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  1. Article ; Online: Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease.

    Dilmore, Amanda Hazel / Martino, Cameron / Neth, Bryan J / West, Kiana A / Zemlin, Jasmine / Rahman, Gibraan / Panitchpakdi, Morgan / Meehan, Michael J / Weldon, Kelly C / Blach, Colette / Schimmel, Leyla / Kaddurah-Daouk, Rima / Dorrestein, Pieter C / Knight, Rob / Craft, Suzanne

    Alzheimer's & dementia : the journal of the Alzheimer's Association

    2023  Volume 19, Issue 11, Page(s) 4805–4816

    Abstract: Introduction: The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's disease (AD) given its protective effects against metabolic dysregulation and seizures. Gut microbiota are essential for KD-mediated neuroprotection against ... ...

    Abstract Introduction: The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's disease (AD) given its protective effects against metabolic dysregulation and seizures. Gut microbiota are essential for KD-mediated neuroprotection against seizures as well as modulation of bile acids, which play a major role in cholesterol metabolism. These relationships motivated our analysis of gut microbiota and metabolites related to cognitive status following a controlled KD intervention compared with a low-fat-diet intervention.
    Methods: Prediabetic adults, either with mild cognitive impairment (MCI) or cognitively normal (CN), were placed on either a low-fat American Heart Association diet or high-fat modified Mediterranean KD (MMKD) for 6 weeks; then, after a 6-week washout period, they crossed over to the alternate diet. We collected stool samples for shotgun metagenomics and untargeted metabolomics at five time points to investigate individuals' microbiome and metabolome throughout the dietary interventions.
    Results: Participants with MCI on the MMKD had lower levels of GABA-producing microbes Alistipes sp. CAG:514 and GABA, and higher levels of GABA-regulating microbes Akkermansia muciniphila. MCI individuals with curcumin in their diet had lower levels of bile salt hydrolase-containing microbes and an altered bile acid pool, suggesting reduced gut motility.
    Discussion: Our results suggest that the MMKD may benefit adults with MCI through modulation of GABA levels and gut-transit time.
    MeSH term(s) United States ; Humans ; Adult ; Alzheimer Disease/metabolism ; Diet, Fat-Restricted ; Microbiota ; Metabolome/physiology ; Seizures ; Ketone Bodies ; gamma-Aminobutyric Acid/metabolism
    Chemical Substances Ketone Bodies ; gamma-Aminobutyric Acid (56-12-2)
    Language English
    Publishing date 2023-04-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2211627-8
    ISSN 1552-5279 ; 1552-5260
    ISSN (online) 1552-5279
    ISSN 1552-5260
    DOI 10.1002/alz.13007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The underappreciated diversity of bile acid modifications.

    Mohanty, Ipsita / Mannochio-Russo, Helena / Schweer, Joshua V / El Abiead, Yasin / Bittremieux, Wout / Xing, Shipei / Schmid, Robin / Zuffa, Simone / Vasquez, Felipe / Muti, Valentina B / Zemlin, Jasmine / Tovar-Herrera, Omar E / Moraïs, Sarah / Desai, Dhimant / Amin, Shantu / Koo, Imhoi / Turck, Christoph W / Mizrahi, Itzhak / Kris-Etherton, Penny M /
    Petersen, Kristina S / Fleming, Jennifer A / Huan, Tao / Patterson, Andrew D / Siegel, Dionicio / Hagey, Lee R / Wang, Mingxun / Aron, Allegra T / Dorrestein, Pieter C

    Cell

    2024  Volume 187, Issue 7, Page(s) 1801–1818.e20

    Abstract: The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by ... ...

    Abstract The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.
    MeSH term(s) Animals ; Humans ; Bile Acids and Salts/chemistry ; Metabolomics/methods ; Polyamines ; Tandem Mass Spectrometry/methods ; Gastrointestinal Microbiome ; Databases, Chemical
    Chemical Substances Bile Acids and Salts ; Polyamines
    Language English
    Publishing date 2024-03-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2024.02.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics.

    Bittremieux, Wout / Avalon, Nicole E / Thomas, Sydney P / Kakhkhorov, Sarvar A / Aksenov, Alexander A / Gomes, Paulo Wender P / Aceves, Christine M / Caraballo-Rodríguez, Andrés Mauricio / Gauglitz, Julia M / Gerwick, William H / Huan, Tao / Jarmusch, Alan K / Kaddurah-Daouk, Rima F / Kang, Kyo Bin / Kim, Hyun Woo / Kondić, Todor / Mannochio-Russo, Helena / Meehan, Michael J / Melnik, Alexey V /
    Nothias, Louis-Felix / O'Donovan, Claire / Panitchpakdi, Morgan / Petras, Daniel / Schmid, Robin / Schymanski, Emma L / van der Hooft, Justin J J / Weldon, Kelly C / Yang, Heejung / Xing, Shipei / Zemlin, Jasmine / Wang, Mingxun / Dorrestein, Pieter C

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 8488

    Abstract: Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated ...

    Abstract Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or "suspects," were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer's brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
    MeSH term(s) Tandem Mass Spectrometry/methods ; Access to Information ; Metabolomics/methods ; Gene Library ; Cluster Analysis
    Language English
    Publishing date 2023-12-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44035-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

    Bittremieux, Wout / Avalon, Nicole E. / Thomas, Sydney P. / Kakhkhorov, Sarvar A. / Aksenov, Alexander A. / Gomes, Paulo Wender P. / Aceves, Christine M. / Caraballo-Rodríguez, Andrés Mauricio / Gauglitz, Julia M. / Gerwick, William H. / Huan, Tao / Jarmusch, Alan K. / Kaddurah-Daouk, Rima F. / Kang, Kyo Bin / Kim, Hyun Woo / Kondić, Todor / Mannochio-Russo, Helena / Meehan, Michael J. / Melnik, Alexey V. /
    Nothias, Louis Felix / O’Donovan, Claire / Panitchpakdi, Morgan / Petras, Daniel / Schmid, Robin / Schymanski, Emma L. / van der Hooft, Justin J.J. / Weldon, Kelly C. / Yang, Heejung / Xing, Shipei / Zemlin, Jasmine / Wang, Mingxun / Dorrestein, Pieter C.

    Nature Communications

    2023  Volume 14, Issue 1

    Abstract: Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated ...

    Abstract Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or “suspects,” were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
    Keywords Life Science
    Subject code 027
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2553671-0
    ISSN 2041-1723
    ISSN 2041-1723
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.

    Zuffa, Simone / Schmid, Robin / Bauermeister, Anelize / P Gomes, Paulo Wender / Caraballo-Rodriguez, Andres M / El Abiead, Yasin / Aron, Allegra T / Gentry, Emily C / Zemlin, Jasmine / Meehan, Michael J / Avalon, Nicole E / Cichewicz, Robert H / Buzun, Ekaterina / Terrazas, Marvic Carrillo / Hsu, Chia-Yun / Oles, Renee / Ayala, Adriana Vasquez / Zhao, Jiaqi / Chu, Hiutung /
    Kuijpers, Mirte C M / Jackrel, Sara L / Tugizimana, Fidele / Nephali, Lerato Pertunia / Dubery, Ian A / Madala, Ntakadzeni Edwin / Moreira, Eduarda Antunes / Costa-Lotufo, Leticia Veras / Lopes, Norberto Peporine / Rezende-Teixeira, Paula / Jimenez, Paula C / Rimal, Bipin / Patterson, Andrew D / Traxler, Matthew F / Pessotti, Rita de Cassia / Alvarado-Villalobos, Daniel / Tamayo-Castillo, Giselle / Chaverri, Priscila / Escudero-Leyva, Efrain / Quiros-Guerrero, Luis-Manuel / Bory, Alexandre Jean / Joubert, Juliette / Rutz, Adriano / Wolfender, Jean-Luc / Allard, Pierre-Marie / Sichert, Andreas / Pontrelli, Sammy / Pullman, Benjamin S / Bandeira, Nuno / Gerwick, William H / Gindro, Katia / Massana-Codina, Josep / Wagner, Berenike C / Forchhammer, Karl / Petras, Daniel / Aiosa, Nicole / Garg, Neha / Liebeke, Manuel / Bourceau, Patric / Kang, Kyo Bin / Gadhavi, Henna / de Carvalho, Luiz Pedro Sorio / Silva Dos Santos, Mariana / Pérez-Lorente, Alicia Isabel / Molina-Santiago, Carlos / Romero, Diego / Franke, Raimo / Brönstrup, Mark / Vera Ponce de León, Arturo / Pope, Phillip Byron / La Rosa, Sabina Leanti / La Barbera, Giorgia / Roager, Henrik M / Laursen, Martin Frederik / Hammerle, Fabian / Siewert, Bianka / Peintner, Ursula / Licona-Cassani, Cuauhtemoc / Rodriguez-Orduña, Lorena / Rampler, Evelyn / Hildebrand, Felina / Koellensperger, Gunda / Schoeny, Harald / Hohenwallner, Katharina / Panzenboeck, Lisa / Gregor, Rachel / O'Neill, Ellis Charles / Roxborough, Eve Tallulah / Odoi, Jane / Bale, Nicole J / Ding, Su / Sinninghe Damsté, Jaap S / Guan, Xue Li / Cui, Jerry J / Ju, Kou-San / Silva, Denise Brentan / Silva, Fernanda Motta Ribeiro / da Silva, Gilvan Ferreira / Koolen, Hector H F / Grundmann, Carlismari / Clement, Jason A / Mohimani, Hosein / Broders, Kirk / McPhail, Kerry L / Ober-Singleton, Sidnee E / Rath, Christopher M / McDonald, Daniel / Knight, Rob / Wang, Mingxun / Dorrestein, Pieter C

    Nature microbiology

    2024  Volume 9, Issue 2, Page(s) 336–345

    Abstract: microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and ...

    Abstract microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.
    MeSH term(s) Humans ; Tandem Mass Spectrometry ; Metabolomics/methods ; Databases, Factual
    Language English
    Publishing date 2024-02-05
    Publishing country England
    Document type Journal Article
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01575-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.

    Zuffa, Simone / Schmid, Robin / Bauermeister, Anelize / Gomes, Paulo Wender P / Caraballo-Rodriguez, Andres M / Abiead, Yasin El / Aron, Allegra T / Gentry, Emily C / Zemlin, Jasmine / Meehan, Michael J / Avalon, Nicole E / Cichewicz, Robert H / Buzun, Ekaterina / Terrazas, Marvic Carrillo / Hsu, Chia-Yun / Oles, Renee / Ayala, Adriana Vasquez / Zhao, Jiaqi / Chu, Hiutung /
    Kuijpers, Mirte C M / Jackrel, Sara L / Tugizimana, Fidele / Nephali, Lerato Pertunia / Dubery, Ian A / Madala, Ntakadzeni Edwin / Moreira, Eduarda Antunes / Costa-Lotufo, Leticia Veras / Lopes, Norberto Peporine / Rezende-Teixeira, Paula / Jimenez, Paula C / Rimal, Bipin / Patterson, Andrew D / Traxler, Matthew F / de Cassia Pessotti, Rita / Alvarado-Villalobos, Daniel / Tamayo-Castillo, Giselle / Chaverri, Priscila / Escudero-Leyva, Efrain / Quiros-Guerrero, Luis-Manuel / Bory, Alexandre Jean / Joubert, Juliette / Rutz, Adriano / Wolfender, Jean-Luc / Allard, Pierre-Marie / Sichert, Andreas / Pontrelli, Sammy / Pullman, Benjamin S / Bandeira, Nuno / Gerwick, William H / Gindro, Katia / Massana-Codina, Josep / Wagner, Berenike C / Forchhammer, Karl / Petras, Daniel / Aiosa, Nicole / Garg, Neha / Liebeke, Manuel / Bourceau, Patric / Kang, Kyo Bin / Gadhavi, Henna / de Carvalho, Luiz Pedro Sorio / Dos Santos, Mariana Silva / Pérez-Lorente, Alicia Isabel / Molina-Santiago, Carlos / Romero, Diego / Franke, Raimo / Brönstrup, Mark / de León, Arturo Vera Ponce / Pope, Phillip Byron / Rosa, Sabina Leanti La / Barbera, Giorgia La / Roager, Henrik M / Laursen, Martin Frederik / Hammerle, Fabian / Siewert, Bianka / Peintner, Ursula / Licona-Cassani, Cuauhtemoc / Rodriguez-Orduña, Lorena / Rampler, Evelyn / Hildebrand, Felina / Koellensperger, Gunda / Schoeny, Harald / Hohenwallner, Katharina / Panzenboeck, Lisa / Gregor, Rachel / O'Neill, Ellis Charles / Roxborough, Eve Tallulah / Odoi, Jane / Bale, Nicole J / Ding, Su / Sinninghe Damsté, Jaap S / Guan, Xueli Li / Cui, Jerry J / Ju, Kou-San / Silva, Denise Brentan / Silva, Fernanda Motta Ribeiro / da Silva, Gilvan Ferreira / Koolen, Hector H F / Grundmann, Carlismari / Clement, Jason A / Mohimani, Hosein / Broders, Kirk / McPhail, Kerry L / Ober-Singleton, Sidnee E / Rath, Christopher M / McDonald, Daniel / Knight, Rob / Wang, Mingxun / Dorrestein, Pieter C

    Research square

    2023  

    Abstract: MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and ...

    Abstract MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without
    Language English
    Publishing date 2023-08-03
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3189768/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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