#METABOLOMICS WORKBENCH bcdefelice_20230828_095809 DATATRACK_ID:4261 STUDY_ID:ST002834 ANALYSIS_ID:AN004629 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                      	POSITIVE
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_AN004629_Results.txt	UNITS:counts, height	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END