{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002741","ANALYSIS_ID":"AN004571","VERSION":"1","CREATED_ON":"August 10, 2023, 11:08 am"},

"PROJECT":{"PROJECT_TITLE":"Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge","PROJECT_SUMMARY":"Multi-omics has the promise to provide a detailed molecular picture for biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimum structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to associate with a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30°C and 37°C, and obtained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofaciens at 37°C.","INSTITUTE":"University of Nebraska -Lincoln","LAST_NAME":"Alvarez","FIRST_NAME":"Sophie","ADDRESS":"1901 Vine st, Lincoln, Nebraska, 68588, USA","EMAIL":"salvarez@unl.edu","PHONE":"4024724575"},

"STUDY":{"STUDY_TITLE":"Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge","STUDY_SUMMARY":"Multi-omics has the promise to provide a detailed molecular picture for biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimum structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to associate with a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30°C and 37°C, and obtained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofaciens at 37°C.","INSTITUTE":"University of Nebraska-Lincoln","LAST_NAME":"Alvarez","FIRST_NAME":"Sophie","ADDRESS":"1901 Vine St","EMAIL":"salvarez@unl.edu","PHONE":"4024724575"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Lentilactobacillus kefiri"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"1130P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_1130P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"230P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_230P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"330P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_330P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"430P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_430P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"530P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_530P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"630P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_630P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"730P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_730P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"830P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_830P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"930P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_930P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"1030P",
"Factors":{"Treatment":"30C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_1030P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"137P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_137P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"237P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_237P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"337P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_337P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"437P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_437P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"537P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_537P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"637P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_637P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"737P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_737P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"837P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_837P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"937P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_937P.abf"}
},
{
"Subject ID":"-",
"Sample ID":"1037P",
"Factors":{"Treatment":"37C"},
"Additional sample data":{"Sample Type":"Cell Pellet (Lactobacillus kefiri and Lactobacillus kefiranofaciens)","RAW_FILE_NAME":"20210730_HP5MS_RI20210225_split_HO_1037P.abf"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"All samples were initially inoculated with a mixed culture of L. kefiri and L. kefiranofaciens inoculum blended from 3-day cultures. 20 mL MRS medium was inocu-lated with 0.5 mL of the combined inoculum and incubated for 3 days, one set of 10 at 30°C, and another set of 10 at 37°C. For controls, L. kefiri and L. kefiranofaciens were inoculated in triplicate for each temperature. The tubes were removed from the incubator after 3 days, and 0.1 mL of each sample was placed in a 96 well plate for OD (600 nm) analysis. Samples were then centrifuged (3000×g, 4°C, 10 min), and the supernatant was removed and frozen for further analysis. The pellet was washed in fresh MRS (pH 5.5), divided in three aliquots, re-pelleted in microcentrifuge tubes, and frozen at -80°C for subsequent transcriptomic, proteomic, and metabolomic analysis.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"All samples were initially inoculated with a mixed culture of L. kefiri and L. kefiranofaciens inoculum blended from 3-day cultures. 20 mL MRS medium was inoculated with 0.5 mL of the combined inoculum and incubated for 3 days, one set of 10 at 30°C, and another set of 10 at 37°C. For controls, L. kefiri and L. kefiranofaciens were inoculated in triplicate for each temperature. The tubes were removed from the incubator after 3 days, and 0.1 mL of each sample was placed in a 96 well plate for OD (600 nm) analysis. Samples were then centrifuged (3000×g, 4°C, 10 min), and the supernatant was removed and frozen for further analysis. The pellet was washed in fresh MRS (pH 5.5), divided in three aliquots, re-pelleted in microcentrifuge tubes, and frozen at -80°C for subsequent metabolomic analysis."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cell pellets were washed 3 times with cold PBS to remove any cell media left after collection. The cell pellets were then extracted using cold 100% methanol and spiked with 40 μL of 10 pinitol (internal standard). A quality control (QC) sample was prepared by mixing the same amount of each sample into one. The supernatants were then dried down using a speed-vac and then resuspended in 20 mg/mL methoxyamine hydrochloride reagent prepared in pure pyridine and incubated for 2 hr at 37 °C on a platform shaker at 1000 rpm. Next, for derivatization, the MSTFA +1% TMCS deri-vatization (ThermoFisher) was added to each sample, incubated for 30 min at 37°C on a platform shaker at 1000 rpm followed by a centrifugation for 10 min at 16,000 g prior to transferring the mixture to GC vials for injection into GC-MS."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The GC-MS analysis was carried out with an Agilent GC (Model 7890B) and MS Quadrupole (Model 5977A) (Agilent Technologies). The liquid injection was done using a PAL System RSI 85 (PAL, Lake Elmo, MN, USA). The injector temperature was 260°C; the MS transfer line was 230°C. Metabolites were separated on a 5% phenyl 95% dimethylarylene siloxane HP-5MS 30 m, 0.25 mm, 0.25 μm capillary column (Agilent Technologies), at constant flow 1.5 ml.min-1 of helium as a carrier gas. One mi-croliter of derivatized sample was injected into the injector operating in 1:5 split mode. The temperature of the column was initially set to 60°C, and increased at a rate of 10°C.min−1 to 325°C.","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890B","COLUMN_NAME":"Agilent HP5-MS (30m x 0.25mm, 0.25 um)","SOLVENT_A":"N/A for GC","SOLVENT_B":"N/A for GC","SOLVENT_C":"N/A for GC","FLOW_GRADIENT":"N/A for GC","FLOW_RATE":"1.5 ml/min","COLUMN_TEMPERATURE":"60"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 5977A","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"The data was analyzed using MS-Dial (version 4.9) for peak detection, deconvolution, alignment, quantification, normalization, and identification. Putative identification of the metabolites was based on the Kovats retention index (RI) and the matching score of the mass spectra with the libraries. Two libraries were used, a local library made from running authentic standards with Kovats RI, and a public spectrum library, the curated Kovats RI with a total of 28,220 compounds (last edited August 21th, 2022, which includes the Fiehn, RIKEN and MoNA databases). The peaks were manually curated reviewed for peak shape, chromatogram alignment integrity and MS/MS match, and the final list of compounds with RI similarities >95% were report-ed. The data was normalized based on the internal standard spiked in the samples during extraction and using LOWESS (locally weighted scatterplot smoothing) for QC-batch normalization."},

"MS_METABOLITE_DATA":{
"Units":"normalized intensity",

"Data":[{"Metabolite":"Pyruvic acid","137P":"4.9E+05","230P":"1.6E+05","237P":"3.0E+05","330P":"2.3E+05","337P":"2.7E+05","430P":"3.1E+05","437P":"2.1E+05","530P":"1.3E+05","537P":"2.1E+05","630P":"4.4E+05","637P":"3.8E+05","730P":"2.1E+05","737P":"5.9E+05","830P":"1.1E+05","837P":"3.1E+05","930P":"6.9E+04","937P":"9.4E+05","1030P":"1.5E+05","1037P":"3.4E+05","1130P":"2.5E+05"},{"Metabolite":"LACTATE","137P":"9.8E+06","230P":"8.4E+06","237P":"8.4E+06","330P":"2.7E+06","337P":"7.8E+06","430P":"2.1E+06","437P":"7.7E+06","530P":"9.5E+06","537P":"8.2E+06","630P":"8.8E+06","637P":"8.7E+06","730P":"9.2E+06","737P":"1.0E+07","830P":"8.9E+06","837P":"9.5E+06","930P":"8.2E+06","937P":"9.1E+06","1030P":"8.1E+06","1037P":"1.0E+07","1130P":"2.5E+06"},{"Metabolite":"Glycolic acid","137P":"3.5E+05","230P":"6.7E+05","237P":"2.5E+05","330P":"3.7E+05","337P":"2.6E+05","430P":"4.3E+05","437P":"2.1E+05","530P":"3.3E+05","537P":"2.2E+05","630P":"5.4E+05","637P":"3.4E+05","730P":"5.0E+05","737P":"4.2E+05","830P":"5.3E+05","837P":"2.4E+05","930P":"2.8E+05","937P":"3.8E+05","1030P":"4.6E+05","1037P":"2.5E+05","1130P":"4.5E+05"},{"Metabolite":"VALINE","137P":"6.0E+06","230P":"8.5E+06","237P":"4.8E+06","330P":"8.1E+06","337P":"5.1E+06","430P":"8.4E+06","437P":"4.1E+06","530P":"7.3E+06","537P":"3.4E+06","630P":"8.7E+06","637P":"6.5E+06","730P":"9.0E+06","737P":"6.6E+06","830P":"8.8E+06","837P":"3.5E+06","930P":"6.4E+06","937P":"7.3E+06","1030P":"8.1E+06","1037P":"3.5E+06","1130P":"8.2E+06"},{"Metabolite":"ALANINE","137P":"9.9E+06","230P":"8.4E+06","237P":"8.4E+06","330P":"8.6E+06","337P":"7.7E+06","430P":"8.8E+06","437P":"7.0E+06","530P":"9.5E+06","537P":"8.2E+06","630P":"8.8E+06","637P":"8.7E+06","730P":"9.2E+06","737P":"1.0E+07","830P":"8.9E+06","837P":"9.4E+06","930P":"8.3E+06","937P":"9.1E+06","1030P":"8.2E+06","1037P":"9.9E+06","1130P":"9.2E+06"},{"Metabolite":"LEUCINE","137P":"9.5E+06","230P":"8.4E+06","237P":"8.0E+06","330P":"8.6E+06","337P":"7.7E+06","430P":"8.9E+06","437P":"7.2E+06","530P":"9.0E+06","537P":"6.3E+06","630P":"8.8E+06","637P":"8.6E+06","730P":"9.2E+06","737P":"9.8E+06","830P":"8.9E+06","837P":"6.5E+06","930P":"7.7E+06","937P":"9.1E+06","1030P":"8.2E+06","1037P":"6.9E+06","1130P":"9.1E+06"},{"Metabolite":"beta-Hydroxybutyric acid","137P":"4.0E+04","230P":"7.8E+04","237P":"2.8E+04","330P":"4.8E+04","337P":"2.8E+04","430P":"5.8E+04","437P":"2.2E+04","530P":"4.3E+04","537P":"2.3E+04","630P":"6.6E+04","637P":"3.8E+04","730P":"6.1E+04","737P":"4.6E+04","830P":"6.9E+04","837P":"2.6E+04","930P":"3.5E+04","937P":"3.8E+04","1030P":"6.2E+04","1037P":"2.8E+04","1130P":"5.3E+04"},{"Metabolite":"ISOLEUCINE","137P":"5.3E+06","230P":"8.3E+06","237P":"4.2E+06","330P":"6.0E+06","337P":"4.5E+06","430P":"6.7E+06","437P":"3.6E+06","530P":"4.8E+06","537P":"2.9E+06","630P":"8.2E+06","637P":"5.8E+06","730P":"6.5E+06","737P":"5.8E+06","830P":"6.6E+06","837P":"3.0E+06","930P":"3.9E+06","937P":"6.8E+06","1030P":"6.6E+06","1037P":"3.2E+06","1130P":"5.7E+06"},{"Metabolite":"NORVALINE","137P":"6.4E+06","230P":"8.9E+06","237P":"4.3E+06","330P":"5.8E+06","337P":"3.7E+06","430P":"5.8E+06","437P":"3.2E+06","530P":"6.3E+06","537P":"4.0E+06","630P":"7.9E+06","637P":"4.6E+06","730P":"8.4E+06","737P":"8.3E+06","830P":"8.3E+06","837P":"5.0E+06","930P":"4.8E+06","937P":"7.3E+06","1030P":"8.4E+06","1037P":"5.6E+06","1130P":"8.1E+06"},{"Metabolite":"SERINE","137P":"4.0E+06","230P":"7.5E+06","237P":"3.6E+06","330P":"5.0E+06","337P":"3.8E+06","430P":"5.6E+06","437P":"3.2E+06","530P":"4.0E+06","537P":"2.6E+06","630P":"6.5E+06","637P":"4.9E+06","730P":"5.3E+06","737P":"4.6E+06","830P":"5.4E+06","837P":"2.5E+06","930P":"3.8E+06","937P":"5.0E+06","1030P":"5.4E+06","1037P":"2.5E+06","1130P":"4.9E+06"},{"Metabolite":"2-Aminoethanol","137P":"7.5E+05","230P":"1.2E+06","237P":"5.3E+05","330P":"6.2E+05","337P":"5.8E+05","430P":"7.3E+05","437P":"4.3E+05","530P":"5.2E+05","537P":"4.3E+05","630P":"1.0E+06","637P":"6.8E+05","730P":"7.9E+05","737P":"8.6E+05","830P":"8.4E+05","837P":"4.6E+05","930P":"3.7E+05","937P":"9.8E+05","1030P":"8.1E+05","1037P":"4.9E+05","1130P":"7.3E+05"},{"Metabolite":"Glycerol","137P":"3.1E+06","230P":"2.5E+06","237P":"2.3E+06","330P":"2.1E+06","337P":"2.2E+06","430P":"2.7E+06","437P":"2.3E+05","530P":"2.3E+06","537P":"2.0E+06","630P":"2.4E+06","637P":"2.7E+06","730P":"2.9E+06","737P":"3.3E+06","830P":"8.4E+05","837P":"2.3E+06","930P":"2.0E+06","937P":"3.0E+06","1030P":"2.9E+06","1037P":"2.6E+06","1130P":"3.0E+06"},{"Metabolite":"PHOSPHOENOLPYRUVATE","137P":"9.9E+06","230P":"5.0E+06","237P":"8.4E+06","330P":"4.8E+06","337P":"7.8E+06","430P":"5.6E+06","437P":"7.7E+06","530P":"9.5E+06","537P":"8.2E+06","630P":"5.1E+06","637P":"8.7E+06","730P":"9.2E+06","737P":"1.0E+07","830P":"8.9E+06","837P":"9.5E+06","930P":"5.0E+06","937P":"9.1E+06","1030P":"8.2E+06","1037P":"1.0E+07","1130P":"9.2E+06"},{"Metabolite":"Nicotinic 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}

}