Summary of Study ST001683

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001074. The data can be accessed directly via it's Project DOI: 10.21228/M8W11P This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST001683
Study Title	A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism.
Study Summary	Gut microbes modulate host phenotypes and are associated with numerous health effects in humans, ranging from cancer immunotherapy response to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microbes has hindered defining mechanistic connections between individual microbial strains and host phenotypes. One key way the gut microbiome influences host physiology is through the production of small molecules hindered by limited tools calibrated to detect products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites (MDMs) in diverse sample types. We report the metabolic profiles of 178 gut microbe strains using our library of 833 metabolites. Leveraging this metabolomics resource we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover novel metabolism in Bacteroides, and employ comparative genomics-based discovery of candidate biochemical pathways. MDMs can be detected in diverse body fluids in gnotobiotic and conventional mice and traced back to corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microbe and microbe-host interactions.
Institute	Stanford University
Department	Microbiology & Immunology
Laboratory	Justin Sonnenburg
Last Name	Han
First Name	Shuo
Address	299 Campus Drive, Stanford, CA, 94305-5124, USA
Email	shuohan@stanford.edu
Phone	-
Submit Date	2021-02-06
Publications	not published, status to be updated
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2021-05-17
Release Version	1

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Treatment:

Treatment ID:	TR001773
Treatment Summary:	Mouse experiments were performed on gnotobiotic Swiss Webster germ-free mice (males, 10-14 weeks of age, n = 3-8 per group for all experiments) maintained in aseptic isolators, and originally obtained from Taconic Bioscience. For mono-association experiments, mice were colonized with Bacteroides thetaiotaomicron VPI 5482, Clostridium sporogenes ATCC 15579, Citrobacter portucalensis BEI HM-34, or Anaerostipes sp. BEI HM-220904a, by oral gavage (200 uL, ~1 x 107 CFU) and were maintained on a standard chow (LabDiet 5K67). For the defined-community experiment, mice with a six-member community were colonized with a 200 uL mixture consisting of equal volumes from saturated cultures of Bacteroides thetaiotaomicron VPI 5482 (8.7 x 109 CFU), Clostridium sporogenes ATCC 15579 (1.4 x 108 CFU), Edwardsiella tarda ATCC 23685 (3.6 x 1010 CFU), Collinsella aerofaciens ATCC 25986 (1.4 x 109), Eubacterium rectale ATCC 33656 (6.9 x 106 CFU), and Parabacteroides distasonis ATCC 8503 (1.5 x 109 CFU). Mice with a five-member community were colonized with all cultures mixed at the same volumes as described above except for Clostridium sporogenes ATCC 15579, which was not included. Successful colonization and stable community members were determined by 16S amplicon sequencing of the V4 (515f, 806r) region of microbial populations present in the feces and cecal contents from individual mice.

Treatment ID:

TR001773

Treatment Summary:

Mouse experiments were performed on gnotobiotic Swiss Webster germ-free mice (males, 10-14 weeks of age, n = 3-8 per group for all experiments) maintained in aseptic isolators, and originally obtained from Taconic Bioscience. For mono-association experiments, mice were colonized with Bacteroides thetaiotaomicron VPI 5482, Clostridium sporogenes ATCC 15579, Citrobacter portucalensis BEI HM-34, or Anaerostipes sp. BEI HM-220904a, by oral gavage (200 uL, ~1 x 107 CFU) and were maintained on a standard chow (LabDiet 5K67). For the defined-community experiment, mice with a six-member community were colonized with a 200 uL mixture consisting of equal volumes from saturated cultures of Bacteroides thetaiotaomicron VPI 5482 (8.7 x 109 CFU), Clostridium sporogenes ATCC 15579 (1.4 x 108 CFU), Edwardsiella tarda ATCC 23685 (3.6 x 1010 CFU), Collinsella aerofaciens ATCC 25986 (1.4 x 109), Eubacterium rectale ATCC 33656 (6.9 x 106 CFU), and Parabacteroides distasonis ATCC 8503 (1.5 x 109 CFU). Mice with a five-member community were colonized with all cultures mixed at the same volumes as described above except for Clostridium sporogenes ATCC 15579, which was not included. Successful colonization and stable community members were determined by 16S amplicon sequencing of the V4 (515f, 806r) region of microbial populations present in the feces and cecal contents from individual mice.