Campus de Campolide","EMAIL":"elisabete.morais@itqb.unl.pt","PHONE":"(+351) 21 446 91 00"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Staphylococcus epidermidis","TAXONOMY_ID":"1282","GENOTYPE_STRAIN":"19N/ICE25"},
"SUBJECT_SAMPLE_FACTORS":[
{
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"Additional sample data":{"RAW_FILE_NAME":"EM_7_0_221012"}
},
{
"Subject ID":"-",
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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"Sample ID":"EM_N7_10b_220812",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"9","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_10b_220812"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_12_221109",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"10","Replica":"1"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_12_221109"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_12b_221109",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"11","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_12b_221109"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_2_220720",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"0","Replica":"1"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_2_220720"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_2a_220811",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"2","Replica":"2"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_2a_220811"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_2b_220812",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"1","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_2b_220812"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_4_220720",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"2","Replica":"1"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_4_220720"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_4a_220811",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"4","Replica":"2"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_4a_220811"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_4b_220812",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"3","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_4b_220812"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_5_221012",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"3","Replica":"1"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_5_221012"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_5a_221012",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"5","Replica":"2"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_5a_221012"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_5b_221012",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"4","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_5b_221012"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_6_220720",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"4","Replica":"1"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_6_220720"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_6a_220811",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"6","Replica":"2"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_6a_220811"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_6b_220812",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"5","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_6b_220812"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_7_221012",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"5","Replica":"1"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_7_221012"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_7a_221012",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"7","Replica":"2"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_7a_221012"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_7b_221012",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"6","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_7b_221012"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_8_220720",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"6","Replica":"1"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_8_220720"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_8a_220811",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"8","Replica":"2"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_8a_220811"}
},
{
"Subject ID":"-",
"Sample ID":"EM_N7_8b_220812",
"Factors":{"Sample source":"19N","Strain":"19N","initial pH":"7.4","Time (h)":"7","Replica":"3"},
"Additional sample data":{"RAW_FILE_NAME":"EM_N7_8b_220812"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Hourly, an 800 µL aliquot was collected to measure OD600nm and the medium was separated from the cells by centrifugation at 5000 g, 5 min and 4°C. The supernatants were kept at -20°C until NMR analysis (for a maximum duration of 3 months).","SAMPLE_TYPE":"Bacterial cells","STORAGE_CONDITIONS":"-20℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"SE growth assays were performed for 19N and ICE25 strains at pH mimicking SE skin colonisation and blood infection (pH 5.5 and 7.4, respectively) in three independent replicates. A total of eight time-points were analysed: t0h collected immediately after inoculation, t2h-6h hourly during the exponential phase, t8h and t10h during the late exponential and beginning of the stationary phase."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"After thawing, 540 µL of the media samples were transferred to 5 mm NMR tubes and 60 µL of the NMR buffer (1 M phosphate potassium buffer, 2 mM sodium azide, 3.22 mM 3-(Trimethylsilyl)propionic-2,2,3,3-d4 acid sodium salt (TSP), pH 7.0) was added."},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR"},

"NM":{"INSTRUMENT_NAME":"Bruker Avance II+ 800 MHz","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","SPECTROMETER_FREQUENCY":"800","NMR_PROBE":"5 mm TXI-Z H/C/N/-D","NMR_SOLVENT":"90% H20 + 10% D2O","NMR_TUBE_SIZE":"5 mm","SHIMMING_METHOD":"Topshim","PULSE_SEQUENCE":"noesygppr1d","RECEIVER_GAIN":"57","CHEMICAL_SHIFT_REF_CPD":"TSP","TEMPERATURE":"25","NUMBER_OF_SCANS":"64","DUMMY_SCANS":"4"},

"NMR_METABOLITE_DATA":{
"Units":"mM",

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acid","HMDB":"HMDB0001488","PubChem":"938","ChEBI":"15940","KEGG":"C00253","METLIN":"6272"},{"Metabolite":"Ornithine","Match":"Ornithine","HMDB":"HMDB0000214","PubChem":"6262","ChEBI":"15729","KEGG":"C00077","METLIN":"27"},{"Metabolite":"Phenylalanine","Match":"Phenylalanine","HMDB":"HMDB0000159","PubChem":"6140","ChEBI":"17295","KEGG":"C00079","METLIN":"28"},{"Metabolite":"Pyroglutamic acid","Match":"Pyroglutamic acid","HMDB":"HMDB0000267","PubChem":"7405","ChEBI":"18183","KEGG":"C01879","METLIN":"3251"},{"Metabolite":"Pyruvic acid","Match":"Pyruvic 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pyrophosphate","HMDB":"HMDB0001372","PubChem":"1132","ChEBI":"9532","KEGG":"C00068","METLIN":"2832"},{"Metabolite":"Threonine","Match":"L-Threonine","HMDB":"HMDB0000167","PubChem":"6288","ChEBI":"16857","KEGG":"C00188","METLIN":"32"},{"Metabolite":"Trehalose","Match":"Trehalose","HMDB":"HMDB0000975","PubChem":"7427","ChEBI":"16551","KEGG":"C01083","METLIN":"5913"},{"Metabolite":"Tryptophan","Match":"L-Tryptophan","HMDB":"HMDB0000929","PubChem":"6305","ChEBI":"16828","KEGG":"C00078","METLIN":"5879"},{"Metabolite":"Tyrosine","Match":"L-Tyrosine","HMDB":"HMDB0000158","PubChem":"6057","ChEBI":"17895","KEGG":"C00082","METLIN":"34"},{"Metabolite":"Uracil","Match":"Uracil","HMDB":"HMDB0000300","PubChem":"1174","ChEBI":"17568","KEGG":"C00106","METLIN":"258"},{"Metabolite":"Uridine","Match":"Uridine","HMDB":"HMDB0000296","PubChem":"6029","ChEBI":"16704","KEGG":"C00299","METLIN":"90"},{"Metabolite":"Valine","Match":"L-Valine","HMDB":"HMDB0000883","PubChem":"6287","ChEBI":"16414","KEGG":"C00183","METLIN":"5842"},{"Metabolite":"cis-Aconitic acid","Match":"cis-Aconitic acid","HMDB":"HMDB0000072","PubChem":"643757","ChEBI":"32805","KEGG":"C00417","METLIN":"5130"},{"Metabolite":"sn-Glycero-3-phosphocholine","Match":"Glycerophosphocholine","HMDB":"HMDB0000086","PubChem":"657272","ChEBI":"16870","KEGG":"C00670","METLIN":"370"}]
}

}