#METABOLOMICS WORKBENCH cbeekman_20240621_055933 DATATRACK_ID:4947 STUDY_ID:ST003288 ANALYSIS_ID:AN005385 PROJECT_ID:PR002040 VERSION 1 CREATED_ON July 2, 2024, 8:17 am #PROJECT PR:PROJECT_TITLE Quantification of amoxicillin in intestinal contents of mice PR:PROJECT_SUMMARY Antibiotics cause collateral damage to resident microbes that is associated with PR:PROJECT_SUMMARY various health risks. To-date, studies have largely focused on impacts of PR:PROJECT_SUMMARY antibiotics on large intestinal and fecal microbiota. Here, we employ a GI-wide PR:PROJECT_SUMMARY integrated multiomic approach to reveal that amoxicillin (AMX) treatment reduces PR:PROJECT_SUMMARY overall bacterial abundance, bile salt hydrolase activity and unconjugated bile PR:PROJECT_SUMMARY acids in the small intestine (SI). An accompanying loss of fatty acids and PR:PROJECT_SUMMARY increase in acyl-carnitines in the large intestine corresponded with PR:PROJECT_SUMMARY spatially-distinct expansions of proteobacteria. Parasuterella excrementihominis PR:PROJECT_SUMMARY utilized fatty acid biosynthesis, becoming dominant in the SI while multiple PR:PROJECT_SUMMARY Klebsiella species employed fatty acid oxidation during expansion in the large PR:PROJECT_SUMMARY intestine. We subsequently demonstrate that restoration of unconjugated bile PR:PROJECT_SUMMARY acids can mitigate losses of commensals in the large intestine while also PR:PROJECT_SUMMARY inhibiting the expansion of Proteobacteria during AMX treatment. PR:INSTITUTE Brown University PR:LAST_NAME Beekman PR:FIRST_NAME Chapman PR:ADDRESS BMC 613, 171 Meeting Street, Providence RI 02912 PR:EMAIL Chapman_Beekman@brown.edu PR:PHONE 4018635953 #STUDY ST:STUDY_TITLE Quantification of amoxicillin in mouse intestinal contents ST:STUDY_SUMMARY Conventionally housed mice were orally treated with amoxicillin for 24 hours ST:STUDY_SUMMARY with and without cholic acid (48h) and small intestinal and cecal contents were ST:STUDY_SUMMARY collected for targeted MS analysis. Samples were flash frozen and stored at -80°C ST:STUDY_SUMMARY prior to analysis. We found that amoxicillin levels in the small intestine were ST:STUDY_SUMMARY 0-40 pmol/mg of contents and no significant difference in amoxicillin ST:STUDY_SUMMARY concentration was detected between small intestine and cecum or between mice ST:STUDY_SUMMARY receiving cholic acid vs amoxicillin alone. ST:INSTITUTE Brown University ST:DEPARTMENT Molecular Microbiology & Immunology ST:LABORATORY Molecular Microbiology & Immunology, Belenky Lab ST:LAST_NAME Beekman ST:FIRST_NAME Chapman ST:ADDRESS BMC 613, 171 Meeting Street, Providence RI 02912 ST:EMAIL Chapman_Beekman@brown.edu ST:PHONE 4018635953 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #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 - Cec_05 Treatment:untreated + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_11.raw SUBJECT_SAMPLE_FACTORS - Cec_06 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_14.raw SUBJECT_SAMPLE_FACTORS - Cec_07 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_15.raw SUBJECT_SAMPLE_FACTORS - Cec_08 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_16.raw SUBJECT_SAMPLE_FACTORS - Cec_13 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_17.raw SUBJECT_SAMPLE_FACTORS - Cec_14 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_18.raw SUBJECT_SAMPLE_FACTORS - Cec_15 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_19.raw SUBJECT_SAMPLE_FACTORS - Cec_16 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_20.raw SUBJECT_SAMPLE_FACTORS - Cec_21 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_21.raw SUBJECT_SAMPLE_FACTORS - Cec_22 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_22.raw SUBJECT_SAMPLE_FACTORS - Cec_23 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_23.raw SUBJECT_SAMPLE_FACTORS - Cec_24 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_24.raw SUBJECT_SAMPLE_FACTORS - Cec_29 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_25.raw SUBJECT_SAMPLE_FACTORS - Cec_30 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_26.raw SUBJECT_SAMPLE_FACTORS - Cec_31 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_27.raw SUBJECT_SAMPLE_FACTORS - Cec_32 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_28.raw SUBJECT_SAMPLE_FACTORS - Cec_33 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_29.raw SUBJECT_SAMPLE_FACTORS - Cec_34 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_30.raw SUBJECT_SAMPLE_FACTORS - Cec_35 Treatment:AMX + std. diet | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_31.raw SUBJECT_SAMPLE_FACTORS - Cec_37 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_32.raw SUBJECT_SAMPLE_FACTORS - Cec_38 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_33.raw SUBJECT_SAMPLE_FACTORS - Cec_39 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_34.raw SUBJECT_SAMPLE_FACTORS - Cec_40 Treatment:AMX + CA | Sample source:mouse cecum RAW_FILE_NAME(File)=Cec_35.raw SUBJECT_SAMPLE_FACTORS - SI_05 Treatment:untreated + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_13.raw SUBJECT_SAMPLE_FACTORS - SI_06 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_14.raw SUBJECT_SAMPLE_FACTORS - SI_07 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_15.raw SUBJECT_SAMPLE_FACTORS - SI_08 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_16.raw SUBJECT_SAMPLE_FACTORS - SI_09 Treatment:untreated + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_17.raw SUBJECT_SAMPLE_FACTORS - SI_10 Treatment:untreated + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_18.raw SUBJECT_SAMPLE_FACTORS - SI_13 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_19.raw SUBJECT_SAMPLE_FACTORS - SI_14 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_20.raw SUBJECT_SAMPLE_FACTORS - SI_15 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_21.raw SUBJECT_SAMPLE_FACTORS - SI_16 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_22.raw SUBJECT_SAMPLE_FACTORS - SI_21 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_23.raw SUBJECT_SAMPLE_FACTORS - SI_22 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_24.raw SUBJECT_SAMPLE_FACTORS - SI_23 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_25.raw SUBJECT_SAMPLE_FACTORS - SI_24 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_26.raw SUBJECT_SAMPLE_FACTORS - SI_29 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_27.raw SUBJECT_SAMPLE_FACTORS - SI_30 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_28.raw SUBJECT_SAMPLE_FACTORS - SI_31 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_29.raw SUBJECT_SAMPLE_FACTORS - SI_32 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_30.raw SUBJECT_SAMPLE_FACTORS - SI_33 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_31.raw SUBJECT_SAMPLE_FACTORS - SI_34 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_32.raw SUBJECT_SAMPLE_FACTORS - SI_35 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_33.raw SUBJECT_SAMPLE_FACTORS - SI_36 Treatment:AMX + std. diet | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_34.raw SUBJECT_SAMPLE_FACTORS - SI_37 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_35.raw SUBJECT_SAMPLE_FACTORS - SI_38 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_36.raw SUBJECT_SAMPLE_FACTORS - SI_39 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_37.raw SUBJECT_SAMPLE_FACTORS - SI_40 Treatment:AMX + CA | Sample source:mouse small intestine RAW_FILE_NAME(File)=SI_38.raw #COLLECTION CO:COLLECTION_SUMMARY SI and cecal contents were homogenized at a concentration of 50-100 mg/mL in 70% CO:COLLECTION_SUMMARY methanol (LCMS grade) containing 50 µM 13C6-labeled AMX as an internal standard CO:COLLECTION_SUMMARY on the Bead Ruptor (Omni Inc.) without beads at a frequency setting of 15 for 5 CO:COLLECTION_SUMMARY minutes. Homogenized samples were then centrifuged at 16,000 X g for 10 minutes CO:COLLECTION_SUMMARY and supernatants were used for analysis. AMX was quantitated with HPLC-MS on an CO:COLLECTION_SUMMARY Ultimate 3000, Dionex coupled to Q Executive Classic (Thermo) with ESI CO:COLLECTION_SUMMARY interface. CO:SAMPLE_TYPE Intestine #TREATMENT TR:TREATMENT_SUMMARY AMX treatment was administered in drinking water (166.7 µg/mL) for a 24-hour TR:TREATMENT_SUMMARY period. This concentration is based on previous studies38,39 and determined to TR:TREATMENT_SUMMARY achieve a dosage of approximately 25mg/kg/day. Untreated mice received TR:TREATMENT_SUMMARY pH-matched water and both AMX and vehicle solutions were sterile filtered prior TR:TREATMENT_SUMMARY to administration. For cholic acid supplementation experiments standard mouse TR:TREATMENT_SUMMARY chow was first blended into a course powder using a blender (Vitamix) and 5mg of TR:TREATMENT_SUMMARY cholic acid was added per gram of powdered chow. Cholic acid was mixed evenly by TR:TREATMENT_SUMMARY re-blending and provided in the powdered chow for a 48-hour period and 24 hours TR:TREATMENT_SUMMARY prior to AMX treatment. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY SI and cecal contents were homogenized at a concentration of 50-100 mg/mL in 70% SP:SAMPLEPREP_SUMMARY methanol (LCMS grade) containing 50 µM 13C6-labeled AMX as an internal standard SP:SAMPLEPREP_SUMMARY on the Bead Ruptor (Omni Inc.) without beads at a frequency setting of 15 for 5 SP:SAMPLEPREP_SUMMARY minutes. Homogenized samples were then centrifuged at 16,000 X g for 10 minutes SP:SAMPLEPREP_SUMMARY and supernatants were used for analysis. AMX was quantitated with HPLC-MS on an SP:SAMPLEPREP_SUMMARY Ultimate 3000, Dionex coupled to Q Executive Classic (Thermo) with ESI SP:SAMPLEPREP_SUMMARY interface. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 CH:COLUMN_NAME Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um) CH:SOLVENT_A 100% Water; 0.2% Formic acid CH:SOLVENT_B 100% Methanol; 0.2% Formic acid CH:FLOW_GRADIENT mobile phase A/B set to 90%/10% from 0.00 to 0.50 min and 90%/10% to 5%/95% from CH:FLOW_GRADIENT 0.5 to 1.6 min and held at A/B ratio of 5%/95% for 0.5 min from 1.6 to 2.1 min (wash) CH:FLOW_GRADIENT and set back to the starting composition A/B 90%/10% from 2.1 to 4.5 (for equilibration) CH:FLOW_RATE 0.35 mL/min CH:COLUMN_TEMPERATURE 30°C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS The mass spectrometer was operated in the positive ion mode in Full MS; at MS:MS_COMMENTS resolution 70,000; AGT target 5 E5 and Scan range 200-500 m/z. Spray voltage and MS:MS_COMMENTS source temperature were set at 3,500 volts, and 320°C, respectively. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS nmol / mg sample MS_METABOLITE_DATA_START Samples Cec_05 Cec_06 Cec_07 Cec_08 Cec_13 Cec_14 Cec_15 Cec_16 Cec_21 Cec_22 Cec_23 Cec_24 Cec_29 Cec_30 Cec_31 Cec_32 Cec_33 Cec_34 Cec_35 Cec_37 Cec_38 Cec_39 Cec_40 SI_05 SI_06 SI_07 SI_08 SI_09 SI_10 SI_13 SI_14 SI_15 SI_16 SI_21 SI_22 SI_23 SI_24 SI_29 SI_30 SI_31 SI_32 SI_33 SI_34 SI_35 SI_36 SI_37 SI_38 SI_39 SI_40 Factors Treatment:untreated + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + std. diet | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:AMX + CA | Sample source:mouse cecum Treatment:untreated + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:untreated + std. diet | Sample source:mouse small intestine Treatment:untreated + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + std. diet | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Treatment:AMX + CA | Sample source:mouse small intestine Amoxicillin 0.000478191 0.010556799 0.006758489 0.013696958 0.002754542 0.011972901 0.011024439 0.005953429 0.009236975 0.011760107 0.023027511 0.016327816 0.00826398 0.002921206 0.008463409 0.013412824 0.018213263 0.023218755 0.010759273 0.020816723 0.00463665 0.013139592 0.00260343 0 0.002334794 3.36128E-05 0.00020701 0 0 0.001905616 0.000887662 0.010664744 0.006486571 0.018839681 0.025742551 0.003630705 0.00555748 0.000134208 0.002879549 0.003637932 0.004152593 0.010777048 0.04371411 0.040085569 0.029802898 0.011073324 0.036184023 0.008376806 0.003273649 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name m/z retention time Amoxicillin 372.13 0.905 METABOLITES_END #END