Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints

Holmes, Andrew J., Chew, Yi Vee, Colakoglu, Feyza, Cliff, John B., Klaassens, Eline, Read, Mark N., Solon-Biet, Samantha M., McMahon, Aisling C. +5 more·2017·Cell Metabolism

DOI 10.1016/j.cmet.2016.10.021

Cited by (183)

Items 101–183 of 183

[Retinal circulation time in diabetic retinopathy treated with photocoagulation (author's transl)].
F. Koerner, Katja Fries, Peter Niesel, P Dubied · 1978 · PubMed
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Christine Poelaert, Xavier Despret, Marianne Sindic, Yves Beckers, Frédéric Francis, Daniel Portetelle, Hélène Soyeurt, André Théwis, Jérôme Bindelle · 2016 · Journal of Agricultural and Food Chemistry
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Kate Larson, Travis Alvine, Dayong Wu, Nishan S. Kalupahana, Naïma Moustaïd‐Moussa, James N. Roemmich · 2020 · Journal of Nutrition
Multiomics assessment of dietary protein titration reveals altered hepatic glucose utilization
Michael Robert MacArthur, Sarah Jayne Mitchell, Katia S. Chadaideh, Jose Humberto Trevino-Villarreal, Jonathan Jung, Krystle C. Kalafut, Justin S. Reynolds, Charlotte G. Mann, Kaspar M. Trocha, Ming Tao et al. · 2022 · Cell Reports
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Herrera, Matthew, Byerley, Lauri O. · 2025 · Nutrients
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Melani K. Muratore, Yvonne Sun, Chelse M. Prather · 2020 · Frontiers in Microbiology
Copper and Gold Nanoparticles Increase Nutrient Excretion Rates of Primary Consumers
Brittany G. Perrotta, Marie Simonin, Jeffrey Alan. Back, Steven M. Anderson, Astrid Avellan, Christina M. Bergemann, Benjamin T. Castellon, Benjamin P. Colman, Gregory Victor Lowry, Cole W. Matson et al. · 2020 · Environmental Science & Technology
Correction to: Dietary intervention using (1,3)/(1,6)-β-glucan, a fungus-derived soluble prebiotic ameliorates high-fat diet-induced metabolic distress and alters beneficially the gut microbiota in mice model
Karthika Muthuramalingam, Vineet Singh, Changmin Choi, Seung In Choi, Youngmee Kim, Tatsuya Unno, Moonjae Cho · 2021 · European Journal of Nutrition
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Sex and Aging
David George Le Couteur, Rozalyn M. Anderson, Rafael de Cabo · 2017 · The Journals of Gerontology Series A
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Vít Všianský, Markéta Svobodová, Jaromír Gumulec, Natalia Cernei, Dagmar Štěrbová, Ondřej Zítka, Rom Kostřica, Pavel Smilek, Jan Plzák, Jan Betka et al. · 2019 · Cells
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Christy S. Carter · 2021 · The Journals of Gerontology Series A
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Alistair McNair Senior, David Raubenheimer, David George Le Couteur, Stephen J. Simpson · 2024 · Annual Review of Animal Biosciences
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Xiaona Zeng, Xiaoyong Zhang, Biao Chen, Liuling Gao, Sha Liu, Feng Wu, Qing Pan · 2021 · Aquaculture Reports
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Xiuhui Zhao, Junning Ye, Xunkai Lin, Huiwen Xue, Xian Zou, Guangbin Liu, Ming Deng, Baoli Sun, Yongqing Guo, Dewu Liu et al. · 2023 · Genes
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Soon Hwee Ng, Michael Stat, Michael Bunce, Stephen James Simpson, Leigh W. Simmons · 2019 · FEMS Microbiology Ecology
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Felipe Paulo da Silva, Tomás Gatica, Carolina Pavéz · 2019 · Revista Médica Clínica Las Condes
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Manuel Kleiner, Angela Kouris, Marlene J. Violette, Grace D’Angelo, Yihua Liu, Abigail Korenek, Nikola Tolić, Timo T. Sachsenberg, Janine McCalder, Mary S. Weir Lipton et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
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Dudley W. Lamming, Emma L. Baar, Sebastian I. Arriola Apelo, Valeria Tosti, Luigi Fontana · 2017 · Nutrition and Healthy Aging
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Rosilene V. Ribeiro, Stephen James Simpson, David George Le Couteur, David Raubenheimer, Joerg Eberhard, Kate Ruiz, Laurence Macia, Yvanna Todorova, Alison K. Gosby · 2019 · Nutrition and Healthy Aging
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Jean‐Bernard Lubin, Michael A. Silverman, Paul Joseph Planet · 2024 · Gut Microbes
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Alison W. S. Luk, Lachlan Mitchell, Yen Chin Koay, John O’Sullivan, Helen T O'Connor, Daniel A. Hackett, Andrew J. Holmes · 2022 · Metabolites
Diet-induced metabolic and faecal microbiome responses in pet dogs fed a minimally processed versus extruded kibble diet
L. C. CAMPBELL, Mary Thompson, Matthew Muir, David Raubenheimer, Andrew J. Holmes · 2026 · Frontiers in Veterinary Science
Comparative analyses of gut microbiota reveal ammonia detoxification and nitrogen assimilation in Cyprinus carpio var. specularis
Chandni Talwar, Shekhar Nagar, Ram Krishan Negi · 2024 · Folia Microbiologica
Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort
Alex E. Mohr, Paniz Jasbi, Irene van Woerden, Jinhua Chi, Haiwei Gu, Meg M. Bruening, Corrie Marie Whisner · 2024 · Gut Microbes Reports
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Jamie Lee, Hiu Lam Athena Wu, Ahmad A. Mannan, Yuumi Nakamura, Masayuki Amagai, Alan David Irvine, Reiko J. Tanaka · 2025 · JID Innovations
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Chaima Dridi, Mathieu Millette, Stéphane Salmieri, Blanca Rosa Aguilar‐Uscanga, Sébastien Lacroix, Tommaso Venneri, Elham Sarmast, Zahra Allahdad, Vincenzo Di Marzo, Cristoforo Silvestri et al. · 2024 · Foods
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Emma Todd, Reem Elnour, Rebecca C. Simpson, Miguel Castaneda, Erin Rose Shanahan · 2021 · Microbiology Australia
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Dharmender K. Gahlot · 2026 · Frontiers in Nutrition
An Ad Libitum‐Fed Diet That Matches the Beneficial Lifespan Effects of Caloric Restriction but Acts via Opposite Effects on the Energy‐Splicing Axis
Amanda E. Brandon, Tamara Pulpitel, Carsten Schmitz‐Peiffer, Lewin Small, Alistair McNair Senior, Sophie Stonehouse, Leteisha A. Prescott, Alyssa Face, K. Saiful Islam, Jenny Elizabeth Gunton et al. · 2025 · Aging Cell
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Juan Pablo Molina Ortiz, Dale David McClure, Erin Rose Shanahan, Fariba Dehghani, Andrew J. Holmes, Mark Norman Read · 2021 · Gut Microbes
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Mirei Okada, Melissa Pehlivan, Jane Miskovic‐Wheatley, Sarah Barakat, Kristi R. Griffiths, Stephen William Touyz, Stephen James Simpson, Sarah Maguire, Andrew J. Holmes · 2023 · Frontiers in Public Health
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Enriqueta García-Gutiérrez · 2019 · UEA Digital Repository (University of East Anglia)
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Han Gao, Chengwei He, Rongxuan Hua, Chen Liang, Boya Wang, Yixuan Du, Yuexin Guo, Lei Gao, Lucia Zhang, Hongwei Shang et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
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Biagina Chiofalo, Rosangela Armone, Andrea Randazzo, Vincenzo Nava, Mario Barbato, Bruno Stefanon · 2025 · Italian Journal of Animal Science
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Siqi Wang, Qinglu Zhou, Xue Han, Mengning Wang, Xuerui Liu, Qun Jiang, Tianqi Liu, Jianhua Qu, Ying Zhang · 2025 · Chemical Engineering Journal
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Zican Li, Lianjie Huang, Qiushuang Zhu, Fanyun Wang, Defang Li, Bo Qu, Runan Zhang, Yue Guan, Akinkunmi Paul Okekunl, Jiaying Yu et al. · 2025 · Food & Function
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Matthew Irick Jackson · 2024 · Metabolites
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Jonathan Z. Shik, Audrey Dussutour, Henrik H. De Fine Licht · 2025 · Ecology Letters
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Yechan Zhao, Zhi-Liang Tan, Zhi-Xiong He, Jian Wu, J. Jiao · 2026 · Microbiome
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Lipeng Wu, Shaozhen Li, Fangkai Han, Jun Guo, Xingtao Zhang, Lisheng Xu · 2026 · Frontiers in Microbiology
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Stephen James Simpson, David George Le Couteur, Lewin Small, Amanda E. Brandon, David Raubenheimer · 2026 · Nature Reviews Endocrinology
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Samantha M. Solon‐Biet, Devin Wahl, David Raubenheimer, David George Le Couteur, Stephen James Simpson, Victoria Carroll Cogger · 2018 · Elsevier eBooks
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Devin Wahl, Rahul Gokarn, Samantha M. Solon‐Biet, Victoria Carroll Cogger, Thomas J. LaRocca, David Raubenheimer, Stephen James Simpson, David George Le Couteur · 2021 · Elsevier eBooks
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Iris A. Holmes, José Gabriel Martínez‐Fonseca, Rudolf von May, Briana A. Sealey, Peter A. Cerda, Maggie R. Grundler, Erin P. Westeen, Daniel Nondorf, Joanna G. Larson, Christopher R. Myers et al. · 2025 · ISME Communications
Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids
Sara C. Di Rienzi, Juliet Jacobson, Elizabeth A. Kennedy, M. Elizabeth Bell, Qiaojuan Shi, Jillian L. Waters, Peter Lawrence, James Thomas Brenna, Robert A. Britton, Jens Walter et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
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Jipeng Jin, Liping Zhang, Qian Chen, Cunming Ma, Jianlei Jia, D. P. Casper · 2021 · Research Square
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Anna F. Bekebrede · 2023
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