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.

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Study IDST001683
Study TitleA gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism.
Study SummaryGut 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
DepartmentMicrobiology & Immunology
LaboratoryJustin Sonnenburg
Last NameHan
First NameShuo
Address299 Campus Drive, Stanford, CA, 94305-5124, USA
Emailshuohan@stanford.edu
Phone-
Submit Date2021-02-06
Publicationsnot published, status to be updated
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-05-17
Release Version1
Shuo Han Shuo Han
https://dx.doi.org/10.21228/M8W11P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Experiment Sample_type Colonization
SA155124s0194community caecal Bt_Ca_Er_Pd_Et
SA155125s0177community caecal Bt_Ca_Er_Pd_Et
SA155126s0195community caecal Bt_Ca_Er_Pd_Et
SA155127s0187community caecal Bt_Ca_Er_Pd_Et
SA155128s0185community caecal Bt_Ca_Er_Pd_Et
SA155129s0176community caecal Bt_Ca_Er_Pd_Et
SA155130s0178community caecal Bt_Ca_Er_Pd_Et
SA155131s0196community caecal Bt_Ca_Er_Pd_Et
SA155132s0186community caecal Bt_Ca_Er_Pd_Et
SA155133s0201community caecal Cs_Bt_Ca_Er_Pd_Et
SA155134s0219community caecal Cs_Bt_Ca_Er_Pd_Et
SA155135s0220community caecal Cs_Bt_Ca_Er_Pd_Et
SA155136s0218community caecal Cs_Bt_Ca_Er_Pd_Et
SA155137s0213community caecal Cs_Bt_Ca_Er_Pd_Et
SA155138s0202community caecal Cs_Bt_Ca_Er_Pd_Et
SA155139s0212community caecal Cs_Bt_Ca_Er_Pd_Et
SA155140s0200community caecal Cs_Bt_Ca_Er_Pd_Et
SA155141s0214community caecal Cs_Bt_Ca_Er_Pd_Et
SA155142s0162community caecal germ-free
SA155143s0161community caecal germ-free
SA155144s0172community caecal germ-free
SA155145s0163community caecal germ-free
SA155146s0167community caecal germ-free
SA155147s0171community caecal germ-free
SA155148s0170community caecal germ-free
SA155149s0169community caecal germ-free
SA155150s0168community caecal germ-free
SA155151s0054community feces Bt_Ca_Er_Pd_Et
SA155152s0070community feces Bt_Ca_Er_Pd_Et
SA155153s0092community feces Cs_Bt_Ca_Er_Pd_Et
SA155154s0100community feces Cs_Bt_Ca_Er_Pd_Et
SA155155s0082community feces Cs_Bt_Ca_Er_Pd_Et
SA155156s0022community feces germ-free
SA155157s0029community feces germ-free
SA155158s0034community feces germ-free
SA155159s0363community serum Bt_Ca_Er_Pd_Et
SA155160s0368community serum Bt_Ca_Er_Pd_Et
SA155161s0362community serum Bt_Ca_Er_Pd_Et
SA155162s0359community serum Bt_Ca_Er_Pd_Et
SA155163s0355community serum Bt_Ca_Er_Pd_Et
SA155164s0374community serum Bt_Ca_Er_Pd_Et
SA155165s0367community serum Bt_Ca_Er_Pd_Et
SA155166s0366community serum Bt_Ca_Er_Pd_Et
SA155167s0360community serum Cs_Bt_Ca_Er_Pd_Et
SA155168s0357community serum Cs_Bt_Ca_Er_Pd_Et
SA155169s0361community serum Cs_Bt_Ca_Er_Pd_Et
SA155170s0356community serum Cs_Bt_Ca_Er_Pd_Et
SA155171s0373community serum Cs_Bt_Ca_Er_Pd_Et
SA155172s0369community serum Cs_Bt_Ca_Er_Pd_Et
SA155173s0372community serum Cs_Bt_Ca_Er_Pd_Et
SA155174s0365community serum germ-free
SA155175s0364community serum germ-free
SA155176s0358community serum germ-free
SA155177s0371community serum germ-free
SA155178s0370community serum germ-free
SA155179s0286community urine Bt_Ca_Er_Pd_Et
SA155180s0281community urine Bt_Ca_Er_Pd_Et
SA155181s0290community urine Bt_Ca_Er_Pd_Et
SA155182s0295community urine Bt_Ca_Er_Pd_Et
SA155183s0309community urine Bt_Ca_Er_Pd_Et
SA155184s0304community urine Bt_Ca_Er_Pd_Et
SA155185s0314community urine Bt_Ca_Er_Pd_Et
SA155186s0245community urine Cs_Bt_Ca_Er_Pd_Et
SA155187s0250community urine Cs_Bt_Ca_Er_Pd_Et
SA155188s0254community urine Cs_Bt_Ca_Er_Pd_Et
SA155189s0259community urine Cs_Bt_Ca_Er_Pd_Et
SA155190s0277community urine Cs_Bt_Ca_Er_Pd_Et
SA155191s0272community urine Cs_Bt_Ca_Er_Pd_Et
SA155192s0227community urine germ-free
SA155193s0231community urine germ-free
SA155194s0236community urine germ-free
SA155195s1073conventional caecal conventional
SA155196s1072conventional caecal conventional
SA155197s1074conventional caecal conventional
SA155198s1065conventional caecal germ-free
SA155199s1067conventional caecal germ-free
SA155200s1066conventional caecal germ-free
SA155201s1064conventional caecal germ-free
SA155202s1077conventional feces conventional
SA155203s1076conventional feces conventional
SA155204s1075conventional feces conventional
SA155205s1069conventional feces germ-free
SA155206s1068conventional feces germ-free
SA155207s1070conventional feces germ-free
SA155208s1071conventional feces germ-free
SA155209s1061conventional serum conventional
SA155210s1062conventional serum conventional
SA155211s1063conventional serum conventional
SA155212s1060conventional serum germ-free
SA155213s1058conventional serum germ-free
SA155214s1057conventional serum germ-free
SA155215s1059conventional serum germ-free
SA155216s1055conventional urine conventional
SA155217s1054conventional urine conventional
SA155218s1056conventional urine conventional
SA155219s1050conventional urine germ-free
SA155220s1051conventional urine germ-free
SA155221s1052conventional urine germ-free
SA155222s1053conventional urine germ-free
SA155223s1100mono-colonization_2 caecal As
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