#METABOLOMICS WORKBENCH bcdefelice_20230828_095809 DATATRACK_ID:4261 STUDY_ID:ST002834 ANALYSIS_ID:AN004630 PROJECT_ID:PR001774 VERSION 1 CREATED_ON August 28, 2023, 2:25 pm #PROJECT PR:PROJECT_TITLE Resource competition predicts assembly of in vitro gut bacterial communities PR:PROJECT_SUMMARY Microbiota dynamics arise from a plethora of interspecies interactions, PR:PROJECT_SUMMARY including resource competition, cross-feeding, and pH modulation. The individual PR:PROJECT_SUMMARY contributions of these mechanisms are challenging to untangle, especially in PR:PROJECT_SUMMARY natural or complex laboratory environments where the landscape of resource PR:PROJECT_SUMMARY competition is unclear. Here, we developed a framework to estimate the extent of PR:PROJECT_SUMMARY multi-species niche overlaps by combining metabolomics data of individual PR:PROJECT_SUMMARY species, growth measurements in pairwise spent media, and mathematical models. PR:PROJECT_SUMMARY When applied to an in vitro model system of human gut commensals in complex PR:PROJECT_SUMMARY media, our framework revealed that a simple model of resource competition PR:PROJECT_SUMMARY described most pairwise interactions. By grouping metabolomic features depleted PR:PROJECT_SUMMARY by the same set of species, we constructed a coarse-grained consumer-resource PR:PROJECT_SUMMARY model that predicted assembly compositions to reasonable accuracy. Moreover, PR:PROJECT_SUMMARY deviations from model predictions enabled us to identify and incorporate into PR:PROJECT_SUMMARY the model additional interactions, including pH-mediated effects and PR:PROJECT_SUMMARY cross-feeding, which improved model performance. In sum, our work provides an PR:PROJECT_SUMMARY experimental and theoretical framework to dissect microbial interactions in PR:PROJECT_SUMMARY complex in vitro environments. PR:INSTITUTE Stanford University PR:LAST_NAME DeFelice PR:FIRST_NAME Brian PR:ADDRESS 1291 Welch Rd., Rm. G0821 (SIM1), Stanford CA, California, 94305, USA PR:EMAIL bcdefelice@ucdavis.edu PR:PHONE 5303564485 #STUDY ST:STUDY_TITLE Resource competition predicts assembly of in vitro gut bacterial communities- ST:STUDY_TITLE 2021-C18 ST:STUDY_SUMMARY Microbiota dynamics arise from a plethora of interspecies interactions, ST:STUDY_SUMMARY including resource competition, cross-feeding, and pH modulation. The individual ST:STUDY_SUMMARY contributions of these mechanisms are challenging to untangle, especially in ST:STUDY_SUMMARY natural or complex laboratory environments where the landscape of resource ST:STUDY_SUMMARY competition is unclear. Here, we developed a framework to estimate the extent of ST:STUDY_SUMMARY multi-species niche overlaps by combining metabolomics data of individual ST:STUDY_SUMMARY species, growth measurements in pairwise spent media, and mathematical models. ST:STUDY_SUMMARY When applied to an in vitro model system of human gut commensals in complex ST:STUDY_SUMMARY media, our framework revealed that a simple model of resource competition ST:STUDY_SUMMARY described most pairwise interactions. By grouping metabolomic features depleted ST:STUDY_SUMMARY by the same set of species, we constructed a coarse-grained consumer-resource ST:STUDY_SUMMARY model that predicted assembly compositions to reasonable accuracy. Moreover, ST:STUDY_SUMMARY deviations from model predictions enabled us to identify and incorporate into ST:STUDY_SUMMARY the model additional interactions, including pH-mediated effects and ST:STUDY_SUMMARY cross-feeding, which improved model performance. In sum, our work provides an ST:STUDY_SUMMARY experimental and theoretical framework to dissect microbial interactions in ST:STUDY_SUMMARY complex in vitro environments. ST:INSTITUTE Stanford University ST:LAST_NAME DeFelice ST:FIRST_NAME Brian ST:ADDRESS 1291 Welch Rd. ST:EMAIL bcdefelice@ucdavis.edu ST:PHONE 5303564485 #SUBJECT SU:SUBJECT_TYPE Bacteria SU:SUBJECT_SPECIES Bacteroides thetaiotaomicron SU:TAXONOMY_ID 8188 SU:SUBJECT_COMMENTS Fecal derived communities and isolates, supernatant was assayed #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 - Pos_1' Genotype:bacterial community | Treatment:BHI spent by Enterococcus hirae RAW_FILE_NAME=Pos_1'.raw SUBJECT_SAMPLE_FACTORS - Pos_1'_r1 Genotype:bacterial community | Treatment:BHI spent by Enterococcus hirae RAW_FILE_NAME=Pos_1'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_1'_r2 Genotype:bacterial community | Treatment:BHI spent by Enterococcus hirae RAW_FILE_NAME=Pos_1'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_2' Genotype:bacterial community | Treatment:BHI spent by Escherichia fergusonii RAW_FILE_NAME=Pos_2'.raw SUBJECT_SAMPLE_FACTORS - Pos_2'_r1 Genotype:bacterial community | Treatment:BHI spent by Escherichia fergusonii RAW_FILE_NAME=Pos_2'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_2'_r2 Genotype:bacterial community | Treatment:BHI spent by Escherichia fergusonii RAW_FILE_NAME=Pos_2'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_3' Genotype:bacterial community | Treatment:BHI spent by Clostridium symbiosum RAW_FILE_NAME=Pos_3'.raw SUBJECT_SAMPLE_FACTORS - Pos_3'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium symbiosum RAW_FILE_NAME=Pos_3'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_3'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium symbiosum RAW_FILE_NAME=Pos_3'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_4' Genotype:bacterial community | Treatment:BHI spent by Bacteroides thetaiotaomicron RAW_FILE_NAME=Pos_4'.raw SUBJECT_SAMPLE_FACTORS - Pos_4'_r1 Genotype:bacterial community | Treatment:BHI spent by Bacteroides thetaiotaomicron RAW_FILE_NAME=Pos_4'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_4'_r2 Genotype:bacterial community | Treatment:BHI spent by Bacteroides thetaiotaomicron RAW_FILE_NAME=Pos_4'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_5' Genotype:bacterial community | Treatment:BHI spent by Clostridium clostridioforme RAW_FILE_NAME=Pos_5'.raw SUBJECT_SAMPLE_FACTORS - Pos_5'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium clostridioforme RAW_FILE_NAME=Pos_5'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_5'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium clostridioforme RAW_FILE_NAME=Pos_5'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_6' Genotype:bacterial community | Treatment:BHI spent by Blautia producta RAW_FILE_NAME=Pos_6'.raw SUBJECT_SAMPLE_FACTORS - Pos_6'_r1 Genotype:bacterial community | Treatment:BHI spent by Blautia producta RAW_FILE_NAME=Pos_6'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_6'_r2 Genotype:bacterial community | Treatment:BHI spent by Blautia producta RAW_FILE_NAME=Pos_6'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_7' Genotype:bacterial community | Treatment:BHI spent by Clostridium scindens RAW_FILE_NAME=Pos_7'.raw SUBJECT_SAMPLE_FACTORS - Pos_7'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium scindens RAW_FILE_NAME=Pos_7'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_7'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium scindens RAW_FILE_NAME=Pos_7'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_8' Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecium RAW_FILE_NAME=Pos_8'.raw SUBJECT_SAMPLE_FACTORS - Pos_8'_r1 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecium RAW_FILE_NAME=Pos_8'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_8'_r2 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecium RAW_FILE_NAME=Pos_8'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_9' Genotype:bacterial community | Treatment:BHI spent by Clostridium hylemonae RAW_FILE_NAME=Pos_9'.raw SUBJECT_SAMPLE_FACTORS - Pos_9'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium hylemonae RAW_FILE_NAME=Pos_9'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_9'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium hylemonae RAW_FILE_NAME=Pos_9'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_10' Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecalis RAW_FILE_NAME=Pos_10'.raw SUBJECT_SAMPLE_FACTORS - Pos_10'_r1 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecalis RAW_FILE_NAME=Pos_10'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_10'_r2 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecalis RAW_FILE_NAME=Pos_10'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_11' Genotype:bacterial community | Treatment:BHI spent by Clostridium hathewayi RAW_FILE_NAME=Pos_11'.raw SUBJECT_SAMPLE_FACTORS - Pos_11'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium hathewayi RAW_FILE_NAME=Pos_11'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_11'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium hathewayi RAW_FILE_NAME=Pos_11'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_12' Genotype:bacterial community | Treatment:BHI spent by Bacteroides fragilis RAW_FILE_NAME=Pos_12'.raw SUBJECT_SAMPLE_FACTORS - Pos_12'_r1 Genotype:bacterial community | Treatment:BHI spent by Bacteroides fragilis RAW_FILE_NAME=Pos_12'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_12'_r2 Genotype:bacterial community | Treatment:BHI spent by Bacteroides fragilis RAW_FILE_NAME=Pos_12'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_13' Genotype:bacterial community | Treatment:BHI spent by Flavonifractor plautii RAW_FILE_NAME=Pos_13'.raw SUBJECT_SAMPLE_FACTORS - Pos_13'_r1 Genotype:bacterial community | Treatment:BHI spent by Flavonifractor plautii RAW_FILE_NAME=Pos_13'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_13'_r2 Genotype:bacterial community | Treatment:BHI spent by Flavonifractor plautii RAW_FILE_NAME=Pos_13'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_14' Genotype:bacterial community | Treatment:BHI spent by Bacteroides uniformis RAW_FILE_NAME=Pos_14'.raw SUBJECT_SAMPLE_FACTORS - Pos_14'_r1 Genotype:bacterial community | Treatment:BHI spent by Bacteroides uniformis RAW_FILE_NAME=Pos_14'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_14'_r2 Genotype:bacterial community | Treatment:BHI spent by Bacteroides uniformis RAW_FILE_NAME=Pos_14'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_15' Genotype:bacterial community | Treatment:BHI spent by Parabacteroides distasonis RAW_FILE_NAME=Pos_15'.raw SUBJECT_SAMPLE_FACTORS - Pos_15'_r1 Genotype:bacterial community | Treatment:BHI spent by Parabacteroides distasonis RAW_FILE_NAME=Pos_15'_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_15'_r2 Genotype:bacterial community | Treatment:BHI spent by Parabacteroides distasonis RAW_FILE_NAME=Pos_15'_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_BHICONTROL(labeled16') Genotype:bacterial community | Treatment:BHI fresh RAW_FILE_NAME=Pos_BHICONTROL(labeled16').raw SUBJECT_SAMPLE_FACTORS - Pos_BHICONTROL(labeled16')_r1 Genotype:bacterial community | Treatment:BHI fresh RAW_FILE_NAME=Pos_BHICONTROL(labeled16')_r1.raw SUBJECT_SAMPLE_FACTORS - Pos_BHICONTROL(labeled16')_r2 Genotype:bacterial community | Treatment:BHI fresh RAW_FILE_NAME=Pos_BHICONTROL(labeled16')_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_1' Genotype:bacterial community | Treatment:BHI spent by Enterococcus hirae RAW_FILE_NAME=Neg_1'.raw SUBJECT_SAMPLE_FACTORS - Neg_1'_r1 Genotype:bacterial community | Treatment:BHI spent by Enterococcus hirae RAW_FILE_NAME=Neg_1'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_1'_r2 Genotype:bacterial community | Treatment:BHI spent by Enterococcus hirae RAW_FILE_NAME=Neg_1'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_2' Genotype:bacterial community | Treatment:BHI spent by Escherichia fergusonii RAW_FILE_NAME=Neg_2'.raw SUBJECT_SAMPLE_FACTORS - Neg_2'_r1 Genotype:bacterial community | Treatment:BHI spent by Escherichia fergusonii RAW_FILE_NAME=Neg_2'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_2'_r2 Genotype:bacterial community | Treatment:BHI spent by Escherichia fergusonii RAW_FILE_NAME=Neg_2'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_3' Genotype:bacterial community | Treatment:BHI spent by Clostridium symbiosum RAW_FILE_NAME=Neg_3'.raw SUBJECT_SAMPLE_FACTORS - Neg_3'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium symbiosum RAW_FILE_NAME=Neg_3'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_3'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium symbiosum RAW_FILE_NAME=Neg_3'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_4' Genotype:bacterial community | Treatment:BHI spent by Bacteroides thetaiotaomicron RAW_FILE_NAME=Neg_4'.raw SUBJECT_SAMPLE_FACTORS - Neg_4'_r1 Genotype:bacterial community | Treatment:BHI spent by Bacteroides thetaiotaomicron RAW_FILE_NAME=Neg_4'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_4'_r2 Genotype:bacterial community | Treatment:BHI spent by Bacteroides thetaiotaomicron RAW_FILE_NAME=Neg_4'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_5' Genotype:bacterial community | Treatment:BHI spent by Clostridium clostridioforme RAW_FILE_NAME=Neg_5'.raw SUBJECT_SAMPLE_FACTORS - Neg_5'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium clostridioforme RAW_FILE_NAME=Neg_5'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_5'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium clostridioforme RAW_FILE_NAME=Neg_5'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_6' Genotype:bacterial community | Treatment:BHI spent by Blautia producta RAW_FILE_NAME=Neg_6'.raw SUBJECT_SAMPLE_FACTORS - Neg_6'_r1 Genotype:bacterial community | Treatment:BHI spent by Blautia producta RAW_FILE_NAME=Neg_6'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_6'_r2 Genotype:bacterial community | Treatment:BHI spent by Blautia producta RAW_FILE_NAME=Neg_6'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_7' Genotype:bacterial community | Treatment:BHI spent by Clostridium scindens RAW_FILE_NAME=Neg_7'.raw SUBJECT_SAMPLE_FACTORS - Neg_7'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium scindens RAW_FILE_NAME=Neg_7'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_7'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium scindens RAW_FILE_NAME=Neg_7'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_8' Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecium RAW_FILE_NAME=Neg_8'.raw SUBJECT_SAMPLE_FACTORS - Neg_8'_r1 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecium RAW_FILE_NAME=Neg_8'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_8'_r2 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecium RAW_FILE_NAME=Neg_8'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_9' Genotype:bacterial community | Treatment:BHI spent by Clostridium hylemonae RAW_FILE_NAME=Neg_9'.raw SUBJECT_SAMPLE_FACTORS - Neg_9'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium hylemonae RAW_FILE_NAME=Neg_9'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_9'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium hylemonae RAW_FILE_NAME=Neg_9'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_10' Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecalis RAW_FILE_NAME=Neg_10'.raw SUBJECT_SAMPLE_FACTORS - Neg_10'_r1 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecalis RAW_FILE_NAME=Neg_10'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_10'_r2 Genotype:bacterial community | Treatment:BHI spent by Enterococcus faecalis RAW_FILE_NAME=Neg_10'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_11' Genotype:bacterial community | Treatment:BHI spent by Clostridium hathewayi RAW_FILE_NAME=Neg_11'.raw SUBJECT_SAMPLE_FACTORS - Neg_11'_r1 Genotype:bacterial community | Treatment:BHI spent by Clostridium hathewayi RAW_FILE_NAME=Neg_11'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_11'_r2 Genotype:bacterial community | Treatment:BHI spent by Clostridium hathewayi RAW_FILE_NAME=Neg_11'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_12' Genotype:bacterial community | Treatment:BHI spent by Bacteroides fragilis RAW_FILE_NAME=Neg_12'.raw SUBJECT_SAMPLE_FACTORS - Neg_12'_r1 Genotype:bacterial community | Treatment:BHI spent by Bacteroides fragilis RAW_FILE_NAME=Neg_12'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_12'_r2 Genotype:bacterial community | Treatment:BHI spent by Bacteroides fragilis RAW_FILE_NAME=Neg_12'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_13' Genotype:bacterial community | Treatment:BHI spent by Flavonifractor plautii RAW_FILE_NAME=Neg_13'.raw SUBJECT_SAMPLE_FACTORS - Neg_13'_r1 Genotype:bacterial community | Treatment:BHI spent by Flavonifractor plautii RAW_FILE_NAME=Neg_13'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_13'_r2 Genotype:bacterial community | Treatment:BHI spent by Flavonifractor plautii RAW_FILE_NAME=Neg_13'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_14' Genotype:bacterial community | Treatment:BHI spent by Bacteroides uniformis RAW_FILE_NAME=Neg_14'.raw SUBJECT_SAMPLE_FACTORS - Neg_14'_r1 Genotype:bacterial community | Treatment:BHI spent by Bacteroides uniformis RAW_FILE_NAME=Neg_14'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_14'_r2 Genotype:bacterial community | Treatment:BHI spent by Bacteroides uniformis RAW_FILE_NAME=Neg_14'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_15' Genotype:bacterial community | Treatment:BHI spent by Parabacteroides distasonis RAW_FILE_NAME=Neg_15'.raw SUBJECT_SAMPLE_FACTORS - Neg_15'_r1 Genotype:bacterial community | Treatment:BHI spent by Parabacteroides distasonis RAW_FILE_NAME=Neg_15'_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_15'_r2 Genotype:bacterial community | Treatment:BHI spent by Parabacteroides distasonis RAW_FILE_NAME=Neg_15'_r2.raw SUBJECT_SAMPLE_FACTORS - Neg_BHICONTROL(labeled16') Genotype:bacterial community | Treatment:BHI fresh RAW_FILE_NAME=Neg_BHICONTROL(labeled16').raw SUBJECT_SAMPLE_FACTORS - Neg_BHICONTROL(labeled16')_r1 Genotype:bacterial community | Treatment:BHI fresh RAW_FILE_NAME=Neg_BHICONTROL(labeled16')_r1.raw SUBJECT_SAMPLE_FACTORS - Neg_BHICONTROL(labeled16')_r2 Genotype:bacterial community | Treatment:BHI fresh RAW_FILE_NAME=Neg_BHICONTROL(labeled16')_r2.raw SUBJECT_SAMPLE_FACTORS - Pos_BK2 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK2.raw SUBJECT_SAMPLE_FACTORS - Pos_BK3 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK3.raw SUBJECT_SAMPLE_FACTORS - Pos_BK4 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK4.raw SUBJECT_SAMPLE_FACTORS - Pos_BK5 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK5.raw SUBJECT_SAMPLE_FACTORS - Pos_BK6 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK6.raw SUBJECT_SAMPLE_FACTORS - Pos_BK7 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK7.raw SUBJECT_SAMPLE_FACTORS - Pos_BK8 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK8.raw SUBJECT_SAMPLE_FACTORS - Pos_BK9 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK9.raw SUBJECT_SAMPLE_FACTORS - Pos_BK10 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK10.raw SUBJECT_SAMPLE_FACTORS - Pos_BK11 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK11.raw SUBJECT_SAMPLE_FACTORS - Pos_BK12 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK12.raw SUBJECT_SAMPLE_FACTORS - Pos_BK13 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK13.raw SUBJECT_SAMPLE_FACTORS - Pos_BK14 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK14.raw SUBJECT_SAMPLE_FACTORS - Pos_BK15 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK15.raw SUBJECT_SAMPLE_FACTORS - Pos_BK16 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK16.raw SUBJECT_SAMPLE_FACTORS - Pos_BK17 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK17.raw SUBJECT_SAMPLE_FACTORS - Pos_BK18 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Pos_BK18.raw SUBJECT_SAMPLE_FACTORS - Pos_QC2 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC2.raw SUBJECT_SAMPLE_FACTORS - Pos_QC3 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC3.raw SUBJECT_SAMPLE_FACTORS - Pos_QC4 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC4.raw SUBJECT_SAMPLE_FACTORS - Pos_QC5 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC5.raw SUBJECT_SAMPLE_FACTORS - Pos_QC6 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC6.raw SUBJECT_SAMPLE_FACTORS - Pos_QC7 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC7.raw SUBJECT_SAMPLE_FACTORS - Pos_QC8 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC8.raw SUBJECT_SAMPLE_FACTORS - Pos_QC9 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC9.raw SUBJECT_SAMPLE_FACTORS - Pos_QC10 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC10.raw SUBJECT_SAMPLE_FACTORS - Pos_QC11 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC11.raw SUBJECT_SAMPLE_FACTORS - Pos_QC12 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC12.raw SUBJECT_SAMPLE_FACTORS - Pos_QC13 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC13.raw SUBJECT_SAMPLE_FACTORS - Pos_QC14 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC14.raw SUBJECT_SAMPLE_FACTORS - Pos_QC15 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC15.raw SUBJECT_SAMPLE_FACTORS - Pos_QC16 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC16.raw SUBJECT_SAMPLE_FACTORS - Pos_QC17 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC17.raw SUBJECT_SAMPLE_FACTORS - Pos_QC18 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Pos_QC18.raw SUBJECT_SAMPLE_FACTORS - Neg_BK2 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK2.raw SUBJECT_SAMPLE_FACTORS - Neg_BK3 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK3.raw SUBJECT_SAMPLE_FACTORS - Neg_BK4 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK4.raw SUBJECT_SAMPLE_FACTORS - Neg_BK5 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK5.raw SUBJECT_SAMPLE_FACTORS - Neg_BK6 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK6.raw SUBJECT_SAMPLE_FACTORS - Neg_BK7 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK7.raw SUBJECT_SAMPLE_FACTORS - Neg_BK8 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK8.raw SUBJECT_SAMPLE_FACTORS - Neg_BK9 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK9.raw SUBJECT_SAMPLE_FACTORS - Neg_BK10 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK10.raw SUBJECT_SAMPLE_FACTORS - Neg_BK11 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK11.raw SUBJECT_SAMPLE_FACTORS - Neg_BK12 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK12.raw SUBJECT_SAMPLE_FACTORS - Neg_BK13 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK13.raw SUBJECT_SAMPLE_FACTORS - Neg_BK14 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK14.raw SUBJECT_SAMPLE_FACTORS - Neg_BK15 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK15.raw SUBJECT_SAMPLE_FACTORS - Neg_BK16 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK16.raw SUBJECT_SAMPLE_FACTORS - Neg_BK17 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK17.raw SUBJECT_SAMPLE_FACTORS - Neg_BK18 Genotype:Analytical Blank | Treatment:Method Blank RAW_FILE_NAME=Neg_BK18.raw SUBJECT_SAMPLE_FACTORS - Neg_QC2 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC2.raw SUBJECT_SAMPLE_FACTORS - Neg_QC3 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC3.raw SUBJECT_SAMPLE_FACTORS - Neg_QC4 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC4.raw SUBJECT_SAMPLE_FACTORS - Neg_QC5 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC5.raw SUBJECT_SAMPLE_FACTORS - Neg_QC6 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC6.raw SUBJECT_SAMPLE_FACTORS - Neg_QC7 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC7.raw SUBJECT_SAMPLE_FACTORS - Neg_QC8 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC8.raw SUBJECT_SAMPLE_FACTORS - Neg_QC9 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC9.raw SUBJECT_SAMPLE_FACTORS - Neg_QC10 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC10.raw SUBJECT_SAMPLE_FACTORS - Neg_QC11 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC11.raw SUBJECT_SAMPLE_FACTORS - Neg_QC12 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC12.raw SUBJECT_SAMPLE_FACTORS - Neg_QC13 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC13.raw SUBJECT_SAMPLE_FACTORS - Neg_QC14 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC14.raw SUBJECT_SAMPLE_FACTORS - Neg_QC15 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC15.raw SUBJECT_SAMPLE_FACTORS - Neg_QC16 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC16.raw SUBJECT_SAMPLE_FACTORS - Neg_QC17 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC17.raw SUBJECT_SAMPLE_FACTORS - Neg_QC18 Genotype:Quality Control | Treatment:Sample Pool RAW_FILE_NAME=Neg_QC18.raw #COLLECTION CO:COLLECTION_SUMMARY Isolates were obtained via plating of in vitro communities –, derived from CO:COLLECTION_SUMMARY culturing fecal samples from humanized mice –, on agar plates made with CO:COLLECTION_SUMMARY various complex media and frozen as glycerol stocks, as previously described CO:COLLECTION_SUMMARY (https://doi.org/https://doi.org/10.1016/j.chom.2021.12.008, CO:COLLECTION_SUMMARY https://www.biorxiv.org/content/10.1101/2023.01.13.523996v1). Frozen stocks were CO:COLLECTION_SUMMARY streaked onto BHI-blood agar plates (5% defibrinated horse blood in 1.5% w/v CO:COLLECTION_SUMMARY agar). Resulting colonies were inoculated into 3 mL of Brain Heart Infusion CO:COLLECTION_SUMMARY (BHI) (BD #2237500) or modified Gifu Anaerobic Medium (mGAM) (HyServe #05433) in CO:COLLECTION_SUMMARY test tubes. All culturing werewas performed at 37 °C without shaking in an CO:COLLECTION_SUMMARY anaerobic chamber (Coy). To minimize potential physiological changes from CO:COLLECTION_SUMMARY freeze-thaw cycles and changes in growth medium, cultures were diluted 1:200 CO:COLLECTION_SUMMARY every 48 h for 3 passages before growth or metabolomics measurements. After the CO:COLLECTION_SUMMARY first passage, subsequent passages were performed in 96-well polystyrene plates CO:COLLECTION_SUMMARY (Greiner Bio-One #655161) filled with 200 μL of growth medium. CO:SAMPLE_TYPE Bacterial cells #TREATMENT TR:TREATMENT_SUMMARY Many combinations of bacterial isolates were assayed. details can be found in TR:TREATMENT_SUMMARY the publicly available preprint here: TR:TREATMENT_SUMMARY https://www.biorxiv.org/content/10.1101/2022.05.30.494065v1.abstract #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Spent media were collected as described above and immediately stored at -80 °C. SP:SAMPLEPREP_SUMMARY Samples were thawed only once, immediately before LC-MS/MS. Thawed samples were SP:SAMPLEPREP_SUMMARY kept on ice, each sample was homogenized by pipetting prior to dispensing. Two SP:SAMPLEPREP_SUMMARY 20-µL aliquots of supernatant were removed from each sample well and dispensed SP:SAMPLEPREP_SUMMARY into two shallow 96-well polypropylene plates, maintained on ice. Additionally, SP:SAMPLEPREP_SUMMARY 5 µL were removed from each sample and combined into a homogenous pool; this SP:SAMPLEPREP_SUMMARY pool was dispensed in 20-µL aliquots and prepared in parallel with samples. SP:SAMPLEPREP_SUMMARY These pooled samples were used for in-run quality control, injected at SP:SAMPLEPREP_SUMMARY predefined intervals over the course of analysis to ensure consistent instrument SP:SAMPLEPREP_SUMMARY performance over time. Samples were analyzed using two complementary SP:SAMPLEPREP_SUMMARY chromatography methods: reversed phase (C18) and hydrophilic interaction SP:SAMPLEPREP_SUMMARY chromatography (HILIC). All samples were analyzed by positive and negative mode SP:SAMPLEPREP_SUMMARY electrospray ionization (ESI+, ESI-). Sample analysis order was randomized to SP:SAMPLEPREP_SUMMARY minimize potential bias in data acquisition. Procedural blanks were prepared by SP:SAMPLEPREP_SUMMARY extracting 20 µL of water in place of bacterial supernatant. Procedural blanks SP:SAMPLEPREP_SUMMARY were inserted throughout the run as additional quality control. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Bacterial supernatant were analyzed via reversed phase (C18) coupled to a Thermo CH:CHROMATOGRAPHY_SUMMARY Q-Exactive HF high resolution mass spectrometer. Prepared samples were injected CH:CHROMATOGRAPHY_SUMMARY onto an Agilent Zorbax SB-C18 column (100 mm length × 3 mm id; 1.8 μm particle CH:CHROMATOGRAPHY_SUMMARY size) with an additional Phenomenex KrudKatcher pre-column (2 μm depth x CH:CHROMATOGRAPHY_SUMMARY 0.004in ID) maintained at 40°C coupled to an Thermo Vanquish UPLC. The mobile CH:CHROMATOGRAPHY_SUMMARY phases were prepared with 0.1% formic acid in either 100% LC-MS grade water for CH:CHROMATOGRAPHY_SUMMARY mobile phase (A), 100% water or mobile phase (B), 100% acetonitrile. Gradient CH:CHROMATOGRAPHY_SUMMARY elution was performed as follows 3% (B) maintained 0–0.43 min to 97% (B) at 9 CH:CHROMATOGRAPHY_SUMMARY min, maintained until 11 min, returning to initial conditions at 11.5 min and CH:CHROMATOGRAPHY_SUMMARY equilibrating until the end of the run at 14 min. Flow rate is maintained at 0.4 CH:CHROMATOGRAPHY_SUMMARY mL/min. Each sample was analyzed in both positive and negative ionization modes CH:CHROMATOGRAPHY_SUMMARY (ESI+, ESI-) via subsequent injections. Full MS-ddMS2 data was collected, an CH:CHROMATOGRAPHY_SUMMARY inclusion list was used to prioritize MS2 selection of metabolites from our CH:CHROMATOGRAPHY_SUMMARY in-house ‘local’ library, when additional scan bandwidth was available MS2 CH:CHROMATOGRAPHY_SUMMARY was collected in a data-dependent manner. Mass range was 60-900 mz, resolution CH:CHROMATOGRAPHY_SUMMARY was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, CH:CHROMATOGRAPHY_SUMMARY isolation window was 1.5 Da. Metabolomics data was processed using MS-DIAL v4.60 CH:CHROMATOGRAPHY_SUMMARY (https://www.nature.com/articles/s41587-020-0531-2) and queried against a CH:CHROMATOGRAPHY_SUMMARY combination of our in-house MS2 library and MassBank of North America, the CH:CHROMATOGRAPHY_SUMMARY largest freely available spectral repository CH:CHROMATOGRAPHY_SUMMARY (https://doi.org/10.1002/mas.21535). Features were excluded from analysis if CH:CHROMATOGRAPHY_SUMMARY peak height was not at least 5-fold greater in one or more samples compared to CH:CHROMATOGRAPHY_SUMMARY the procedural blank average. CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Agilent Zorbax SB-C18 (100 x 3.0 mm, 1.8 um) CH:SOLVENT_A Water + 0.1% formic acid CH:SOLVENT_B Acetonitrile + 0.1% formic acid CH:FLOW_GRADIENT Gradient elution was performed from 100% (B) at 0–2 min to 70% (B) at 7.7 min, CH:FLOW_GRADIENT 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min, isocratic until CH:FLOW_GRADIENT 16.75 min with a column flow ofGradient elution was performed as follows 3% (B) CH:FLOW_GRADIENT maintained 0–0.43 min to 97% (B) at 9 min, maintained until 11 min, returning CH:FLOW_GRADIENT to initial conditions at 11.5 min and equilibrating until the end of the run at CH:FLOW_GRADIENT 14 min. CH:FLOW_RATE 0.4 mL/min. CH:COLUMN_TEMPERATURE 40C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 MS:MS_COMMENTS selection of metabolites from our in-house ‘local’ library, when additional MS:MS_COMMENTS scan bandwidth was available MS2 was collected in a data-dependent manner. Mass MS:MS_COMMENTS range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was MS:MS_COMMENTS collected, loop count was 4, isolation window was 1.5 Da. Metabolomics data was MS:MS_COMMENTS processed using MS-DIAL v4.60. Features were excluded from analysis if peak MS:MS_COMMENTS height was not at least 5-fold greater in one or more samples compared to the MS:MS_COMMENTS procedural blank average. MS:MS_RESULTS_FILE ST002834_AN004630_Results.txt UNITS:counts, height Has m/z:Yes Has RT:Yes RT units:Minutes #END