American Gut: an Open Platform for Citizen-Science Microbiome Research

McDonalda, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar +51 more·2018·mSystems

DOI 10.1101/277970

Cited by (884)

Items 201–300 of 884

Multi-cohort analysis of depression-associated gut bacteria sheds insight on bacterial biomarkers across populations
Suisha Liang, Zhen Ye Sin, Juelei Yu, Shilin Zhao, Xi Zhang, Roberto Bruzzone, Hein M. Tun · 2022 · Cellular and Molecular Life Sciences
Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets
Anukriti Sharma, Miles Richardson, Lauren E. Cralle, Christopher E. Stamper, Juan Pedro Maestre, Kelly A. Stearns‐Yoder, Teodor T. Postolache, Katherine L. Bates, Kerry A. Kinney, Lisa A. Brenner et al. · 2019 · Microbiome
Challenges in the construction of knowledge bases for human microbiome-disease associations
Varsha D. Badal, Dustin Wright, Yannis Katsis, Ho‐Cheol Kim, Austin D.-E. Swafford, Rob D. Knight, Chun‐Nan Hsu · 2019 · Microbiome
Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study
Mi Young Lim, Seung Pyo Hong, Bomin Kim, Yongju Ahn, Hyun‐Jin Kim, Young‐Do Nam · 2020 · Scientific Reports
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses
Stephen Woloszynek, Zhengqiao Zhao, Jian Chen, GAIL L. ROSEN · 2019 · PLoS Computational Biology
Framing the discussion of microorganisms as a facet of social equity in human health
Suzanne Lynn Ishaq, Maurisa Rapp, Risa Byerly, Loretta S. McClellan, Maya R. O’Boyle, Anika Nykanen, Patrick J. Fuller, Calvin Aas, Jude M. Stone, Sean Killpatrick et al. · 2019 · PLoS Biology
Critical evaluation of faecal microbiome preservation using metagenomic analysis
Alena L. Pribyl, Donovan H. Parks, Nicola Z. Angel, Joel A. Boyd, Alexander Hasson, Liang Fang, Samantha MacDonald, Blake Wills, David Wood, Lutz Krause et al. · 2021 · ISME Communications
Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
Søren Michael Karst, Ryan M. Ziels, Rasmus Hansen Kirkegaard, Emil Aarre Sørensen, Daniel T. McDonald, Qiyun Zhu, Rob D. Knight, Mads Albertsen · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes
George Armstrong, Kalen Cantrell, Shi Wei Huang, Daniel T. McDonald, Niina Haiminen, Anna Paola Carrieri, Qiyun Zhu, Antonio González, Imran McGrath, Kristen L. Beck et al. · 2021 · Genome Research
Estimating the Time Since Deposition of Saliva Stains With a Targeted Bacterial DNA Approach: A Proof-of-Principle Study
Celia Díez López, Manfred Kayser, Athina Vidaki · 2021 · Frontiers in Microbiology
Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk
Chan Wang, Leopoldo N. Segal, Jiyuan Hu, Boyan Zhou, Richard B. Hayes, Jiyoung Ahn, Huilin Li · 2022 · Microbiome
Gut Microbiota–MicroRNA Interactions in Intestinal Homeostasis and Cancer Development
Nataliia Nikolaieva, Aneta Ševčíková, Radoslav Omelka, Monika Martiniaková, Michal Mego, Soňa Čierniková · 2022 · Microorganisms
Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status
Laura Anthamatten, Philipp Rogalla von Bieberstein, Carmen Menzi, Janina N. Zünd, Christophe Lacroix, Tomás de Wouters, Gabriel E. Leventhal · 2024 · Microbiome
Gut Microbiota: An Important Participant in Childhood Obesity
Yu Luo, Maojun Li, Dan Luo, Binzhi Tang · 2024 · Advances in Nutrition
Mechanistic Implications of the Mediterranean Diet in Patients With Newly Diagnosed Crohn's Disease: Multiomic Results From a Prospective Cohort
Lihi Godny, Sarine Elial-Fatal, Jessica Arrouasse, Tali Sharar Fischler, Leah Reshef, Yelena Kutukov, Shaked Cohen, Tamar Pfeffer‐Gik, Revital Barkan, Shelly R. Shakhman et al. · 2025 · Gastroenterology
Comparative Analysis of Gut Microbiota Following Changes in Training Volume Among Swimmers
Jarrad Hampton‐Marcell, Tifani W. Eshoo-Anton, Marc D. Cook, Jack A. Gilbert, Craig A. Horswill, Rachel Susan Poretsky · 2020 · International Journal of Sports Medicine
Potential of gut microbiome for detection of autism spectrum disorder
Tong Wu, Hongchao Wang, Wenwei Lu, Qixiao Zhai, Qiuxiang Zhang, Weiwei Yuan, Zhennan Gu, Jianxin Zhao, Hao Zhang, Wei Chen · 2020 · Microbial Pathogenesis
Age and sex-dependent patterns of gut microbial diversity in human adults
Jacobo de la Cuesta‐Zuluaga, Scott Theodore Kelley, Yingfeng Chen, Juan Sebastián Escobar, Noel Theodore Mueller, Ruth E. Ley, Daniel T. McDonald, Shi Wei Huang, Austin D.-E. Swafford, Rob D. Knight et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions
Celia Díez López, Athina Vidaki, Manfred Kayser · 2021 · Forensic Science International Genetics
Predicting Neurodegenerative Disease Using Prepathology Gut Microbiota Composition: a Longitudinal Study in Mice Modeling Alzheimer’s Disease Pathologies
Emily M. Borsom, Kathryn A Conn, Christopher R. Keefe, Chloe Herman, Gabrielle M Orsini, Allyson H. Hirsch, Melanie Palma Avila, George Testo, Sierra A. Jaramillo, Evan K Bolyen et al. · 2023 · Microbiology Spectrum
Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients
Chen Liao, Bradford P. Taylor, Camilla Ceccarani, Emily Fontana, Luigi A. Amoretti, Roberta J. Wright, Antonio L. C. Gomes, Jonathan U. Peled, Ying Taur, Miguel‐Angel Perales et al. · 2021 · Scientific Data
Is adolescence the missing developmental link in Microbiome–Gut–Brain axis communication?
Jessica Flannery, Bridget L. Callaghan, Thomas J. Sharpton, Philip A. Fisher, Jennifer H. Pfeifer · 2019 · Developmental Psychobiology
Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species
Alice Risely, Mark A. F. Gillingham, Arnaud Béchet, Stefan Dominik Brändel, Alexander Christoph Heni, Marco Heurich, Sebastian Menke, Marta B. Manser, Marco Tschapka, Wasimuddin et al. · 2021 · Frontiers in Microbiology
Exploring the role of gut microbiota in advancing personalized medicine
Guoxin Huang, Raees Khan, Yilin Zheng, Ping-Chin Lee, Qingnan Li, Imran Khan · 2023 · Frontiers in Microbiology
In Vitro Evaluation of Different Prebiotics on the Modulation of Gut Microbiota Composition and Function in Morbid Obese and Normal-Weight Subjects
Alicja Maria Nogacka, Nuria Salazar, Silvia Arboleya, Patricia Ruas‐Madiedo, Leonardo Mancabelli, Adolfo Suárez, Ceferino Martinez Faedo, Marco Ventura, Takumi Tochio, Katsuaki Hirano et al. · 2020 · International Journal of Molecular Sciences
Effects of exercise and physical activity on gut microbiota composition and function in older adults: a systematic review
Viviana Aya, Paula Jiménez, Enrique Muñoz, Juan David Ramírez · 2023 · BMC Geriatrics
Multi-site microbiota alteration is a hallmark of kidney stone formation
Kait F. Al, Benjamin R. Joris, Brendan A. Daisley, John A. Chmiel, Jennifer Bjazevic, Gregor Reid, Gregory Brian Gloor, John D. Denstedt, HASSAN A. RAZVI, Jeremy P. Burton · 2023 · Microbiome
Microbial communities of a variety of 75 homemade fermented vegetables
Anne Thierry, Marie‐Noëlle Madec, Victoria Chuat, Anne-Sophie Bage, Olivier Picard, Cécile Grondin, Olivier Rué, Mahendra Mariadassou, Laurent Marché, Florence Valence · 2023 · Frontiers in Microbiology
Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome
Julien Tap, Stine Störsrud, Boris Le Nevé, Aurélie Cotillard, Nicolas Pons, Joel M. Dore, Lena Öhman, Hans Törnblom, Muriel Derrien, Magnus Simrén · 2021 · Microbiome
Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease
Ryszard Kubinski, Jean-Yves Djamen-Kepaou, Timur Zhanabaev, Álex Hernández-García, Stefan Bauer, Falk Hildebrand, Tamas Douglas Korcsmaros, Sani Karam, Prévost Jantchou, Kamran Kafi et al. · 2022 · Frontiers in Genetics
Benchmarking differential abundance analysis methods for correlated microbiome sequencing data
Lu Yang, Jun Chen · 2022 · Briefings in Bioinformatics
Challenges and research priorities to progress the impact of antimicrobial stewardship
Matteo Bassetti, Daniele Roberto Giacobbe, Antonio Vena, Adrian John Brink · 2019 · Drugs in Context
Inflammation in Mental Disorders: Is the Microbiota the Missing Link?
Sophie Marin, Ying Hé, Keith Butler, Ming T. Tsuang · 2020 · Neuroscience Bulletin
Shared Environment and Genetics Shape the Gut Microbiome after Infant Adoption
Hannah F. Tavalire, Diana M. Christie, Leslie D. Leve, Nelson Ting, William A. Cresko, Brendan J. M. Bohannan · 2021 · mBio
The Kitty Microbiome Project: Defining the Healthy Fecal “Core Microbiome” in Pet Domestic Cats
Holly H. Ganz, Guillaume Jospin, Connie A. Rojas, Alex L. Martin, Katherine E. Dahlhausen, Dawn D. Kingsbury, Carlton X. Osborne, Zhandra Entrolezo, Syd Redner, Bryan Ramirez et al. · 2022 · Veterinary Sciences
Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults
Leila M Shinn, Yutong Li, Aditya Mansharamani, Loretta Sue Auvil, Michael E. Welge, Colleen Bushell, Naiman A. Khan, Craig S. Charron, Janet A. Novotny, David J. Baer et al. · 2020 · Journal of Nutrition
Shrinkage improves estimation of microbial associations under different normalization methods
Michelle H. Badri, Zachary D. Kurtz, Richard Bonneau, Christian L. Müller · 2020 · NAR Genomics and Bioinformatics
The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices
Celia Fuentes‐Chust, Claudio Parolo, Giulio Rosati, Lourdes Rivas, Karla Perez‐Toralla, Stéphanie Simon, Itziar de Lecuona, Christophe Junot, Jonel Trebicka, Arben Merkoçi · 2021 · Advanced Materials
Association of Loneliness and Wisdom With Gut Microbial Diversity and Composition: An Exploratory Study
Tanya T. Nguyen, Xinlian Zhang, Tsung‐Chin Wu, Jinyuan Liu, Collin Le, Xin Ming Tu, Rob D. Knight, Dilip V. Jeste · 2021 · Frontiers in Psychiatry
Fecal Microbiota Transplants for Inflammatory Bowel Disease Treatment: Synthetic- and Engineered Communities-Based Microbiota Transplants Are the Future
Raees Khan, Nazish Roy, Hussain Ali, Muhammad Naeem · 2022 · Gastroenterology Research and Practice
Artificial intelligence approaches to human-microbiome protein–protein interactions
Lim, Hansaim, Cankara, Fatma, Tsai, Chung-Jung, Keskin, Ozlem, Nussinov, Ruth, Gursoy, Attila · 2022 · Current Opinion in Structural Biology
A Guide to Dietary Pattern–Microbiome Data Integration
Yuni Choi, Suzie Hoops, Calvin J. Thoma, Abigail J. Johnson · 2022 · Journal of Nutrition
Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome
German A. Ashniev, Sergey N. Petrov, Stanislav N. Iablokov, Dmitry A. Rodionov · 2022 · Microorganisms
Identifying and Predicting Novelty in Microbiome Studies
Xiaoquan Su, Gongchao Jing, Daniel T. McDonald, Honglei Wang, Zengbin Wang, Antonio Gonzalez, Zheng Sun, Shi Wei Huang, Jose Navas, Rob D. Knight et al. · 2018 · mBio
Testing for differential abundance in compositional counts data, with application to microbiome studies
Barak Brill, Amnon Amir, Ruth Heller · 2022 · The Annals of Applied Statistics
Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma
Sean P. Polster, Anukriti Sharma, Ceylan Tanes, Alan T. Tang, Patricia A. Mericko, Ying Jun Cao, Julián Carrión‐Penagos, Romuald Girard, Janne Koskimäki, Dongdong Zhang et al. · 2020 · Nature Communications
Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth
Alexander Mahnert, Cyprien Verseux, Petra Schwendner, Kaisa Koskinen, Christina Kumpitsch, Marcus Blohs, Lisa Wink, Daniela Brunner, Theodora Goessler, Daniela Billi et al. · 2021 · Microbiome
MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition
Xing Hua, Lei Song, Guoqin Yu, Emily Vogtmann, James J. Goedert, Christian C. Abnet, Maria Teresa Landi, Jianxin Shi · 2022 · Genes
Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs)
Mancabelli, Leonardo, Tarracchini, Chiara, Milani, Christian, Lugli, Gabriele Andrea, Fontana, Federico, Turroni, Francesca, van Sinderen, Douwe, Ventura, Marco · 2020 · Computational and Structural Biotechnology Journal
Temporal variations in the gut microbial diversity in response to high-fat diet and exercise
Saba Imdad, Byunghun So, Jun-Ho Jang, Jin-Han Park, Sam‐Jun Lee, Jinhee Kim, Chounghun Kang · 2024 · Scientific Reports
The Influence of Diet Interventions Using Whole, Plant Food on the Gut Microbiome: A Narrative Review
Holly J Willis, Joanne L. Slavin · 2019 · Journal of the Academy of Nutrition and Dietetics
Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort
Mary E. Kable, Elizabeth L. Chin, David H. Storms, Danielle G. Lemay, Charles Bolt Stephensen · 2021 · Journal of Nutrition
Toward a health-associated core keystone index for the human gut microbiome
Goel, Abhishek, Shete, Omprakash, Goswami, Sourav, Samal, Amit, C.B., Lavanya, Kedia, Saurabh, Ahuja, Vineet, O’Toole, Paul W., Shanahan, Fergus, Ghosh, Tarini Shankar · 2025 · Cell Reports
Machine Learning Based Microbiome Signature to Predict Inflammatory Bowel Disease Subtypes
José Liñares-Blanco, Carlos Fernandez-Lozano, José Antonio Seoane, Guillermo López–Campos · 2022 · Frontiers in Microbiology
Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
Consuelo Sauceda, Charlie F. Bayne, Khadijeh Sudqi, Antonio González, Parambir Singh Dulai, Rob D. Knight, David J. Gonzalez, Carlos G. Gonzalez · 2022 · Gut Microbes
Combing fecal microbial community data to identify consistent obesity-specific microbial signatures and shared metabolic pathways
Yu Lin, Zhilu Xu, Yun Kit Yeoh, Hein Min Tun, Wenli Huang, Wei Jiang, Francis K.L. Chan, Siew C. Ng · 2023 · iScience
Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome
Stefan Gavriliuc, Mason R. Stothart, Astrid Henry, Jocelyn Poissant · 2021 · PeerJ
Bioinformatic approaches for studying the microbiome of fermented food
Liam H. Walsh, Mairéad Coakley, Aaron M. Walsh, Paul William O’Toole, Paul D. Cotter · 2022 · Critical Reviews in Microbiology
Lower gut dysbiosis and mortality in acute critical illness: a systematic review and meta-analysis
Tess Evans, Umar Ali, Ryan S. Anderton, Edward Raby, Laurens A. Manning, Edward Litton · 2023 · Intensive Care Medicine Experimental
Local and Systemic Effects of Bioactive Food Ingredients: Is There a Role for Functional Foods to Prime the Gut for Resilience?
Emma F. Jacquier, Marcel van de Wouw, Elena Nekrasov, Nikhat Contractor, Amira Nemr Kassis, Diana E. Marcu · 2024 · Foods
Citizen science to further precision medicine: from vision to implementation
Carolyn Collins Petersen, Robin R. Austin, Uba Backonja, Hugo Campos, Arlene E. Chung, Eric B. Hekler, Pei-Yun Sabrina Hsueh, Katherine K. Kim, Anthony T. Pho, Liz Salmi et al. · 2019 · JAMIA Open
A Distinct Microbiome Signature in Posttreatment Lyme Disease Patients
Madeleine Morrissette, Norman Pitt, Antonio González, Philip Strandwitz, Mariaelena Caboni, Alison W. Rebman, Rob D. Knight, Anthony E. Donofrio, John N. Aucott, Mark J. Soloski et al. · 2020 · mBio
Analysing indoor mycobiomes through a large‐scale citizen science study in Norway
Pedro Maria Martin-Sanchez, Eva Lena F. Estensmo, Luís Neves Morgado, Sundy Maurice, Ingeborg Bjorvand Engh, Inger Skrede, Håvard Kauserud · 2021 · Molecular Ecology
Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas
Suet‐Ying Kwan, Caroline M. Sabotta, Aron Y. Joon, Peng Wei, Lauren E. Petty, Jennifer Elizabeth Below, Xiaogang Wu, Jianhua Zhang, Robert R. Jenq, Ernest T. Hawk et al. · 2022 · mSystems
Machine learning–based feature selection to search stable microbial biomarkers: application to inflammatory bowel disease
Youngro Lee, Marco Cappellato, Barbara Di Camillo · 2022 · GigaScience
A toolbox of machine learning software to support microbiome analysis
Laura Judith Marcos-Zambrano, Víctor Manuel López-Molina, Burcu Bakır-Güngör, Marcus Frohme, Kanita Karađuzović-Hadžiabdić, Thomas Klammsteiner, Eliana Ibrahimi, Leo Lahti, Tatjana Lončar-Turukalo, Xhilda Dhamo et al. · 2023 · Frontiers in Microbiology
The Emerging Role of Gut Dysbiosis in Cardio-metabolic Risk Factors for Heart Failure
Yusuke Sata, Francine Z. Marques, David M. Kaye · 2020 · Current Hypertension Reports
Randomised, double-blind, placebo-controlled trial of Probiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC): a clinical trial protocol
Helen Tang, Lauren M. Bohannon, M. Lew, David Jensen, Sin‐Ho Jung, Aaron T. Zhao, Anthony Derek Sung, Paul Edmund Wischmeyer · 2021 · BMJ Open
Predictable and host‐species specific humanization of the gut microbiota in captive primates
Jennifer L. Houtz, Jon G. Sanders, Anthony Denice, Andrew H. Moeller · 2021 · Molecular Ecology
Gut Microbiome Structure and Association with Host Factors in a Korean Population
Mi Young Lim, Seung Pyo Hong, So-Jung Bang, Won‐Hyong Chung, Ji‐Hee Shin, Jung‐Ha Kim, Young‐Do Nam · 2021 · mSystems
Microbiome and Metabolome Insights into the Role of the Gastrointestinal–Brain Axis in Parkinson’s and Alzheimer’s Disease: Unveiling Potential Therapeutic Targets
Helena U. Zacharias, Christoph Kaleta, François Cossais, Eva Schaeffer, Henry Berndt, Lena Best, Thomas Dost, Svea Glüsing, Mathieu Groussin, Mathilde Poyet et al. · 2022 · Metabolites
Dietary and microbiome evidence in multiple myeloma and other plasma cell disorders
Urvi Ashok Shah, Richa Parikh, Francesca Castro, Matteo Bellone, Alexander M. Lesokhin · 2023 · Leukemia
Connect the dots: sketching out microbiome interactions through networking approaches
Marco Fabbrini, Daniel Scicchitano, Marco Candela, Silvia Turroni, Simone Rampelli · 2023 · Microbiome Research Reports
Pharmaceuticals and Personal Care Products in the Aquatic Environment: How Can Regions at Risk be Identified in the Future?
John L. Wilkinson, Ian Thornhill, Rik Oldenkamp, Anthony Ngure Gachanja, Rosa Busquets · 2023 · Environmental Toxicology and Chemistry
Harnessing the Power of Microbiome Assessment Tools as Part of Neuroprotective Nutrition and Lifestyle Medicine Interventions
Miguel A Toribio-Mateas · 2018 · Microorganisms
Microbial Transformations of Organically Fermented Foods
Ruma Raghuvanshi, Allyssa G. Grayson, Isabella Schena, Onyebuchi Amanze, Kezia Suwintono, Robert A. Quinn · 2019 · Metabolites
Fermented foods and cardiometabolic health: Definitions, current evidence, and future perspectives
Katherine J. Li, Kathryn J. Burton-Pimentel, Guy Vergères, Edith J. M. Feskens, Elske Maria Brouwer-Brolsma · 2022 · Frontiers in Nutrition
Existing and Future Strategies to Manipulate the Gut Microbiota With Diet as a Potential Adjuvant Treatment for Psychiatric Disorders
Fiona C. Ross, D.E. Mayer, Arpana Gupta, Chris I. R. Gill, Daniele Del Rio, John F. Cryan, Aonghus Lavelle, R. Paul Ross, Catherine Stanton, Emeran A. Mayer · 2023 · Biological Psychiatry
Clinician Guide to Microbiome Testing
Christopher M. Staley, Thomas Kaiser, Alexander Khoruts · 2018 · Digestive Diseases and Sciences
A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data
Jian Yun Xiao, Li Chen, Yue Yu, Xianyang Zhang, Jun Chen · 2018 · Frontiers in Microbiology
tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies
Tianhua Liao, Yuchen Wei, Mingjing Luo, Guoping Zhao, Haokui Zhou · 2019 · Genome biology
Leveling up citizen science
Jérôme Waldispühl, Attila Szantner, Rob D. Knight, Sébastien Caisse, Randy Pitchford · 2020 · Nature Biotechnology
Dietary fiber and the microbiota: A narrative review by a group of experts from the Asociación Mexicana de Gastroenterología
A.T. Abreu y Abreu, María del Pilar Milke-García, G.A. Argüello-Arévalo, Ana María Calderón de la Barca, Ramón Carmona-Sánchez, Alejandra Consuelo‐Sánchez, Enrique Coss‐Adame, Maria F. Garcia Cedillo, Vanessa Hernández-Rosiles, María Eugenia Icaza-Chávez et al. · 2021 · Revista de Gastroenterología de México (English Edition)
Clean room microbiome complexity impacts planetary protection bioburden
Ryan Hendrickson, Camilla Urbaniak, Jeremiah J. Minich, Heidi S. Aronson, Cameron Martino, Ramūnas Stepanauskas, Rob D. Knight, Kasthuri J. Venkateswaran · 2021 · Microbiome
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity
Cameron Martino, Benjamin P. Kellman, Daniel R. Sandoval, Thomas Mandel Clausen, Clarisse A. Marotz, Se Jin Song, Stephen Wandro, Livia Soares Zaramela, Rodolfo Antonio Salido Benítez, Qiyun Zhu et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
Beta-diversity distance matrices for microbiome sample size and power calculations — How to obtain good estimates
By IMPACTT investigators · 2022 · Computational and Structural Biotechnology Journal
Calour: an Interactive, Microbe-Centric Analysis Tool
Zhenjiang Zech Xu, Amnon Amir, Jon G. Sanders, Qiyun Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Wei Huang, Daniel T. McDonald, Lingjing Jiang et al. · 2019 · mSystems
Equivolumetric Protocol Generates Library Sizes Proportional to Total Microbial Load in 16S Amplicon Sequencing
Giuliano Netto Flores Cruz, Ana Paula Christoff, Luiz Felipe Valter de Oliveira · 2021 · Frontiers in Microbiology
Best Practices for Microbiome Study Design in Companion Animal Research
Jessica K. Jarett, Dawn D. Kingsbury, Katherine E. Dahlhausen, Holly H. Ganz · 2021 · Frontiers in Veterinary Science
Tree-aggregated predictive modeling of microbiome data
Jacob Bien, Xiaohan Yan, Léo Simpson, Christian L. Müller · 2021 · Scientific Reports
Associations between the Gut Microbiome and Migraines in Children Aged 7-18 Years: An Analysis of the American Gut Project Cohort
Jinbing Bai, Natalie Shen, Yanqun Liu · 2022 · Pain Management Nursing
NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters
Tiago Leão, Mingxun Wang, Ricardo Silva, Alexey A. Gurevich, Anelize Bauermeister, Paulo Wender Portal Gomes, Asker Brejnrod, Evgenia Glukhov, Allegra T. Aron, Joris J. R. Louwen et al. · 2022 · PNAS Nexus
Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy
Grazia Maria Vernaci, Edoardo Vincenzo Savarino, Ilaria Patuzzi, Sonia Facchin, Fabiana Zingone, Davide Massa, Giovanni Faggioni, Tommaso Giarratano, Federica Miglietta, Gaia Griguolo et al. · 2023 · The Oncologist
Are microbiome studies ready for hypothesis-driven research?
Anupriya Tripathi, Clarisse A. Marotz, Antonio González, Yoshiki Vázquez‐Baeza, Se Jin Song, Amina Bouslimani, Daniel T. McDonald, Qiyun Zhu, Jon G. Sanders, Larry L. Smarr et al. · 2018 · Current Opinion in Microbiology
Method development for cross-study microbiome data mining: Challenges and opportunities
Xiaoquan Su, Gongchao Jing, Yufeng Zhang, Shunyao Wu · 2020 · Computational and Structural Biotechnology Journal
Yeast β-glucan reduces obesity-associated Bilophila abundance and modulates bile acid metabolism in healthy and high-fat diet mouse models
Sik Yu So, Qinglong Wu, Kin Sum Leung, Zuzanna Maria Kundi, Tor Savidge, Hani S El-Nezami · 2021 · American Journal of Physiology-Gastrointestinal and Liver Physiology
Ecosystem-specific microbiota and microbiome databases in the era of big data
Victor P. Lobanov, Angélique Gobet, Alyssa Joyce · 2022 · Environmental Microbiome
Role of the Microbiome and Diet for Response to Cancer Checkpoint Immunotherapy: A Narrative Review of Clinical Trials
Gamrath, Lone, Pedersen, Tobias Bruun, Møller, Martin Vad, Volmer, Lone Marie, Holst-Christensen, Linda, Vestermark, Lene Weber, Donskov, Frede · 2025 · Current Oncology Reports
Detecting personal microbiota signatures at artificial crime scenes
Jarrad Hampton‐Marcell, Peter Emil Larsen, Tifani Anton, Lauren E. Cralle, Naseer Sangwan, Simon M. Lax, Neil Gottel, Mariana Salas Garcia, Candace Young, George T. Duncan et al. · 2020 · Forensic Science International
D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies
Jun Chen, Xianyang Zhang · 2021 · Bioinformatics