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2. Microbiome and metabolome insights into the role of the gastrointestinal-brain axis in neurodegenerative diseases: unveiling potential therapeutic targets

Author

Zacharias, Helena U., Kaleta, Christoph, Cossais, Francois, Schaeffer, Eva, Berndt, Henry, Best, Lena, Dost, Thomas, Glüsing, Svea, Groussin, Mathieu, Poyet, Mathilde, Heinzel, Sebastian, Bang, Corinna, Siebert, Leonard, Demetrowitsch, Tobias, Leypoldt, Frank, Adelung, Rainer, Bartsch, Thorsten, Bosy-Westphal, Anja, Schwarz, Karin, and Berg, Daniela

Subjects
Quantitative Biology - Tissues and Organs, Quantitative Biology - Molecular Networks, Quantitative Biology - Neurons and Cognition
Abstract

Due to the aging of the world population and westernization of lifestyles, the prevalence of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD) is rapidly rising and is expected to put a strong socioeconomic burden on health systems worldwide. Due to the limited success of clinical trials of therapies against neurodegenerative diseases, research has extended its scope to a systems medicine point of view, with a particular focus on the gastrointestinal-brain axis as a potential main actor in disease development and progression. Microbiome as well as metabolome studies along the gastrointestinal-brain axis have already revealed important insights into disease pathomechanisms. Both the microbiome and metabolome can be easily manipulated by dietary and lifestyle interventions, and might thus offer novel, readily available therapeutic options to prevent the onset as well as the progression of PD and AD. This review summarizes our current knowledge on the association between microbiota, metabolites, and neurodegeneration in light of the gastrointestinal-brain axis. In this context, we also illustrate state-of-the art methods of microbiome and metabolome research as well as metabolic modeling that facilitate the identification of disease pathomechanisms. We conclude our review with therapeutic options to modulate microbiome composition to prevent or delay neurodegeneration and illustrate potential future research directions to fight PD and AD.

Published
2022

3. A global initiative for ecological and evolutionary hologenomics

Author

Abalos, Javier, Adhola, Titus, Aguirre, Windsor, Aizpurua, Ostaizka, Ali, Shahzad, Andreone, Franco, Aubret, Fabien, Ávila-Palma, Hefer D., Alcantara, Lizbeth Fabiola Bautista, Beltrán, Juan F., Berg, Rachel, Berg, Thomas Bjørneboe, Bertolino, Sandro, Blumstein, Daniel T., Boldgiv, Bazartseren, Borowski, Zbigniew, Boubli, Jean Philippe, Büchner, Sven, Cabido, Carlos, Camacho, Carlos, Chaparro, Juan C., Charmantier, Anne, D'Elía, Guillermo, da Silva, Luis P., Dalsgaard, Bo, de Franceschi, Christophe, de la Cruz, Ferran, de la Sancha, Noé U., Denoël, Mathieu, Eisenhofer, Raphael, Feiner, Nathalie, Fernandes, Joana M., Figuerola, Jordi, Fusani, Leonida, Gangoso, Laura, García-Roa, Roberto, Gasperini, Stefania, Gaun, Nanna, Thomas, M., Gilbert, P., Gomez-Mestre, Ivan, Graves, Gary R., Groombridge, Jim, Hardouin, Emilie A., Hernández, Mauricio, Herrera M., L. Gerardo, Hodder, Kathy, Hosner, Peter A., Hurtado, Natali, Juste, Javier, Knowles, Sarah C.L., Kohl, Kevin D., Korine, Carmi, Kornilev, Yurii V., Kramer-Schadt, Stephanie, Lambin, Xavier, Lattenkamp, Ella Z., Lauritsen, Jonas, Li, Guoliang, López, Celeste María, Baucells, Adrià López, Cohen, Tali Magory, Manzo, Emiliano, Marteau, Mélanie, Martin, Lynn B., Bideguren, Garazi Martin, Mazzamuto, Maria Vittoria, Monadjem, Ara, Nietlisbach, Pirmin, Øksnebjerg, Daniel Bilyeli, Packer, Jasmin G., Pepke, Michael L., Peralta-Sánchez, Juan M., Perdomo, Adrián, de Lanuza, Guillem Pérez i, Pietroni, Carlotta, Poyet, Mathilde, Rahbek, Carsten, Ramaraj, Thiruvarangan, Caldas, Yuliaxis Ramayo, Razgour, Orly, Rebelo, Hugo, Reif, Jiří, Rimbach, Rebecca, Rocha, Ricardo, Rocha, Rita G., Fernandes, Carlos Rodríguez, Romeo, Claudia, Ruuskanen, Suvi, Sakaluk, Scott K., Santicchia, Francesca, Sarraude, Tom, Sørås, Rune, Spada, Martina, Steele, Michael A., Stothart, Mason R., Sunje, Emina, Sutton, Alex O., Szulkin, Marta, Takahata, Yu, Thompson, Charles F., Thorup, Kasper, Tomazetto, Geizecler, Torrent, Laura, Toshkova, Nia, Tranquillo, Claudia, Turcios-Casco, Manfredo Alejandro, Uller, Tobias, van Riemsdijk, Isolde, Velo-Antón, Guillermo, Verbeylen, Goedele, Videvall, Elin, Voigt, Christian C., Wauters, Lucas A., Wellenreuther, Maren, Yanchukov, Alexey, Leonard, Aoife, and Alberdi, Antton

Published
2024
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4. Elevated rates of horizontal gene transfer in the industrialized human microbiome

Author

Groussin, Mathieu, Poyet, Mathilde, Sistiaga, Ainara, Kearney, Sean M., Moniz, Katya, Noel, Mary, Hooker, Jeff, Gibbons, Sean M., Segurel, Laure, Froment, Alain, Mohamed, Rihlat Said, Fezeu, Alain, Juimo, Vanessa A., Lafosse, Sophie, Tabe, Francis E., Girard, Catherine, Iqaluk, Deborah, Nguyen, Le Thanh Tu, Shapiro, B. Jesse, Lehtimäki, Jenni, Ruokolainen, Lasse, Kettunen, Pinja P., Vatanen, Tommi, Sigwazi, Shani, Mabulla, Audax, Domínguez-Rodrigo, Manuel, Nartey, Yvonne A., Agyei-Nkansah, Adwoa, Duah, Amoako, Awuku, Yaw A., Valles, Kenneth A., Asibey, Shadrack O., Afihene, Mary Y., Roberts, Lewis R., Plymoth, Amelie, Onyekwere, Charles A., Summons, Roger E., Xavier, Ramnik J., and Alm, Eric J.

Published
2021
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5. A global initiative for ecological and evolutionary hologenomics

Author

Leonard, Aoife, primary, Abalos, Javier, additional, Adhola, Titus, additional, Aguirre, Windsor, additional, Aizpurua, Ostaizka, additional, Ali, Shahzad, additional, Andreone, Franco, additional, Aubret, Fabien, additional, Ávila-Palma, Hefer D., additional, Alcantara, Lizbeth Fabiola Bautista, additional, Beltrán, Juan F., additional, Berg, Rachel, additional, Berg, Thomas Bjørneboe, additional, Bertolino, Sandro, additional, Blumstein, Daniel T., additional, Boldgiv, Bazartseren, additional, Borowski, Zbigniew, additional, Boubli, Jean Philippe, additional, Büchner, Sven, additional, Cabido, Carlos, additional, Camacho, Carlos, additional, Chaparro, Juan C., additional, Charmantier, Anne, additional, D'Elía, Guillermo, additional, da Silva, Luis P., additional, Dalsgaard, Bo, additional, de Franceschi, Christophe, additional, de la Cruz, Ferran, additional, de la Sancha, Noé U., additional, Denoël, Mathieu, additional, Eisenhofer, Raphael, additional, Feiner, Nathalie, additional, Fernandes, Joana M., additional, Figuerola, Jordi, additional, Fusani, Leonida, additional, Gangoso, Laura, additional, García-Roa, Roberto, additional, Gasperini, Stefania, additional, Gaun, Nanna, additional, Thomas, M., additional, Gilbert, P., additional, Gomez-Mestre, Ivan, additional, Graves, Gary R., additional, Groombridge, Jim, additional, Hardouin, Emilie A., additional, Hernández, Mauricio, additional, Herrera M., L. Gerardo, additional, Hodder, Kathy, additional, Hosner, Peter A., additional, Hurtado, Natali, additional, Juste, Javier, additional, Knowles, Sarah C.L., additional, Kohl, Kevin D., additional, Korine, Carmi, additional, Kornilev, Yurii V., additional, Kramer-Schadt, Stephanie, additional, Lambin, Xavier, additional, Lattenkamp, Ella Z., additional, Lauritsen, Jonas, additional, Li, Guoliang, additional, López, Celeste María, additional, Baucells, Adrià López, additional, Cohen, Tali Magory, additional, Manzo, Emiliano, additional, Marteau, Mélanie, additional, Martin, Lynn B., additional, Bideguren, Garazi Martin, additional, Mazzamuto, Maria Vittoria, additional, Monadjem, Ara, additional, Nietlisbach, Pirmin, additional, Øksnebjerg, Daniel Bilyeli, additional, Packer, Jasmin G., additional, Pepke, Michael L., additional, Peralta-Sánchez, Juan M., additional, Perdomo, Adrián, additional, de Lanuza, Guillem Pérez i, additional, Pietroni, Carlotta, additional, Poyet, Mathilde, additional, Rahbek, Carsten, additional, Ramaraj, Thiruvarangan, additional, Caldas, Yuliaxis Ramayo, additional, Razgour, Orly, additional, Rebelo, Hugo, additional, Reif, Jiří, additional, Rimbach, Rebecca, additional, Rocha, Ricardo, additional, Rocha, Rita G., additional, Fernandes, Carlos Rodríguez, additional, Romeo, Claudia, additional, Ruuskanen, Suvi, additional, Sakaluk, Scott K., additional, Santicchia, Francesca, additional, Sarraude, Tom, additional, Sørås, Rune, additional, Spada, Martina, additional, Steele, Michael A., additional, Stothart, Mason R., additional, Sunje, Emina, additional, Sutton, Alex O., additional, Szulkin, Marta, additional, Takahata, Yu, additional, Thompson, Charles F., additional, Thorup, Kasper, additional, Tomazetto, Geizecler, additional, Torrent, Laura, additional, Toshkova, Nia, additional, Tranquillo, Claudia, additional, Turcios-Casco, Manfredo Alejandro, additional, Uller, Tobias, additional, van Riemsdijk, Isolde, additional, Velo-Antón, Guillermo, additional, Verbeylen, Goedele, additional, Videvall, Elin, additional, Voigt, Christian C., additional, Wauters, Lucas A., additional, Wellenreuther, Maren, additional, Yanchukov, Alexey, additional, and Alberdi, Antton, additional

Published
2024
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7. A global initiative for ecological and evolutionary hologenomics

Author

Leonard, Aoife, Abalos, Javier, Adhola, Titus, Aguirre, Windsor, Aizpurua, Ostaizka, Ali, Shahzad, Andreone, Franco, Aubret, Fabien, Ávila-Palma, Hefer D., Alcantara, Lizbeth Fabiola Bautista, Beltrán, Juan F., Berg, Rachel, Berg, Thomas Bjørneboe, Bertolino, Sandro, Blumstein, Daniel T., Boldgiv, Bazartseren, Borowski, Zbigniew, Boubli, Jean Philippe, Büchner, Sven, Cabido, Carlos, Camacho, Carlos, Chaparro, Juan C., Charmantier, Anne, D'Elía, Guillermo, da Silva, Luis P., Dalsgaard, Bo, de Franceschi, Christophe, de la Cruz, Ferran, de la Sancha, Noé U., Denoël, Mathieu, Eisenhofer, Raphael, Feiner, Nathalie, Fernandes, Joana M., Figuerola, Jordi, Fusani, Leonida, Gangoso, Laura, García-Roa, Roberto, Gasperini, Stefania, Gaun, Nanna, Thomas, M., Gilbert, P., Gomez-Mestre, Ivan, Graves, Gary R., Groombridge, Jim J., Hardouin, Emilie A., Hernández, Mauricio, Herrera M., L. Gerardo, Hodder, Kathy, Hosner, Peter A., Hurtado, Natali, Juste, Javier, Knowles, Sarah C.L., Kohl, Kevin D., Korine, Carmi, Kornilev, Yurii V., Kramer-Schadt, Stephanie, Lambin, Xavier, Lattenkamp, Ella Z., Lauritsen, Jonas, Li, Guoliang, López, Celeste María, Baucells, Adrià López, Cohen, Tali Magory, Manzo, Emiliano, Marteau, Mélanie, Martin, Lynn B., Bideguren, Garazi Martin, Mazzamuto, Maria Vittoria, Monadjem, Ara, Nietlisbach, Pirmin, Øksnebjerg, Daniel Bilyeli, Packer, Jasmin G., Pepke, Michael L., Peralta-Sánchez, Juan M., Perdomo, Adrián, de Lanuza, Guillem Pérez i, Pietroni, Carlotta, Poyet, Mathilde, Rahbek, Carsten, Ramaraj, Thiruvarangan, Caldas, Yuliaxis Ramayo, Razgour, Orly, Rebelo, Hugo, Reif, Jiří, Rimbach, Rebecca, Rocha, Ricardo, Rocha, Rita G., Fernandes, Carlos Rodríguez, Romeo, Claudia, Ruuskanen, Suvi, Sakaluk, Scott K., Santicchia, Francesca, Sarraude, Tom, Sørås, Rune, Spada, Martina, Steele, Michael A., Stothart, Mason R., Sunje, Emina, Sutton, Alex O., Szulkin, Marta, Takahata, Yu, Thompson, Charles F., Thorup, Kasper, Tomazetto, Geizecler, Torrent, Laura, Toshkova, Nia, Tranquillo, Claudia, Turcios-Casco, Manfredo Alejandro, Uller, Tobias, van Riemsdijk, Isolde, Velo-Antón, Guillermo, Verbeylen, Goedele, Videvall, Elin, Voigt, Christian C., Wauters, Lucas A., Wellenreuther, Maren, Yanchukov, Alexey, Alberdi, Antton, Leonard, Aoife, Abalos, Javier, Adhola, Titus, Aguirre, Windsor, Aizpurua, Ostaizka, Ali, Shahzad, Andreone, Franco, Aubret, Fabien, Ávila-Palma, Hefer D., Alcantara, Lizbeth Fabiola Bautista, Beltrán, Juan F., Berg, Rachel, Berg, Thomas Bjørneboe, Bertolino, Sandro, Blumstein, Daniel T., Boldgiv, Bazartseren, Borowski, Zbigniew, Boubli, Jean Philippe, Büchner, Sven, Cabido, Carlos, Camacho, Carlos, Chaparro, Juan C., Charmantier, Anne, D'Elía, Guillermo, da Silva, Luis P., Dalsgaard, Bo, de Franceschi, Christophe, de la Cruz, Ferran, de la Sancha, Noé U., Denoël, Mathieu, Eisenhofer, Raphael, Feiner, Nathalie, Fernandes, Joana M., Figuerola, Jordi, Fusani, Leonida, Gangoso, Laura, García-Roa, Roberto, Gasperini, Stefania, Gaun, Nanna, Thomas, M., Gilbert, P., Gomez-Mestre, Ivan, Graves, Gary R., Groombridge, Jim J., Hardouin, Emilie A., Hernández, Mauricio, Herrera M., L. Gerardo, Hodder, Kathy, Hosner, Peter A., Hurtado, Natali, Juste, Javier, Knowles, Sarah C.L., Kohl, Kevin D., Korine, Carmi, Kornilev, Yurii V., Kramer-Schadt, Stephanie, Lambin, Xavier, Lattenkamp, Ella Z., Lauritsen, Jonas, Li, Guoliang, López, Celeste María, Baucells, Adrià López, Cohen, Tali Magory, Manzo, Emiliano, Marteau, Mélanie, Martin, Lynn B., Bideguren, Garazi Martin, Mazzamuto, Maria Vittoria, Monadjem, Ara, Nietlisbach, Pirmin, Øksnebjerg, Daniel Bilyeli, Packer, Jasmin G., Pepke, Michael L., Peralta-Sánchez, Juan M., Perdomo, Adrián, de Lanuza, Guillem Pérez i, Pietroni, Carlotta, Poyet, Mathilde, Rahbek, Carsten, Ramaraj, Thiruvarangan, Caldas, Yuliaxis Ramayo, Razgour, Orly, Rebelo, Hugo, Reif, Jiří, Rimbach, Rebecca, Rocha, Ricardo, Rocha, Rita G., Fernandes, Carlos Rodríguez, Romeo, Claudia, Ruuskanen, Suvi, Sakaluk, Scott K., Santicchia, Francesca, Sarraude, Tom, Sørås, Rune, Spada, Martina, Steele, Michael A., Stothart, Mason R., Sunje, Emina, Sutton, Alex O., Szulkin, Marta, Takahata, Yu, Thompson, Charles F., Thorup, Kasper, Tomazetto, Geizecler, Torrent, Laura, Toshkova, Nia, Tranquillo, Claudia, Turcios-Casco, Manfredo Alejandro, Uller, Tobias, van Riemsdijk, Isolde, Velo-Antón, Guillermo, Verbeylen, Goedele, Videvall, Elin, Voigt, Christian C., Wauters, Lucas A., Wellenreuther, Maren, Yanchukov, Alexey, and Alberdi, Antton

Abstract

The Earth Hologenome Initiative (EHI) is a global collaboration to generate and analyse hologenomic data from wild animals and associated microorganisms using standardised methodologies underpinned by open and inclusive research principles. Initially focused on vertebrates, it aims to re-examine ecological and evolutionary questions by studying host–microbiota interactions from a systemic perspective.

Published
2024

11. Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease

Author

Ruehlemann, Malte Christoph, primary, Waschina, Silvio, additional, Wacker, Eike Matthias, additional, Rausch, Philipp, additional, Schaan, Ana, additional, Zafroon, Zaira, additional, Franzpoetter, Katrin, additional, Jacobs, Gunnar, additional, Ellinghaus, David, additional, Kruse, Robert, additional, Bergemalm, Daniel, additional, Halfvarson, Jonas, additional, Ziemann, Malte, additional, Goerg, Siegfried, additional, Lieb, Wolfgang, additional, Schreiber, Stefan, additional, Poyet, Mathilde, additional, Bang, Corinna, additional, Franke, Andre, additional, and Groussin, Mathieu, additional

Published
2023
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13. Advancing evolutionary medicine in Northern Germany: Collaboration between Kiel University's Medical Faculty and the Max Planck Institute for Evolutionary Biology.

Author

Baines, John F, Baldus, Claudia D, Bertels, Frederic, Brüggemann, Monika, Kaleta, Christoph, Laudes, Matthias, Mueller, Franz-Josef, Odenthal-Hesse, Linda, Poyet, Mathilde, Rainey, Paul B, Rosenstiel, Philip, Scheffold, Alexander, Sebens, Susanne, Thiery, Joachim, and Traulsen, Arne

Subjects
BIOLOGICAL evolution, HORIZONTAL gene transfer, MEDICAL sciences, INFLAMMATORY bowel diseases, HOMOLOGOUS recombination, DOUBLE-strand DNA breaks, BACTERIAL evolution
Published
2024
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15. One Health Assessment of an Urban Temporary Settlement Reveals Gut Microbiome Serving as Antimicrobial Resistance Gene Reservoir

Author

Napit, Rajindra, primary, Gurung, Anupama, additional, Poudel, Ajit, additional, Manandhar, Prajwol, additional, Chaudhary, Ashok B, additional, Sharma, Ajay N., additional, Raut, Samita, additional, Pradhan, Saman M., additional, Joshi, Jyotsna, additional, Poyet, Mathilde, additional, Groussin, Mathieu, additional, Rajbhandari, Rajesh M, additional, and Karmacharya, Dibesh, additional

Published
2023
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16. Microbiome and Metabolome Insights into the Role of the Gastrointestinal–Brain Axis in Parkinson’s and Alzheimer’s Disease: Unveiling Potential Therapeutic Targets

Author

Zacharias, Helena U., primary, Kaleta, Christoph, additional, Cossais, François, additional, Schaeffer, Eva, additional, Berndt, Henry, additional, Best, Lena, additional, Dost, Thomas, additional, Glüsing, Svea, additional, Groussin, Mathieu, additional, Poyet, Mathilde, additional, Heinzel, Sebastian, additional, Bang, Corinna, additional, Siebert, Leonard, additional, Demetrowitsch, Tobias, additional, Leypoldt, Frank, additional, Adelung, Rainer, additional, Bartsch, Thorsten, additional, Bosy-Westphal, Anja, additional, Schwarz, Karin, additional, and Berg, Daniela, additional

Published
2022
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18. A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes

Author

Bousbaine, Djenet, primary, Fisch, Laura I., additional, London, Mariya, additional, Bhagchandani, Preksha, additional, Rezende de Castro, Tiago B., additional, Mimee, Mark, additional, Olesen, Scott, additional, Reis, Bernardo S., additional, VanInsberghe, David, additional, Bortolatto, Juliana, additional, Poyet, Mathilde, additional, Cheloha, Ross W., additional, Sidney, John, additional, Ling, Jingjing, additional, Gupta, Aaron, additional, Lu, Timothy K., additional, Sette, Alessandro, additional, Alm, Eric J., additional, Moon, James J., additional, Victora, Gabriel D., additional, Mucida, Daniel, additional, Ploegh, Hidde L., additional, and Bilate, Angelina M., additional

Published
2022
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19. Microbiome and Metabolome Insights into the Role of the Gastrointestinal–Brain Axis in Parkinson’s and Alzheimer’s Disease: Unveiling Potential Therapeutic Targets

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Zacharias, Helena U., Kaleta, Christoph, Cossais, François, Schaeffer, Eva, Berndt, Henry, Best, Lena, Dost, Thomas, Glüsing, Svea, Groussin, Mathieu, Poyet, Mathilde, Heinzel, Sebastian, Bang, Corinna, Siebert, Leonard, Demetrowitsch, Tobias, Leypoldt, Frank, Adelung, Rainer, Bartsch, Thorsten, Bosy-Westphal, Anja, Schwarz, Karin, Berg, Daniela, Massachusetts Institute of Technology. Department of Biological Engineering, Zacharias, Helena U., Kaleta, Christoph, Cossais, François, Schaeffer, Eva, Berndt, Henry, Best, Lena, Dost, Thomas, Glüsing, Svea, Groussin, Mathieu, Poyet, Mathilde, Heinzel, Sebastian, Bang, Corinna, Siebert, Leonard, Demetrowitsch, Tobias, Leypoldt, Frank, Adelung, Rainer, Bartsch, Thorsten, Bosy-Westphal, Anja, Schwarz, Karin, and Berg, Daniela

Abstract

Neurodegenerative diseases such as Parkinson’s (PD) and Alzheimer’s disease (AD), the prevalence of which is rapidly rising due to an aging world population and westernization of lifestyles, are expected to put a strong socioeconomic burden on health systems worldwide. Clinical trials of therapies against PD and AD have only shown limited success so far. Therefore, research has extended its scope to a systems medicine point of view, with a particular focus on the gastrointestinal–brain axis as a potential main actor in disease development and progression. Microbiome and metabolome studies have already revealed important insights into disease mechanisms. Both the microbiome and metabolome can be easily manipulated by dietary and lifestyle interventions, and might thus offer novel, readily available therapeutic options to prevent the onset as well as the progression of PD and AD. This review summarizes our current knowledge on the interplay between microbiota, metabolites, and neurodegeneration along the gastrointestinal–brain axis. We further illustrate state-of-the art methods of microbiome and metabolome research as well as metabolic modeling that facilitate the identification of disease pathomechanisms. We conclude with therapeutic options to modulate microbiome composition to prevent or delay neurodegeneration and illustrate potential future research directions to fight PD and AD.

Published
2022

20. An omics-based framework for assessing the health risk of antimicrobial resistance genes

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Zhang, An-Ni, Gaston, Jeffry M., Dai, Chengzhen L., Zhao, Shijie, Poyet, Mathilde, Groussin, Mathieu, Yin, Xiaole, Li, Li-Guan, van Loosdrecht, Mark C. M., Topp, Edward, Gillings, Michael R., Hanage, William P., Tiedje, James M., Moniz, Katya, Alm, Eric J., Zhang, Tong, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Zhang, An-Ni, Gaston, Jeffry M., Dai, Chengzhen L., Zhao, Shijie, Poyet, Mathilde, Groussin, Mathieu, Yin, Xiaole, Li, Li-Guan, van Loosdrecht, Mark C. M., Topp, Edward, Gillings, Michael R., Hanage, William P., Tiedje, James M., Moniz, Katya, Alm, Eric J., and Zhang, Tong

Abstract

AbstractAntibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an ‘omics-based’ framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as ‘current threats’ (Rank I; 3%) - already present among pathogens - and ‘future threats’ (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 ‘current threat’ ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II (‘future threats’). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.

Published
2022

21. Elevated rates of horizontal gene transfer in the industrialized human microbiome

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Groussin, Mathieu, Poyet, Mathilde, Sistiaga Guiterrez, Maria Ainara, Kearney, Sean Michael, Moniz, Katya H, Noel, Mary, Hooker, Jeff, Gibbons, Sean Michael, Segurel, Laure, Froment, Alain, Mohamed, Rihlat Said, Fezeu, Alain, Juimo, Vanessa A., Lafosse, Sophie, Tabe, Francis E., Girard, Catherine, Iqaluk, Deborah, Nguyen, Le Thanh Tu, Shapiro, B. Jesse, Lehtimäki, Jenni, Ruokolainen, Lasse, Kettunen, Pinja P., Vatanen, Tommi, Sigwazi, Shani, Mabulla, Audax, Domínguez-Rodrigo, Manuel, Nartey, Yvonne A., Agyei-Nkansah, Adwoa, Duah, Amoako, Awuku, Yaw A., Valles, Kenneth A., Asibey, Shadrack O., Afihene, Mary Y., Roberts, Lewis R., Plymoth, Amelie, Onyekwere, Charles A., Summons, Roger E, Xavier, Ramnik Joseph, Alm, Eric J, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Groussin, Mathieu, Poyet, Mathilde, Sistiaga Guiterrez, Maria Ainara, Kearney, Sean Michael, Moniz, Katya H, Noel, Mary, Hooker, Jeff, Gibbons, Sean Michael, Segurel, Laure, Froment, Alain, Mohamed, Rihlat Said, Fezeu, Alain, Juimo, Vanessa A., Lafosse, Sophie, Tabe, Francis E., Girard, Catherine, Iqaluk, Deborah, Nguyen, Le Thanh Tu, Shapiro, B. Jesse, Lehtimäki, Jenni, Ruokolainen, Lasse, Kettunen, Pinja P., Vatanen, Tommi, Sigwazi, Shani, Mabulla, Audax, Domínguez-Rodrigo, Manuel, Nartey, Yvonne A., Agyei-Nkansah, Adwoa, Duah, Amoako, Awuku, Yaw A., Valles, Kenneth A., Asibey, Shadrack O., Afihene, Mary Y., Roberts, Lewis R., Plymoth, Amelie, Onyekwere, Charles A., Summons, Roger E, Xavier, Ramnik Joseph, and Alm, Eric J

Abstract

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

Published
2022

22. An omics-based framework for assessing the health risk of antimicrobial resistance genes

Author

Zhang, An Ni (author), Gaston, Jeffry M. (author), Dai, Chengzhen L. (author), Zhao, Shijie (author), Poyet, Mathilde (author), Groussin, Mathieu (author), Li, Li Guan (author), van Loosdrecht, Mark C.M. (author), Zhang, Tong (author), Zhang, An Ni (author), Gaston, Jeffry M. (author), Dai, Chengzhen L. (author), Zhao, Shijie (author), Poyet, Mathilde (author), Groussin, Mathieu (author), Li, Li Guan (author), van Loosdrecht, Mark C.M. (author), and Zhang, Tong (author)

Abstract

Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an ‘omics-based’ framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as ‘current threats’ (Rank I; 3%) - already present among pathogens - and ‘future threats’ (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 ‘current threat’ ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II (‘future threats’). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions., BT/Environmental Biotechnology

Published
2021
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23. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases

Author

Wu, Fuqing, primary, Zhang, Jianbo, additional, Xiao, Amy, additional, Gu, Xiaoqiong, additional, Lee, Wei Lin, additional, Armas, Federica, additional, Kauffman, Kathryn, additional, Hanage, William, additional, Matus, Mariana, additional, Ghaeli, Newsha, additional, Endo, Noriko, additional, Duvallet, Claire, additional, Poyet, Mathilde, additional, Moniz, Katya, additional, Washburne, Alex D., additional, Erickson, Timothy B., additional, Chai, Peter R., additional, Thompson, Janelle, additional, and Alm, Eric J., additional

Published
2020
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24. Antigen-specific induction of CD4+CD8αα+ intraepithelial T lymphocytes by Bacteroidetes species

Author

Bousbaine, Djenet, primary, Bhagchandani, Preksha, additional, London, Mariya, additional, Mimee, Mark, additional, Olesen, Scott, additional, Poyet, Mathilde, additional, Cheloha, Ross W., additional, Sidney, John, additional, Ling, Jingjing, additional, Gupta, Aaron, additional, Lu, Timothy K., additional, Sette, Alessandro, additional, Alm, Eric J., additional, Mucida, Daniel, additional, Bilate, Angelina M., additional, and Ploegh, Hidde L., additional

Published
2020
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25. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases

Author

Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Broad Institute of MIT and Harvard, Koch Institute for Integrative Cancer Research at MIT, Wu, Fuqing, Zhang, Jianbo, Xiao, Amy, Gu, Xiaoqiong, Lee, Wei Lin, Armas, Federica, Kauffman, Kathryn, Hanage, William, Matus, Mariana, Ghaeli, Newsha, Endo, Noriko, Duvallet, Claire, Poyet, Mathilde, Moniz, Katya H, Washburne, Alex D., Erickson, Timothy B., Chai, Peter R., Thompson, Janelle, Alm, Eric J, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Broad Institute of MIT and Harvard, Koch Institute for Integrative Cancer Research at MIT, Wu, Fuqing, Zhang, Jianbo, Xiao, Amy, Gu, Xiaoqiong, Lee, Wei Lin, Armas, Federica, Kauffman, Kathryn, Hanage, William, Matus, Mariana, Ghaeli, Newsha, Endo, Noriko, Duvallet, Claire, Poyet, Mathilde, Moniz, Katya H, Washburne, Alex D., Erickson, Timothy B., Chai, Peter R., Thompson, Janelle, and Alm, Eric J

Abstract

Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks. IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.

Published
2020

26. Adaptive Evolution within Gut Microbiomes of Healthy People

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Zhao, Shijie, Lieberman, Tami, Poyet, Mathilde, Kauffman, Kathryn, Gibbons, Sean M., Groussin, Mathieu, Xavier, Ramnik J., Alm, Eric J, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Zhao, Shijie, Lieberman, Tami, Poyet, Mathilde, Kauffman, Kathryn, Gibbons, Sean M., Groussin, Mathieu, Xavier, Ramnik J., and Alm, Eric J

Abstract

Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization. Bacteria acquire adaptive mutations during infections, but the role of mutations in the gut microbiome is unknown. Zhao and Lieberman et al. report that Bacteroides fragilis adapts via mutation within healthy people. They discover genes important to survival in humans and detail dynamics within individuals and across populations. Keywords: adaptive evolution; human microbiome; Bacteroides; microbial evolution; microbial genomics; de novo mutation; horizontal gene transfer; metagenomics; whole-genome sequencing

Published
2020

27. Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Jiang, Xiaofang, Hall, A. Brantley, Arthur, Timothy D., Plitchta, Damian R., Covington, Christian T., Poyet, Mathilde, Crothers, Jessica, Moses, Peter L., Tolonen, Andrew C., Vlamakis, Hera, Alm, Eric J., Xavier, Ramnik J., Massachusetts Institute of Technology. Department of Biological Engineering, Jiang, Xiaofang, Hall, A. Brantley, Arthur, Timothy D., Plitchta, Damian R., Covington, Christian T., Poyet, Mathilde, Crothers, Jessica, Moses, Peter L., Tolonen, Andrew C., Vlamakis, Hera, Alm, Eric J., and Xavier, Ramnik J.

Abstract

Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion–mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces., National Institutes of Health (U.S.) (Grant AT009708), National Institutes of Health (U.S.) (Grant DK043351)

Published
2020

29. Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome

Author

Groussin, Mathieu, primary, Poyet, Mathilde, additional, Sistiaga, Ainara, additional, Kearney, Sean M., additional, Moniz, Katya, additional, Noel, Mary, additional, Hooker, Jeff, additional, Gibbons, Sean M., additional, Segurel, Laure, additional, Froment, Alain, additional, Said Mohamed, Rihlat, additional, Fezeu, Alain, additional, Juimo, Vanessa A., additional, Girard, Catherine, additional, Nguyen, Le Thanh Tu, additional, Shapiro, B. Jesse, additional, Lehtimäki, Jenni M. S., additional, Ruokolainen, Lasse, additional, Kettunen, Pinja P., additional, Vatanen, Tommi, additional, Sigwazi, Shani, additional, Mabulla, Audax, additional, Domínguez-Rodrigo, Manuel, additional, Summons, Roger E., additional, Xavier, Ramnik J., additional, and Alm, Eric J., additional

Published
2020
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30. Response of life-history traits to artificial and natural selection for virulence and nonvirulence in a Drosophila parastitoid, Asobara tabida

Author

Moiroux , Joffrey, van Baaren , Joan, POYET , Mathilde, Couty , Aude, Eslin , Patrice, Prévost , Geneviève, Seguin , Jérémy, Le Roux , Vincent, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Ecologie et Dynamique des Systèmes Anthropisés ( EDYSAN ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Picardie Jules Verne ( UPJV ), Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique ( CNRS ), Ecosystèmes, biodiversité, évolution [Rennes] ( ECOBIO ), Université de Rennes 1 ( UR1 ), and Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -INEE-Observatoire des Sciences de l'Univers de Rennes ( OSUR ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Male, [ SDV.MP.PAR ] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Virulence, [ SDV.BA.ZI ] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Climate, Reproduction, Wasps, geographic variation, host resistance, Host-Parasite Interactions, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Drosophila melanogaster, trade-offs, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Animals, encapsulation, Female, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Selection, Genetic, Life History Traits, Locomotion, Selective Breeding, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Co-evolution of host-parasitoid interactions is determined by the costs of host resistance, which received empirical evidence, and the costs of parasitoid virulence, which have been mostly hypothesized. Asobara tabida is a parasitoid, which mainly parasitizes Drosophila melanogaster and D. subobscura, the first species being able to resist to the parasitoid development while the second species is not. To parasitize resistant hosts, including D. melanogaster, A. tabida develops sticky eggs, which prevent encapsulation, but this virulence mechanism may be costly. Interindividual and interpopulation variation in the proportion of sticky eggs respectively allowed us to (i) artificially select and compare life-history traits of a virulent and a nonvirulent laboratory strain, and (ii) compare a virulent and a nonvirulent field strain, to investigate the hypothetical costs of virulence. We observed strong differences between the 2 laboratory strains. The nonvirulent strain invested fewer resources in reproduction and walked less than the virulent one but lived longer. Concerning the field strains, we observed that the nonvirulent strain had larger wings while the virulent one walked more and faster. All together, our results suggest that virulence may not always be costly, but rather that different life histories associated with different levels of virulence may coexist at both intra- and interpopulation levels.

Published
2018
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31. Choosing Your Battles: Which Resistance Genes Warrant Global Action?

Author

Zhang, An-Ni, primary, Li, Li-Guan, additional, Yin, Xiaole, additional, Dai, Chengzhen L, additional, Groussin, Mathieu, additional, Poyet, Mathilde, additional, Topp, Edward, additional, Gillings, Michael R, additional, Hanage, William P, additional, Tiedje, James M, additional, Alm, Eric J, additional, and Zhang, Tong, additional

Published
2019
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33. Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

Author

Kearney, Sean M, Gibbons, Sean Michael, Poyet, Mathilde, Gurry, Thomas Jerome, Alm, Eric J, Bullock, Kevin, Allegretti, Jessica R., Clish, Clary B., Kearney, Sean M, Gibbons, Sean Michael, Poyet, Mathilde, Gurry, Thomas Jerome, Alm, Eric J, Bullock, Kevin, Allegretti, Jessica R., and Clish, Clary B.

Abstract

Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.

Published
2018

36. The Wide Potential Trophic Niche of the Asiatic Fruit Fly Drosophila suzukii: The Key of Its Invasion Success in Temperate Europe?

Author

Poyet, Mathilde, Le Roux, Vincent, Gibert, P., Meirland, Antoine, Prevost, Geneviève, Eslin, Patrice, CHABRERIE, OLIVIER, Desneux, Nicolas, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN), Laboratoire de biologie des Entomophages, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDE.MCG]Environmental Sciences/Global Changes, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience

Published
2015
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37. Drosophila suzukii benefits from niche opportunity to invade France

Author

Poyet, Mathilde, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard - Lyon I, Patricia Gibert, and Patrice Eslin

Subjects
Médication, Niche écologique, Parasitoids, Invasion, Plantes hôtes, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Niche, Drosophila suzukii, Parasitoïde, Host plants
Abstract

Successful biological invasion is divided into three stages: the introduction of a non-native population on a new geographical area, the establishment of viable populations and their exponential growth in the area of introduction. In 2002, Shea and Chesson proposed the Opportunity Niche Hypothesis in order to explain the success of the establishment and the spread of invasive species. According to these authors, alien species introduced into a new range can jointly benefit from a decrease of the pressure applied by natural enemies and from an increase in the availability of resources. Drosophila suzukii has been reported to be an invasive species. Native of Asia, it has been now widely observed in North America and throughout Western Europe. Since its introduction in 2008, especially in Europe, the invasion of D. suzukii is particularly rapid and, as it grows on ripe fruits, a lot of concerns have been raised on the damage it causes on crops. In our work, we have highlighted some characters of this species as elements that facilitate the success of its invasion. D. suzukii is highly resistant against parasitoids, known as its major natural enemies. We have then showed the existence of a link between the ability to resist to larval parasitoids and a high hemocyte load. Furthermore, thanks to a very large sample, we have illustrated the great polyphagia of this species. This property provides available resources throughout the year. Finally, with a study of tritrophic interactions, we have shown that the nutritional quality of host plants used by D. suzukii can have an impact on the level of resistance to entomophages. Indeed, D. suzukii increases its resistance to several species of parasitoids when it growths on an alkaloid-rich substrate. Our recent results suggest that it would even be able to achieve a form of self-medication. The different studies performed in this thesis seem to confirm that D. suzukii makes the most of niche opportunity to efficiently invade temperate Europe; Une invasion biologique réussie se décompose en trois étapes : l'introduction d'une population allochtone sur une nouvelle aire de répartition géographique, l'établissement de populations viables et leur prolifération exponentielle dans l'aire d'introduction. En 2002, Shea et Chesson ont énoncé l'hypothèse d'Opportunité de Niche dans le but d'expliquer la réussite de l'établissement et de la prolifération des espèces envahissantes. Selon ces auteurs, les espèces exogènes introduites sur une nouvelle aire géographique peuvent y profiter d'une part de la diminution de la pression exercée par leurs ennemis naturels et d'autre part d'une augmentation de la disponibilité de leurs ressources. Drosophila suzukii est une de ces espèces dites envahissantes. Originaire d'Asie, sa présence est aujourd'hui largement recensée en Amérique du Nord et dans tout l'ouest de l'Europe. Depuis son introduction en 2008, en Europe notamment, l'invasion de D. suzukii est particulièrement rapide et les dégâts engendrés dans les cultures par cette espèce qui se développe sur les fruits en cours de maturité sont très préoccupants. Au cours de nos travaux, nous avons mis en évidence certains caractères chez cette espèce comme étant des éléments facilitant le succès de son invasion. D. suzukii présente tout d'abord une grande résistance face à ses principaux ennemis naturels, les parasitoïdes. Nous avons ensuite montré l'existence d'un lien entre sa capacité à mettre en échec les parasitoïdes larvaires et son importante charge hémocytaire. Par ailleurs, grâce à un échantillonnage très large, nous avons illustré la grande polyphagie de cette espèce. Ce caractère lui assure potentiellement une disponibilité en ressources tout au long de l'année. Enfin, à l'aide d'une étude portant sur les relations tritrophiques, nous avons montré que la qualité nutritive des plantes hôtes utilisées par D. suzukii peut avoir un impact sur le niveau de sa résistance aux entomophages. D. suzukii parvient en effet à augmenter sa résistance à plusieurs espèces de parasitoïdes lorsqu'elle réalise son développement sur un substrat riche en alcaloïde. Nos derniers résultats suggèrent qu'elle serait même capable de réaliser une forme d'automédication. Les différentes études réalisées au cours de cette thèse semblent confirmer que D. suzukii profite d'une opportunité de niche en Europe tempérée

Published
2014

38. Invasive host for invasive pest: when the Asiatic cherry fly ( Drosophila suzukii ) meets the American black cherry ( Prunus serotina ) in Europe

Author

Poyet, Mathilde, Eslin, Patrice, Heraude, Marie, Le Roux, Vincent, Prevost, Geneviève, Gibert, Patricia, CHABRERIE, OLIVIER, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Université de Picardie Jules Verne (UPJV), and Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV)

Subjects
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], [SDE.MCG]Environmental Sciences/Global Changes, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience

Published
2014
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40. Response of life‐history traits to artificial and natural selection for virulence and nonvirulence in a <italic>Drosophila</italic> parastitoid, <italic>Asobara tabida</italic>.

Author

Moiroux, Joffrey, van Baaren, Joan, Poyet, Mathilde, Couty, Aude, Eslin, Patrice, Prévost, Geneviève, Séguin, Jérémy, and Le Roux, Vincent

Subjects
ASOBARA tabida, NATURAL selection, HOST-parasite relationships, MICROBIAL virulence, PARASITOIDS
Abstract

Abstract: Co‐evolution of host–parasitoid interactions is determined by the costs of host resistance, which received empirical evidence, and the costs of parasitoid virulence, which have been mostly hypothesized. Asobara tabida is a parasitoid, which mainly parasitizes Drosophila melanogaster and D. subobscura, the first species being able to resist to the parasitoid development while the second species is not. To parasitize resistant hosts, including D. melanogaster, A. tabida develops sticky eggs, which prevent encapsulation, but this virulence mechanism may be costly. Interindividual and interpopulation variation in the proportion of sticky eggs respectively allowed us to (i) artificially select and compare life‐history traits of a virulent and a nonvirulent laboratory strain, and (ii) compare a virulent and a nonvirulent field strain, to investigate the hypothetical costs of virulence. We observed strong differences between the 2 laboratory strains. The nonvirulent strain invested fewer resources in reproduction and walked less than the virulent one but lived longer. Concerning the field strains, we observed that the nonvirulent strain had larger wings while the virulent one walked more and faster. All together, our results suggest that virulence may not always be costly, but rather that different life histories associated with different levels of virulence may coexist at both intra‐ and interpopulation levels. [ABSTRACT FROM AUTHOR]

Published
2018
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42. Response of the human gut and saliva microbiome to urbanization in Cameroon

Author

Lokmer, Ana, Aflalo, Sophie, Amougou, Norbert, Lafosse, Sophie, Froment, Alain, Tabe, Francis Ekwin, Poyet, Mathilde, Groussin, Mathieu, Said-Mohamed, Rihlat, and Ségurel, Laure

Subjects
2. Zero hunger, Adult, Male, Adolescent, Bacteria, Urban Population, Urbanization, 1. No poverty, Middle Aged, Diet, Gastrointestinal Microbiome, Entamoeba, Feces, Young Adult, Humans, Female, Cameroon, Saliva, human activities, Aged
Abstract

Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.

43. Response of the human gut and saliva microbiome to urbanization in Cameroon

Author

Laure Ségurel, Mathieu Groussin, Francis Ekwin Tabe, Norbert Amougou, Rihlat Said-Mohamed, Sophie Lafosse, Alain Froment, Sophie Aflalo, Mathilde Poyet, Ana Lokmer, Lokmer, Ana [0000-0003-4579-6607], Poyet, Mathilde [0000-0002-0942-7217], Apollo - University of Cambridge Repository, Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Fractionnement des AgroRessources et Environnement (FARE), Université de Reims Champagne-Ardenne (URCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), ANR-15-CE02-0003,MICROREGAL,Adaptations du microbiome intestinal humain aux changements passés et présents d'alimentation et de mode de vies(2015), and Éco-Anthropologie (EA)

Subjects
0301 basic medicine, Adult, Male, Saliva, Adolescent, Urban Population, media_common.quotation_subject, 030106 microbiology, Zoology, lcsh:Medicine, Biology, Positive correlation, Article, Entamoeba, Microbial ecology, 03 medical and health sciences, Feces, Young Adult, Human gut, Urbanization, Humans, Microbiome, Cameroon, lcsh:Science, media_common, Aged, 2. Zero hunger, Stool consistency, Multidisciplinary, Bacteria, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], lcsh:R, 1. No poverty, Middle Aged, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Diet, Gastrointestinal Microbiome, 030104 developmental biology, Female, lcsh:Q, Rural area, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities, Diversity (politics), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.

Published
2020
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44. Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

Author

Clary B. Clish, Thomas Gurry, Kevin Bullock, Eric J. Alm, Jessica R. Allegretti, Sean M. Kearney, Mathilde Poyet, Sean M. Gibbons, Kearney, Sean M, Gibbons, Sean Michael, Poyet, Mathilde, Gurry, Thomas Jerome, and Alm, Eric J

Subjects
0301 basic medicine, Genetics, Human feces, Spores, Bacterial, Endospore formation, Bacteria, Transmission (medicine), 030106 microbiology, Human microbiome, Biodiversity, Biology, Microbiology, Endospore, Article, Gastrointestinal Microbiome, 03 medical and health sciences, Feces, 030104 developmental biology, Humans, Colonization, Microbiome, Gene, Ecology, Evolution, Behavior and Systematics
Abstract

Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endosporesin situand how sporulation varies across individuals and over time. Here, we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.

Published
2018

45. Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome.

Author

Yuan Y, DeMott MS, Byrne SR, Flores K, Poyet M, Groussin M, Microbiome Conservancy G, Berdy B, Comstock L, Alm EJ, and Dedon PC

Abstract

Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by dnd and ssp gene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possessed dnd or ssp genes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis uncovered several putative new PT synthesis systems, including Type 4 Bacteriophage Exclusion (BREX) brx genes, which were genetically validated in Bacteroides salyersiae. Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessing dnd , ssp , and brx genes revealed 8 PT dinucleotide settings confirmed in 6 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes.

Published
2024
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