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3. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.

Author

Kennedy, Katherine, de Goffau, Marcus, Perez-Muñoz, Maria, Arrieta, Marie-Claire, Bäckhed, Fredrik, Bork, Peer, Braun, Thorsten, Bushman, Frederic, Dore, Joel, de Vos, Willem, Earl, Ashlee, Eisen, Jonathan, Elovitz, Michal, Ganal-Vonarburg, Stephanie, Gänzle, Michael, Garrett, Wendy, Hall, Lindsay, Hornef, Mathias, Huttenhower, Curtis, Konnikova, Liza, Lebeer, Sarah, Macpherson, Andrew, Massey, Ruth, McHardy, Alice, Koren, Omry, Lawley, Trevor, Ley, Ruth, OMahony, Liam, OToole, Paul, Pamer, Eric, Parkhill, Julian, Raes, Jeroen, Rattei, Thomas, Salonen, Anne, Segal, Eran, Segata, Nicola, Shanahan, Fergus, Sloboda, Deborah, Smith, Gordon, Sokol, Harry, Spector, Tim, Surette, Michael, Tannock, Gerald, Walker, Alan, Yassour, Moran, and Walter, Jens

Subjects
Animals, Female, Humans, Pregnancy, Amniotic Fluid, Biomass, Mammals, Microbiota, Placenta, Fetus, DNA Contamination, Reproducibility of Results
Abstract

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.

Published
2023

4. Safety and efficacy of faecal microbiota transplantation in patients with mild to moderate Parkinson's disease (GUT-PARFECT): a double-blind, placebo-controlled, randomised, phase 2 trial

Author

Bruggeman, Arnout, Vandendriessche, Charysse, Hamerlinck, Hannelore, De Looze, Danny, Tate, David J., Vuylsteke, Marnik, De Commer, Lindsey, Devolder, Lindsay, Raes, Jeroen, Verhasselt, Bruno, Laukens, Debby, Vandenbroucke, Roosmarijn E., and Santens, Patrick

Published
2024
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8. Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide

Author

Andrikopoulos, Petros, Aron-Wisnewsky, Judith, Chakaroun, Rima, Myridakis, Antonis, Forslund, Sofia K., Nielsen, Trine, Adriouch, Solia, Holmes, Bridget, Chilloux, Julien, Vieira-Silva, Sara, Falony, Gwen, Salem, Joe-Elie, Andreelli, Fabrizio, Belda, Eugeni, Kieswich, Julius, Chechi, Kanta, Puig-Castellvi, Francesc, Chevalier, Mickael, Le Chatelier, Emmanuelle, Olanipekun, Michael T., Hoyles, Lesley, Alves, Renato, Helft, Gerard, Isnard, Richard, Køber, Lars, Coelho, Luis Pedro, Rouault, Christine, Gauguier, Dominique, Gøtze, Jens Peter, Prifti, Edi, Froguel, Philippe, Zucker, Jean-Daniel, Bäckhed, Fredrik, Vestergaard, Henrik, Hansen, Torben, Oppert, Jean-Michel, Blüher, Matthias, Nielsen, Jens, Raes, Jeroen, Bork, Peer, Yaqoob, Muhammad M., Stumvoll, Michael, Pedersen, Oluf, Ehrlich, S. Dusko, Clément, Karine, and Dumas, Marc-Emmanuel

Published
2023
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9. Author Correction: Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer

Author

Hatcher, Charlie, Richenberg, George, Waterson, Samuel, Nguyen, Long H., Joshi, Amit D., Carreras-Torres, Robert, Moreno, Victor, Chan, Andrew T., Gunter, Marc, Lin, Yi, Qu, Conghui, Song, Mingyang, Casey, Graham, Figueiredo, Jane C., Gruber, Stephen B., Hampe, Jochen, Hampel, Heather, Jenkins, Mark A., Keku, Temitope O., Peters, Ulrike, Tangen, Catherine M., Wu, Anna H., Hughes, David A., Rühlemann, Malte C., Raes, Jeroen, Timpson, Nicholas J., and Wade, Kaitlin H.

Published
2023
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10. Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer

Author

Hatcher, Charlie, Richenberg, George, Waterson, Samuel, Nguyen, Long H., Joshi, Amit D., Carreras-Torres, Robert, Moreno, Victor, Chan, Andrew T., Gunter, Marc, Lin, Yi, Qu, Conghui, Song, Mingyang, Casey, Graham, Figueiredo, Jane C., Gruber, Stephen B., Hampe, Jochen, Hampel, Heather, Jenkins, Mark A., Keku, Temitope O., Peters, Ulrike, Tangen, Catherine M., Wu, Anna H., Hughes, David A., Rühlemann, Malte C., Raes, Jeroen, Timpson, Nicholas J., and Wade, Kaitlin H.

Published
2023
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11. The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice

Author

Fan, Yong, Støving, René Klinkby, Berreira Ibraim, Samar, Hyötyläinen, Tuulia, Thirion, Florence, Arora, Tulika, Lyu, Liwei, Stankevic, Evelina, Hansen, Tue Haldor, Déchelotte, Pierre, Sinioja, Tim, Ragnarsdottir, Oddny, Pons, Nicolas, Galleron, Nathalie, Quinquis, Benoît, Levenez, Florence, Roume, Hugo, Falony, Gwen, Vieira-Silva, Sara, Raes, Jeroen, Clausen, Loa, Telléus, Gry Kjaersdam, Bäckhed, Fredrik, Oresic, Matej, Ehrlich, S. Dusko, and Pedersen, Oluf

Published
2023
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13. Reporting guidelines for human microbiome research: the STORMS checklist

Author

Mirzayi, Chloe, Renson, Audrey, Zohra, Fatima, Elsafoury, Shaimaa, Geistlinger, Ludwig, Kasselman, Lora J, Eckenrode, Kelly, van de Wijgert, Janneke, Loughman, Amy, Marques, Francine Z, MacIntyre, David A, Arumugam, Manimozhiyan, Azhar, Rimsha, Beghini, Francesco, Bergstrom, Kirk, Bhatt, Ami, Bisanz, Jordan E, Braun, Jonathan, Bravo, Hector Corrada, Buck, Gregory A, Bushman, Frederic, Casero, David, Clarke, Gerard, Collado, Maria Carmen, Cotter, Paul D, Cryan, John F, Demmer, Ryan T, Devkota, Suzanne, Elinav, Eran, Escobar, Juan S, Fettweis, Jennifer, Finn, Robert D, Fodor, Anthony A, Forslund, Sofia, Franke, Andre, Furlanello, Cesare, Gilbert, Jack, Grice, Elizabeth, Haibe-Kains, Benjamin, Handley, Scott, Herd, Pamela, Holmes, Susan, Jacobs, Jonathan P, Karstens, Lisa, Knight, Rob, Knights, Dan, Koren, Omry, Kwon, Douglas S, Langille, Morgan, Lindsay, Brianna, McGovern, Dermot, McHardy, Alice C, McWeeney, Shannon, Mueller, Noel T, Nezi, Luigi, Olm, Matthew, Palm, Noah, Pasolli, Edoardo, Raes, Jeroen, Redinbo, Matthew R, Rühlemann, Malte, Balfour Sartor, R, Schloss, Patrick D, Schriml, Lynn, Segal, Eran, Shardell, Michelle, Sharpton, Thomas, Smirnova, Ekaterina, Sokol, Harry, Sonnenburg, Justin L, Srinivasan, Sujatha, Thingholm, Louise B, Turnbaugh, Peter J, Upadhyay, Vaibhav, Walls, Ramona L, Wilmes, Paul, Yamada, Takuji, Zeller, Georg, Zhang, Mingyu, Zhao, Ni, Zhao, Liping, Bao, Wenjun, Culhane, Aedin, Devanarayan, Viswanath, Dopazo, Joaquin, Fan, Xiaohui, Fischer, Matthias, Jones, Wendell, Kusko, Rebecca, Mason, Christopher E, Mercer, Tim R, Sansone, Susanna-Assunta, Scherer, Andreas, Shi, Leming, Thakkar, Shraddha, Tong, Weida, Wolfinger, Russ, Hunter, Christopher, Segata, Nicola, and Huttenhower, Curtis

Subjects
Human Genome, Genetics, Computational Biology, Dysbiosis, Humans, Microbiota, Observational Studies as Topic, Research Design, Translational Science, Biomedical, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Medical and Health Sciences, Immunology
Abstract

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Published
2021

14. Beyond the Norm: Epidemiology of Irritable Bowel Syndrome and Mental Health Among Sexual and Gender-Diverse Young Adults in a Large Representative Cohort

Author

Voorspoels, Wouter, Proost, Sebastian, Mortier, Philippe, Kiekens, Glenn, Alonso, Jordi, Raes, Jeroen, Falony, Gwen, Vieira-Silva, Sara, van Oudenhove, Lukas, Cuijpers, Pim, Auerbach, Randy P., Bootsma, Erik, Jansen, Leontien, Van Den Houte, Karen, Kessler, Ronald C., Tack, Jan, and Bruffaerts, Ronny

Published
2024
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15. Rigorous Donor Selection for Fecal Microbiota Transplantation in Active Ulcerative Colitis: Key Lessons From a Randomized Controlled Trial Halted for Futility

Author

Caenepeel, Clara, Deleu, Sara, Vazquez Castellanos, Jorge Francisco, Arnauts, Kaline, Braekeleire, Sara, Machiels, Kathleen, Baert, Filip, Mana, Fazia, Pouillon, Lieven, Hindryckx, Pieter, Lobaton, Triana, Louis, Edouard, Franchimont, Denis, Verstockt, Bram, Ferrante, Marc, Sabino, João, Vieira-Silva, Sara, Falony, Gwen, Raes, Jeroen, and Vermeire, Séverine

Published
2024
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17. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.

Author

Acinas, Silvia G, Sánchez, Pablo, Salazar, Guillem, Cornejo-Castillo, Francisco M, Sebastián, Marta, Logares, Ramiro, Royo-Llonch, Marta, Paoli, Lucas, Sunagawa, Shinichi, Hingamp, Pascal, Ogata, Hiroyuki, Lima-Mendez, Gipsi, Roux, Simon, González, José M, Arrieta, Jesús M, Alam, Intikhab S, Kamau, Allan, Bowler, Chris, Raes, Jeroen, Pesant, Stéphane, Bork, Peer, Agustí, Susana, Gojobori, Takashi, Vaqué, Dolors, Sullivan, Matthew B, Pedrós-Alió, Carlos, Massana, Ramon, Duarte, Carlos M, and Gasol, Josep M

Subjects
Bacteria, DNA, Bacterial, Seawater, Photosynthesis, Metagenome, Carbon Cycle
Abstract

The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

Published
2021

18. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Author

Kennedy, Katherine M., de Goffau, Marcus C., Perez-Muñoz, Maria Elisa, Arrieta, Marie-Claire, Bäckhed, Fredrik, Bork, Peer, Braun, Thorsten, Bushman, Frederic D., Dore, Joel, de Vos, Willem M., Earl, Ashlee M., Eisen, Jonathan A., Elovitz, Michal A., Ganal-Vonarburg, Stephanie C., Gänzle, Michael G., Garrett, Wendy S., Hall, Lindsay J., Hornef, Mathias W., Huttenhower, Curtis, Konnikova, Liza, Lebeer, Sarah, Macpherson, Andrew J., Massey, Ruth C., McHardy, Alice Carolyn, Koren, Omry, Lawley, Trevor D., Ley, Ruth E., O’Mahony, Liam, O’Toole, Paul W., Pamer, Eric G., Parkhill, Julian, Raes, Jeroen, Rattei, Thomas, Salonen, Anne, Segal, Eran, Segata, Nicola, Shanahan, Fergus, Sloboda, Deborah M., Smith, Gordon C. S., Sokol, Harry, Spector, Tim D., Surette, Michael G., Tannock, Gerald W., Walker, Alan W., Yassour, Moran, and Walter, Jens

Published
2023
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19. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author

Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, Christopher M, Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C, Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A, Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, and Wincker, Patrick

Subjects
Genetics, Climate Action, Gene Expression Regulation, Geography, Metagenome, Microbiota, Molecular Sequence Annotation, Oceans and Seas, RNA, Messenger, Seawater, Temperature, Transcriptome, Tara Oceans Coordinators, Tara Oceans, biogeochemistry, community turnover, eco-systems biology, gene expression change, global ocean microbiome, metagenome, metatranscriptome, microbial ecology, ocean warming, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.

Published
2019

21. Revitalizing the Gut Microbiome in Chronic Kidney Disease: A Comprehensive Exploration of the Therapeutic Potential of Physical Activity

Author

Vandecruys, Marieke, primary, De Smet, Stefan, additional, De Beir, Jasmine, additional, Renier, Marie, additional, Leunis, Sofie, additional, Van Criekinge, Hanne, additional, Glorieux, Griet, additional, Raes, Jeroen, additional, Vanden Wyngaert, Karsten, additional, Nagler, Evi, additional, Calders, Patrick, additional, Monbaliu, Diethard, additional, Cornelissen, Véronique, additional, Evenepoel, Pieter, additional, and Van Craenenbroeck, Amaryllis H. Van, additional

Published
2024
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22. RIGOROUS DONOR SELECTION FOR FMT IN ACTIVE ULCERATIVE COLITIS: KEY LESSONS FROM A RANDOMIZED CONTROLLED TRIAL HALTED FOR FUTILITY

Author

Caenepeel, Clara, primary, Deleu, Sara, additional, Vazquez Castellanos, Jorge Francisco, additional, Arnauts, Kaline, additional, Braekeleire, Sara, additional, Machiels, Kathleen, additional, Baert, Filip, additional, Mana, Fazia, additional, Pouillon, Lieven, additional, Hindryckx, Pieter, additional, Lobaton, Triana, additional, Louis, Edouard, additional, Franchimont, Denis, additional, Verstockt, Bram, additional, Ferrante, Marc, additional, Sabino, João, additional, Vieira-Silva, Sara, additional, Falony, Gwen, additional, Raes, Jeroen, additional, and Vermeire, Séverine, additional

Published
2024
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24. Early-Career Scientists Shaping the World

Author

Cristea, Ileana M, Dorrestein, Pieter C, Eisen, Jonathan A, Gilbert, Jack A, Huber, Julie A, Jansson, Janet K, Knight, Rob, Pollard, Katherine S, Raes, Jeroen, Silver, Pamela A, Webster, Nicole S, and Xu, Jian

Published
2019

25. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author

Gregory, Ann C, Zayed, Ahmed A, Conceição-Neto, Nádia, Temperton, Ben, Bolduc, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, Jean-Éric, Vik, Dean, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I, Dutilh, Bas E, and Roux, Simon

Subjects
Genetics, Infection, Life Below Water, Aquatic Organisms, Biodiversity, DNA Viruses, DNA, Viral, Metagenome, Water Microbiology, Tara Oceans Coordinators, community ecology, diversity gradients, marine biology, metagenomics, population ecology, species, viruses, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.

Published
2019

26. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author

Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, and Pelletier, Eric

Published
2022
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27. Microbiome and metabolome features of the cardiometabolic disease spectrum

Author

Fromentin, Sebastien, Forslund, Sofia K., Chechi, Kanta, Aron-Wisnewsky, Judith, Chakaroun, Rima, Nielsen, Trine, Tremaroli, Valentina, Ji, Boyang, Prifti, Edi, Myridakis, Antonis, Chilloux, Julien, Andrikopoulos, Petros, Fan, Yong, Olanipekun, Michael T., Alves, Renato, Adiouch, Solia, Bar, Noam, Talmor-Barkan, Yeela, Belda, Eugeni, Caesar, Robert, Coelho, Luis Pedro, Falony, Gwen, Fellahi, Soraya, Galan, Pilar, Galleron, Nathalie, Helft, Gerard, Hoyles, Lesley, Isnard, Richard, Le Chatelier, Emmanuelle, Julienne, Hanna, Olsson, Lisa, Pedersen, Helle Krogh, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Schmidt, Thomas S. B., Vieira-Silva, Sara, Li, Peishun, Zimmermann-Kogadeeva, Maria, Lewinter, Christian, Søndertoft, Nadja B., Hansen, Tue H., Gauguier, Dominique, Gøtze, Jens Peter, Køber, Lars, Kornowski, Ran, Vestergaard, Henrik, Hansen, Torben, Zucker, Jean-Daniel, Hercberg, Serge, Letunic, Ivica, Bäckhed, Fredrik, Oppert, Jean-Michel, Nielsen, Jens, Raes, Jeroen, Bork, Peer, Stumvoll, Michael, Segal, Eran, Clément, Karine, Dumas, Marc-Emmanuel, Ehrlich, S. Dusko, and Pedersen, Oluf

Published
2022
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33. Effect of Mutant and Engineered High-Acetate-Producing Saccharomyces cerevisiae var. boulardii Strains in Dextran Sodium Sulphate-Induced Colitis.

Author

Deleu, Sara, Jacobs, Inge, Vazquez Castellanos, Jorge F., Verstockt, Sare, Trindade de Carvalho, Bruna, Subotić, Ana, Verstockt, Bram, Arnauts, Kaline, Deprez, Lowie, Vissers, Eva, Lenfant, Matthias, Vandermeulen, Greet, De Hertogh, Gert, Verbeke, Kristin, Matteoli, Gianluca, Huys, Geert R. B., Thevelein, Johan M., Raes, Jeroen, and Vermeire, Séverine

Abstract

Acetate-producing Saccharomyces cerevisiae var. boulardii strains could exert improved effects on ulcerative colitis, which here, was preclinically evaluated in an acute dextran sodium sulphate induced model of colitis. Nine-week-old female mice were divided into 12 groups, receiving either drinking water or 2.75% dextran sodium sulphate for 7 days, combined with a daily gavage of various treatments with different levels of acetate accumulation: sham control (phosphate buffered saline, no acetate), non-probiotic control (Baker's yeast, no acetate), probiotic control (Enterol®, transient acetate), and additionally several Saccharomyces cerevisiae var. boulardii strains with respectively no, high, and extra-high acetate accumulation. Disease activity was monitored daily, and feces samples were collected at different timepoints. On day 14, the mice were sacrificed, upon which blood and colonic tissue were collected for analysis. Disease activity in inflamed mice was lower when treated with the high-acetate-producing strain compared to sham and non-probiotic controls. The non-acetate-producing strain showed higher disease activity compared to the acetate-producing strains. Accordingly, higher histologic inflammation was observed in non- or transient-acetate-producing strains compared to the sham control, whereas this increase was not observed for high- and extra-high-acetate-producing strains upon induction of inflammation. These anti-inflammatory findings were confirmed by transcriptomic analysis of differentially expressed genes. Moreover, only the strain with the highest acetate production was superior in maintaining a stable gut microbial alpha-diversity upon inflammation. These findings support new possibilities for acetate-mediated management of inflammation in inflammatory bowel disease by administrating high-acetate-producing Saccharomyces cerevisae var. boulardii strains. [ABSTRACT FROM AUTHOR]

Published
2024
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36. Combinatorial, additive and dose-dependent drug–microbiome associations

Author

Forslund, Sofia K., Chakaroun, Rima, Zimmermann-Kogadeeva, Maria, Markó, Lajos, Aron-Wisnewsky, Judith, Nielsen, Trine, Moitinho-Silva, Lucas, Schmidt, Thomas S. B., Falony, Gwen, Vieira-Silva, Sara, Adriouch, Solia, Alves, Renato J., Assmann, Karen, Bastard, Jean-Philippe, Birkner, Till, Caesar, Robert, Chilloux, Julien, Coelho, Luis Pedro, Fezeu, Leopold, Galleron, Nathalie, Helft, Gerard, Isnard, Richard, Ji, Boyang, Kuhn, Michael, Le Chatelier, Emmanuelle, Myridakis, Antonis, Olsson, Lisa, Pons, Nicolas, Prifti, Edi, Quinquis, Benoit, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Tremaroli, Valentina, Valles-Colomer, Mireia, Lewinter, Christian, Søndertoft, Nadja B., Pedersen, Helle Krogh, Hansen, Tue H., Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Zucker, Jean-Daniel, Hercberg, Serge, Oppert, Jean-Michel, Letunic, Ivica, Nielsen, Jens, Bäckhed, Fredrik, Ehrlich, S. Dusko, Dumas, Marc-Emmanuel, Raes, Jeroen, Pedersen, Oluf, Clément, Karine, Stumvoll, Michael, and Bork, Peer

Published
2021
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37. Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative.

Author

Wang, Jun, Kurilshikov, Alexander, Radjabzadeh, Djawad, Turpin, Williams, Croitoru, Kenneth, Bonder, Marc, Jackson, Matthew, Medina-Gomez, Carolina, Frost, Fabian, Homuth, Georg, Rühlemann, Malte, Hughes, David, Kim, Han-Na, Spector, Tim, Bell, Jordana, Steves, Claire, Timpson, Nicolas, Franke, Andre, Wijmenga, Cisca, Meyer, Katie, Kacprowski, Tim, Franke, Lude, Paterson, Andrew, Raes, Jeroen, Kraaij, Robert, and Zhernakova, Alexandra

Subjects
Genome-wide association studies (GWAS), Gut microbiome, Meta-analysis, Bacteria, Cohort Studies, Gastrointestinal Microbiome, Genetic Variation, Genome, Human, Genome-Wide Association Study, Humans, RNA, Ribosomal, 16S
Abstract

BACKGROUND: In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. RESULTS: Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. CONCLUSION: We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.

Published
2018

38. Enterotypes in the landscape of gut microbial community composition.

Author

Costea, Paul I, Hildebrand, Falk, Arumugam, Manimozhiyan, Bäckhed, Fredrik, Blaser, Martin J, Bushman, Frederic D, de Vos, Willem M, Ehrlich, S Dusko, Fraser, Claire M, Hattori, Masahira, Huttenhower, Curtis, Jeffery, Ian B, Knights, Dan, Lewis, James D, Ley, Ruth E, Ochman, Howard, O'Toole, Paul W, Quince, Christopher, Relman, David A, Shanahan, Fergus, Sunagawa, Shinichi, Wang, Jun, Weinstock, George M, Wu, Gary D, Zeller, Georg, Zhao, Liping, Raes, Jeroen, Knight, Rob, and Bork, Peer

Subjects
Gastrointestinal Tract, Animals, Humans, Bacteria, RNA, Ribosomal, 16S, Bacterial Typing Techniques, Biodiversity, Metagenome, Metagenomics, Gastrointestinal Microbiome, Human Genome, Genetics, Clinical Research, Microbiology, Medical Microbiology
Abstract

Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.

Published
2018

40. Heritable components of the human fecal microbiome are associated with visceral fat

Author

Beaumont, Michelle, Goodrich, Julia K, Jackson, Matthew A, Yet, Idil, Davenport, Emily R, Vieira-Silva, Sara, Debelius, Justine, Pallister, Tess, Mangino, Massimo, Raes, Jeroen, Knight, Rob, Clark, Andrew G, Ley, Ruth E, Spector, Tim D, and Bell, Jordana T

Subjects
Human Genome, Aging, Genetics, Clinical Research, Obesity, Nutrition, Prevention, 2.1 Biological and endogenous factors, Aetiology, Cardiovascular, Oral and gastrointestinal, Metabolic and endocrine, Cancer, Stroke, Fecal microbiome, Visceral fat, Heritability, Genetic association, Twins, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundVariation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures.ResultsWe profile six adiposity measures in 3666 twins and estimate their heritability, finding novel evidence for strong genetic effects underlying visceral fat and android/gynoid ratio. We confirm the association of lower diversity of the fecal microbiome with obesity and adiposity measures, and then compare the association between fecal microbial composition and the adiposity phenotypes in a discovery subsample of twins. We identify associations between the relative abundances of fecal microbial operational taxonomic units (OTUs) and abdominal adiposity measures. Most of these results involve visceral fat associations, with the strongest associations between visceral fat and Oscillospira members. Using BMI as a surrogate phenotype, we pursue replication in independent samples from three population-based cohorts including American Gut, Flemish Gut Flora Project and the extended TwinsUK cohort. Meta-analyses across the replication samples indicate that 8 OTUs replicate at a stringent threshold across all cohorts, while 49 OTUs achieve nominal significance in at least one replication sample. Heritability analysis of the adiposity-associated microbial OTUs prompted us to assess host genetic-microbe interactions at obesity-associated human candidate loci. We observe significant associations of adiposity-OTU abundances with host genetic variants in the FHIT, TDRG1 and ELAVL4 genes, suggesting a potential role for host genes to mediate the link between the fecal microbiome and obesity.ConclusionsOur results provide novel insights into the role of the fecal microbiota in cardio-metabolic disease with clear potential for prevention and novel therapies.

Published
2016

43. Local immune response to food antigens drives meal-induced abdominal pain

Author

Aguilera-Lizarraga, Javier, Florens, Morgane V., Viola, Maria Francesca, Jain, Piyush, Decraecker, Lisse, Appeltans, Iris, Cuende-Estevez, Maria, Fabre, Naomi, Van Beek, Kim, Perna, Eluisa, Balemans, Dafne, Stakenborg, Nathalie, Theofanous, Stavroula, Bosmans, Goele, Mondelaers, Stéphanie U., Matteoli, Gianluca, Ibiza Martínez, Sales, Lopez-Lopez, Cintya, Jaramillo-Polanco, Josue, Talavera, Karel, Alpizar, Yeranddy A., Feyerabend, Thorsten B., Rodewald, Hans-Reimer, Farre, Ricard, Redegeld, Frank A., Si, Jiyeon, Raes, Jeroen, Breynaert, Christine, Schrijvers, Rik, Bosteels, Cédric, Lambrecht, Bart N., Boyd, Scott D., Hoh, Ramona A., Cabooter, Deirdre, Nelis, Maxim, Augustijns, Patrick, Hendrix, Sven, Strid, Jessica, Bisschops, Raf, Reed, David E., Vanner, Stephen J., Denadai-Souza, Alexandre, Wouters, Mira M., and Boeckxstaens, Guy E.

Published
2021
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44. Large-scale association analyses identify host factors influencing human gut microbiome composition

Author

Kurilshikov, Alexander, Medina-Gomez, Carolina, Bacigalupe, Rodrigo, Radjabzadeh, Djawad, Wang, Jun, Demirkan, Ayse, Le Roy, Caroline I., Raygoza Garay, Juan Antonio, Finnicum, Casey T., Liu, Xingrong, Zhernakova, Daria V., Bonder, Marc Jan, Hansen, Tue H., Frost, Fabian, Rühlemann, Malte C., Turpin, Williams, Moon, Jee-Young, Kim, Han-Na, Lüll, Kreete, Barkan, Elad, Shah, Shiraz A., Fornage, Myriam, Szopinska-Tokov, Joanna, Wallen, Zachary D., Borisevich, Dmitrii, Agreus, Lars, Andreasson, Anna, Bang, Corinna, Bedrani, Larbi, Bell, Jordana T., Bisgaard, Hans, Boehnke, Michael, Boomsma, Dorret I., Burk, Robert D., Claringbould, Annique, Croitoru, Kenneth, Davies, Gareth E., van Duijn, Cornelia M., Duijts, Liesbeth, Falony, Gwen, Fu, Jingyuan, van der Graaf, Adriaan, Hansen, Torben, Homuth, Georg, Hughes, David A., Ijzerman, Richard G., Jackson, Matthew A., Jaddoe, Vincent W. V., Joossens, Marie, Jørgensen, Torben, Keszthelyi, Daniel, Knight, Rob, Laakso, Markku, Laudes, Matthias, Launer, Lenore J., Lieb, Wolfgang, Lusis, Aldons J., Masclee, Ad A. M., Moll, Henriette A., Mujagic, Zlatan, Qibin, Qi, Rothschild, Daphna, Shin, Hocheol, Sørensen, Søren J., Steves, Claire J., Thorsen, Jonathan, Timpson, Nicholas J., Tito, Raul Y., Vieira-Silva, Sara, Völker, Uwe, Völzke, Henry, Võsa, Urmo, Wade, Kaitlin H., Walter, Susanna, Watanabe, Kyoko, Weiss, Stefan, Weiss, Frank U., Weissbrod, Omer, Westra, Harm-Jan, Willemsen, Gonneke, Payami, Haydeh, Jonkers, Daisy M. A. E., Arias Vasquez, Alejandro, de Geus, Eco J. C., Meyer, Katie A., Stokholm, Jakob, Segal, Eran, Org, Elin, Wijmenga, Cisca, Kim, Hyung-Lae, Kaplan, Robert C., Spector, Tim D., Uitterlinden, Andre G., Rivadeneira, Fernando, Franke, Andre, Lerch, Markus M., Franke, Lude, Sanna, Serena, D’Amato, Mauro, Pedersen, Oluf, Paterson, Andrew D., Kraaij, Robert, Raes, Jeroen, and Zhernakova, Alexandra

Published
2021
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46. Gut environmental factors explain variations in the gut microbiome composition and metabolism within and between healthy adults

Author

Prochazkova, Nicola, primary, Laursen, Martin Fredrik, additional, La Barbera, Giorgia, additional, Tsekitsidi, Eirini, additional, Joergensen, Malte Studnitz, additional, Rasmussen, Morten Arendt, additional, Raes, Jeroen, additional, Dragsted, Lars Ove, additional, Licht, Tine Rask, additional, and Roager, Henrik Munch, additional

Published
2024
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48. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

Author

Weiss, Sophie, Van Treuren, Will, Lozupone, Catherine, Faust, Karoline, Friedman, Jonathan, Deng, Ye, Xia, Li Charlie, Xu, Zhenjiang Zech, Ursell, Luke, Alm, Eric J, Birmingham, Amanda, Cram, Jacob A, Fuhrman, Jed A, Raes, Jeroen, Sun, Fengzhu, Zhou, Jizhong, and Knight, Rob

Subjects
Microbiology, Biological Sciences, Bacteria, Benchmarking, Computational Biology, Humans, Microbial Interactions, Microbiota, Models, Statistical, RNA, Ribosomal, 16S, Statistics as Topic, Environmental Sciences, Technology, Biological sciences, Environmental sciences
Abstract

Disruption of healthy microbial communities has been linked to numerous diseases, yet microbial interactions are little understood. This is due in part to the large number of bacteria, and the much larger number of interactions (easily in the millions), making experimental investigation very difficult at best and necessitating the nascent field of computational exploration through microbial correlation networks. We benchmark the performance of eight correlation techniques on simulated and real data in response to challenges specific to microbiome studies: fractional sampling of ribosomal RNA sequences, uneven sampling depths, rare microbes and a high proportion of zero counts. Also tested is the ability to distinguish signals from noise, and detect a range of ecological and time-series relationships. Finally, we provide specific recommendations for correlation technique usage. Although some methods perform better than others, there is still considerable need for improvement in current techniques.

Published
2016

49. Plankton networks driving carbon export in the oligotrophic ocean

Author

Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Subjects
Aquatic Organisms, Carbon, Chlorophyll, Dinoflagellida, Ecosystem, Expeditions, Genes, Bacterial, Genes, Viral, Geography, Oceans and Seas, Photosynthesis, Plankton, Seawater, Synechococcus, Tara Oceans coordinators, General Science & Technology
Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2016

50. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

Author

Cornejo-Castillo, Francisco M, Cabello, Ana M, Salazar, Guillem, Sánchez-Baracaldo, Patricia, Lima-Mendez, Gipsi, Hingamp, Pascal, Alberti, Adriana, Sunagawa, Shinichi, Bork, Peer, de Vargas, Colomban, Raes, Jeroen, Bowler, Chris, Wincker, Patrick, Zehr, Jonathan P, Gasol, Josep M, Massana, Ramon, and Acinas, Silvia G

Subjects
Phytoplankton, Cyanobacteria, Genomics, Seawater, Nitrogen Fixation, Symbiosis, Atlantic Ocean, Biological Evolution, Haptophyta, Genetics, Human Genome
Abstract

The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled phytoplankton. UCYN-A includes several closely related lineages whose partner fidelity, genome-wide expression and time of evolutionary divergence remain to be resolved. Here we detect and distinguish UCYN-A1 and UCYN-A2 lineages in symbiosis with two distinct prymnesiophyte partners in the South Atlantic Ocean. Both symbiotic systems are lineage specific and differ in the number of UCYN-A cells involved. Our analyses infer a streamlined genome expression towards nitrogen fixation in both UCYN-A lineages. Comparative genomics reveal a strong purifying selection in UCYN-A1 and UCYN-A2 with a diversification process ∼91 Myr ago, in the late Cretaceous, after the low-nutrient regime period occurred during the Jurassic. These findings suggest that UCYN-A diversified in a co-evolutionary process, wherein their prymnesiophyte partners acted as a barrier driving an allopatric speciation of extant UCYN-A lineages.

Published
2016

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