Reference Data Based Insights Expand Understanding of Human Metabolomes

Gauglitz, Julia M.; Bittremieux, Wout; Williams, Candace L.; Weldon, Kelly C.; Panitchpakdi, Morgan; Ottavio, Francesca Di; Aceves, Christine M.; Brown, Élizabeth; Sikora, Nicole; Jarmusch, Alan K.; Martino, Cameron; Tripathi, Anupriya; Sayyari, Erfan; Shaffer, Justin P.; Coras, Roxana; Vargas, Fernando; Goldasich, Lindsay DeRight; Schwartz, Tara; Bryant, MacKenzie; Humphrey, Gregory; Johnson, Abigail; Spengler, Katharina; Belda-Ferre, Pedro; Diaz, Edgar; McDonald, Daniel; Zhu, Qiyun; Nguyen, Dominic; Elijah, Emmanuel O.; Wang, Mingxun; Marotz, Clarisse; Sprecher, Kate E.; Vargas-Robles, Daniela; Withrow, Dana; Ackermann, Gail; Herrera, Lourdes; Bradford, B.J.; Marques, Lucas Maciel Mauriz; Amaral, Juliano Geraldo; Silva, Rodrigo Moreira da; Veras, Flávio Protaso; Cunha, Thiago Mattar; Oliveira, Renê Donizeti Ribeiro de; Louzada‐Júnior, Paulo; Mills, Robert H.; Galasko, Douglas; Dulai, Parambir S.; Wittenberg, Curt; Gonzalez, David J.; Terkeltaub, Robert; Doty, Megan M.; Kim, Jaehwan; Rhee, Kyung E.; Beauchamp‐Walters, Julia; Wright, Kenneth P.; Bello, Maria Gloria Dominguez; Manary, Mark; Oliveira, Michelli F.; Boland, Brigid S.; Lopes, Norberto Peporine; Gumá, Mónica; Swafford, Austin D.; Dutton, Rachel J.; Knight, Rob; Dorrestein, Pieter C.

doi:10.2139/ssrn.3661950

Cited by 5 publications

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“…Co-networking of HOMEChem data with other public datasets to enable tracing of potential sources, a reference data–driven metabolomics approach ( 8 ), revealed that the molecules found in the indoor space overlap with other sample types and thus may, at least in part, originate from those sources: food (~15.7%), human-associated microbes (~1.1%), feces (~8.6%; although feces contain both food and microbial molecules), building materials and microbes that grow on them (~2.6%), and building materials in humid conditions (~4.7%).…”

Section: Resultsmentioning

confidence: 99%

“…Because eating or cooking had the most significant impact on the chemistries of specific locations within the house, we used the Global FoodOmics project ( 8 ) of molecular composition of foods and a reference data–driven approach to track the overlap of molecules detected in the house with those found in various foods, as described in Materials and Methods and references therein. The test house inhabitants contributed an assortment of molecules that we could bioinformatically relate to a wide variety of possible food sources (fig.…”

Section: Resultsmentioning

confidence: 99%

“…S7A can be found at https://ccms-ucsd.github.io/GNPSDocumentation/tutorials/rdd/ and is linked out to GitHub and the MassIVE Repository, as shown in Gauglitz et al . ( 8 ).…”

Section: Methodsmentioning

confidence: 99%

“…The chemical molecular ontology analysis using Qemistree ( 28 ) for the FoodOmics ( 8 ) and nestedness analysis ( 9 ) were performed using the GNPS workflow. The results can be viewed at https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=732ee57912dc4420afc7e5b83f3d8594.…”

Section: Methodsmentioning

confidence: 99%

“…Reference data–based metabolomics ( 8 ) was performed to conetwork HOMEChem data with other public datasets to trace the potential source. The common features were considered an overlap.…”

Section: Methodsmentioning

confidence: 99%

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The molecular impact of life in an indoor environment

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The chemistry of indoor surfaces and the role of microbes in shaping and responding to that chemistry are largely unexplored. We found that, over 1 month, people’s presence and activities profoundly reshaped the chemistry of a house. Molecules associated with eating/cooking, bathroom use, and personal care were found throughout the entire house, while molecules associated with medications, outdoor biocides, and microbially derived compounds were distributed in a location-dependent manner. The house and its microbial occupants, in turn, also introduced chemical transformations such as oxidation and transformations of foodborne molecules. The awareness of and the ability to observe the molecular changes introduced by people should influence future building designs.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…S7A can be found at https://ccms-ucsd.github.io/GNPSDocumentation/tutorials/rdd/ and is linked out to GitHub and the MassIVE Repository, as shown in Gauglitz et al . ( 8 ).…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The molecular impact of life in an indoor environment

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Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation

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et al. 2022

J. Agric. Food Chem.

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Understanding the microbial and chemical diversities, as well as what affects these diversities, is important for modern manufacturing of traditional fermented foods. In this work, Chinese dark teas (CDTs) that are traditional microbial fermented beverages with relatively high sample diversity were collected. Microbial DNA amplicon sequencing and mass spectrometry-based untargeted metabolomics show that the CDT microbial β diversity, as well as the nonvolatile chemical α and β diversities, is determined by the primary impact factors of geography and manufacturing procedures, in particular, latitude and pile fermentation after blending. A large number of metabolites sharing between CDTs and fungi were discovered by Feature-based Molecular Networking (FBMN) on the Global Natural Products Social Molecular Networking (GNPS) web platform. These molecules, such as prenylated cyclic dipeptides and B-vitamins, are functionally important for nutrition, biofunctions, and flavor. Molecular networking has revealed patterns in metabolite profiles on a chemical family level in addition to individual structures.

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Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease

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Inflammatory Bowel Disease (IBD) is a chronic immune-mediated inflammatory disease of the gastrointestinal tract that is a growing public burden. Gut microbes and their interactions with hosts play a crucial role in disease pathogenesis and progression. These interactions are complex, spanning multiple physiological systems and data types, making comprehensive disease assessment difficult, and often overwhelming single-omic capabilities. Stool-based multi-omics is a promising approach for characterizing host-gut microbiome interactions using deep integration of technologies such as 16S rRNA sequencing, shotgun metagenomics, meta-transcriptomics, metabolomics, and metaproteomics. The wealth of information generated through multi-omic studies is poised to usher in advancements in IBD research and precision medicine. This review highlights historical and recent findings from stool-based muti-omic studies that have contributed to unraveling IBD’s complexity. Finally, we discuss common pitfalls, issues, and limitations, and how future pipelines should address them to standardize multi-omics in IBD research and beyond.

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Reference Data Based Insights Expand Understanding of Human Metabolomes

Cited by 5 publications

References 0 publications

The molecular impact of life in an indoor environment

The molecular impact of life in an indoor environment

Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation

Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease

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