#METABOLOMICS WORKBENCH bastiseelbinder_20230323_053437 DATATRACK_ID:3813 STUDY_ID:ST002523 ANALYSIS_ID:AN004157 PROJECT_ID:PR001625 VERSION 1 CREATED_ON March 23, 2023, 7:43 am #PROJECT PR:PROJECT_TITLE Metabolomics of human urine PR:PROJECT_TYPE MS quantitative analysis PR:PROJECT_SUMMARY Metabolomics of human urine to support the findings in Candida expansion in the PR:PROJECT_SUMMARY gut of lung cancer patients associates with an ecological signature that PR:PROJECT_SUMMARY supports growth under dysbiotic conditions PR:INSTITUTE Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll PR:INSTITUTE Institute (Leibniz-HKI) PR:DEPARTMENT Microbiome Dynamics PR:LAST_NAME Seelbinder PR:FIRST_NAME Bastian PR:ADDRESS Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany PR:EMAIL bastian.seelbinder@leibniz-hki.de PR:PHONE +4936415321360 #STUDY ST:STUDY_TITLE Candida expansion in the human gut is associated with an ecological signature ST:STUDY_TITLE that supports growth under dysbiotic conditions ST:STUDY_SUMMARY The overgrowth of Candida species in the human gut is considered a prerequisite ST:STUDY_SUMMARY for invasive candidiasis. However, our understanding of how gut bacteria promote ST:STUDY_SUMMARY or restrict overgrowth of Candida species in the human gut is still limited. By ST:STUDY_SUMMARY integrating mycobiome and shotgun metagenomics data from stool of 75 patients at ST:STUDY_SUMMARY risk but with no systemic candidiasis, we revealed that bacterial communities ST:STUDY_SUMMARY from high Candida samples had greater metabolic potential whereas communities ST:STUDY_SUMMARY from low Candida had greater functional redundancy. In addition, we developed ST:STUDY_SUMMARY machine learning models that used only bacterial taxa or functional relative ST:STUDY_SUMMARY abundances to predict the levels of Candida genus and species in an external ST:STUDY_SUMMARY validation cohort with an area under the curve of 78.6-81.1%. Last, we proposed ST:STUDY_SUMMARY an intriguing mechanism for Candida species overgrowth based on a decrease in ST:STUDY_SUMMARY short-chain fatty acid producing-bacteria resulting in increased oxygen levels. ST:STUDY_SUMMARY These conditions create a metabolic niche for Candida species to use lactate as ST:STUDY_SUMMARY a carbon source and overtake their fungal competitors in the human gut. ST:INSTITUTE Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll ST:INSTITUTE Institute (Leibniz-HKI) ST:DEPARTMENT Microbiome Dynamics ST:LAST_NAME Bastian ST:FIRST_NAME Seelbinder ST:ADDRESS Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany ST:EMAIL bastian.seelbinder@leibniz-hki.de ST:PHONE +4936415321360 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:AGE_OR_AGE_RANGE 68 (63, 73) SU:WEIGHT_OR_WEIGHT_RANGE 77 (62, 87) SU:HEIGHT_OR_HEIGHT_RANGE 170 (160, 176) SU:GENDER Male and female SU:HUMAN_ETHNICITY White SU:HUMAN_MEDICATIONS anti-PD-1 immune checkpoint inhibitors (nivolumab or pembrolizumab) SU:HUMAN_INCLUSION_CRITERIA consecutive advanced cancer patients #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - MK115 Candida:Low | Gender:Female | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-030-SA008756.mzML SUBJECT_SAMPLE_FACTORS - MK175 Candida:High | Gender:Female | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-036-SA008762.mzML SUBJECT_SAMPLE_FACTORS - MK209 Candida:High | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-027-SA008757.mzML SUBJECT_SAMPLE_FACTORS - MK227 Candida:Low | Gender:Female | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-039-SA008759.mzML SUBJECT_SAMPLE_FACTORS - MK251 Candida:Low | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-024-SA008768.mzML SUBJECT_SAMPLE_FACTORS - MK279 Candida:Low | Gender:Male | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-032-SA008765.mzML SUBJECT_SAMPLE_FACTORS - MK287 Candida:Low | Gender:Female | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-019-SA008754.mzML SUBJECT_SAMPLE_FACTORS - MK300 Candida:High | Gender:Male | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-031-SA008764.mzML SUBJECT_SAMPLE_FACTORS - MK304 Candida:High | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-026-SA008763.mzML SUBJECT_SAMPLE_FACTORS - MK311 Candida:High | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-022-SA008767.mzML SUBJECT_SAMPLE_FACTORS - MK324 Candida:High | Gender:Male | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-038-SA008751.mzML SUBJECT_SAMPLE_FACTORS - MK329 Candida:High | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-028-SA008758.mzML SUBJECT_SAMPLE_FACTORS - MT196 Candida:High | Gender:Male | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-025-SA008753.mzML SUBJECT_SAMPLE_FACTORS - MT238 Candida:Low | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-034-SA008749.mzML SUBJECT_SAMPLE_FACTORS - MT239 Candida:High | Gender:Female | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-040-SA008755.mzML SUBJECT_SAMPLE_FACTORS - MT241 Candida:High | Gender:Male | Immunotherapy:Pembrolizumab RAW_FILE_NAME=220922-LC1-PAN-1-037-SA008752.mzML SUBJECT_SAMPLE_FACTORS - MT242 Candida:Low | Gender:Female | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-018-SA008750.mzML SUBJECT_SAMPLE_FACTORS - MT245 Candida:Low | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-033-SA008760.mzML SUBJECT_SAMPLE_FACTORS - MT252 Candida:Low | Gender:Male | Immunotherapy:Nivolumab RAW_FILE_NAME=220922-LC1-PAN-1-020-SA008761.mzML #COLLECTION CO:COLLECTION_SUMMARY Human urine samples were collected by from lung cancer patients and frozen at CO:COLLECTION_SUMMARY -80 °C. Samples were shipped to MS-OMICS for metabolomic analysis. CO:SAMPLE_TYPE Urine CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY To unfreeze samples at MS-OMICS, samples were assigned to their SpinX filters TR:TREATMENT_SUMMARY and centrifugated at 15,000 RPM for 5 minutes at 4 °C. Urine samples were then TR:TREATMENT_SUMMARY diluted 11 times in mobile phase eluent A and fortified with stable isotope TR:TREATMENT_SUMMARY labelled standards before analysis. TR:TREATMENT_COMPOUND mobile phase eluent A #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Urine samples were then diluted 11 times in mobile phase eluent A and fortified SP:SAMPLEPREP_SUMMARY with stable isotope labelled standards before analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The samples were analysed with our semi-polar metabolites method, which is a CH:CHROMATOGRAPHY_SUMMARY slightly modified version of the protocol described by Catalin et al. (UPLC/MS CH:CHROMATOGRAPHY_SUMMARY Monitoring of Water-Soluble Vitamin Bs in Cell Culture Media in Minutes, Water CH:CHROMATOGRAPHY_SUMMARY Application note 2011, 720004042en). The analysis was carried out in a CH:CHROMATOGRAPHY_SUMMARY randomised order using a UPLC system (Vanquish, Thermo Fisher Scientific) CH:CHROMATOGRAPHY_SUMMARY coupled with a high-resolution quadrupole-orbitrap mass spectrometer Orbitrap CH:CHROMATOGRAPHY_SUMMARY Exploris 240 MS, Thermo Fisher Scientific. CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) CH:SOLVENT_A 10 mM ammonium formate, 0.1% formic acid in water (pH 3.1) CH:SOLVENT_B 10 mM ammonium formate, 0.1% formic acid in methanol CH:FLOW_GRADIENT 300 μL/min: 0-2 min: 0% B, 2-12 min: 35% B, 12-13 min: 90% B, 13-14 min: 90% B, CH:FLOW_GRADIENT 14-15 min: 0% B CH:FLOW_RATE 300 μL/min CH:COLUMN_TEMPERATURE 30 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Orbitrap Exploris 240 MS:INSTRUMENT_TYPE QTRAP MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS The ionization was achieved with an electrospray ionization interface operated MS:MS_COMMENTS in positive and negative ionization mode under polarity switching. Data were MS:MS_COMMENTS processed using Compound Discoverer 3.3 (Thermo Fisher Scientific) and Skyline MS:MS_COMMENTS 21.2. MS:MS_RESULTS_FILE ST002523_AN004157_Results.txt UNITS:Peak area Has m/z:Neutral masses Has RT:Yes RT units:Minutes #END