Multivariable association discovery in population-scale meta-omics studies

Mallick, Himel, Rahnavard, Ali, McIver, Lauren J., Ma, Siyuan, Zhang, Yancong, Nguyen, Long H., Tickle, Timothy L., Weingart, George, Ren, Boyu, Schwager, Emma H., Chatterjee, Suvo, Thompson, Kelsey N., Wilkinson, Jeremy E., Subramanian, Ayshwarya, Lu, Yiren, Waldron, Levi, Paulson, Joseph N., Franzosa, Eric A., Bravo, Hector Corrada, Huttenhower, Curtis·2021·PLOS Computational Biology

DOI 10.1371/journal.pcbi.1009442

Cited by (1,002)

Items 101–200 of 1,002

A statistical model for describing and simulating microbial community profiles
Siyuan Ma, Boyu Ren, Himel Mallick, Yo Sup Moon, Emma Schwager, Sagun Maharjan, Timothy L. Tickle, Yiren Lu, Rachel N. Carmody, Eric A. Franzosa et al. · 2021 · PLoS Computational Biology
Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics
Teija Ojala, Aino-Elina Häkkinen, Esko M Kankuri, Matti Kankainen · 2023 · Trends in Genetics
Staphylococcal diversity in atopic dermatitis from an individual to a global scale
Sara Saheb Kashaf, Catriona P. Harkins, Clay Deming, Payal Joglekar, Sean Conlan, Cassandra J. Holmes, Alexandre Almeida, Robert D. Finn, Julia A. Segre, Heidi H. Kong · 2023 · Cell Host & Microbe
Host and environmental factors shape upper airway microbiota and respiratory health across the human lifespan
Mari-Lee Odendaal, Wouter A. A. de Steenhuijsen Piters, Eelco Franz, Mei Ling J. N. Chu, James A. Groot, Elske M. van Logchem, Raïza Hasrat, Sjoerd Kuiling, Roan Pijnacker, Rob Mariman et al. · 2024 · Cell
Investigating differential abundance methods in microbiome data: A benchmark study
Marco Cappellato, Giacomo Baruzzo, Barbara Di Camillo · 2022 · PLoS Computational Biology
RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities
Ya Wang, Kelsey N. Thompson, Yan Yan, Meghan I. Short, Yancong Zhang, Eric A. Franzosa, Jiaxian Shen, Erica Marie Hartmann, Curtis Huttenhower · 2023 · Microbiome
The infant gut resistome is associated with E. coli and early-life exposures
Rebecca M. Lebeaux, Modupe Oluseun Coker, Erika F. Dade, Thomas J. Palys, Hilary G. Morrison, Benjamin D. Ross, Emily Baker, Margaret Rita Karagas, Juliette C. Madan, Anne Gatewood Hoen · 2021 · BMC Microbiology
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Jean-Sébastien Gounot, Minghao Chia, Denis Bertrand, Woei‐Yuh Saw, Aarthi Ravikrishnan, Adrian Low, Yichen Ding, Amanda Hui Qi Ng, Linda Wei Lin Tan, Yik‐Ying Teo et al. · 2022 · Nature Communications
Flavonifractor plautii Protects Against Elevated Arterial Stiffness
Shiyun Luo, Yawen Zhao, Shanshan Zhu, Ludi Liu, Ken Cheng, Bingqi Ye, Yueyuan Han, Jiahua Fan, Min Xia · 2022 · Circulation Research
Integrated Multi‐Cohort Analysis of the Parkinson's Disease Gut Metagenome
Joseph C. Boktor, Gil Sharon, Leo Verhagen Metman, Deborah A. Hall, Phillip A. Engen, Zoe J. Zreloff, Daniel Hakim, John W. Bostick, James A. Ousey, Danielle Lange et al. · 2023 · Movement Disorders
The gut microbiome affects response of treatments in HER2‐negative advanced gastric cancer
Zihan Han, Siyuan Cheng, Die Dai, Yan Kou, Xiaotian Zhang, Fang Li, Xiaochen Yin, Jingjing Ji, Zhikuan Zhang, Xi Wang et al. · 2023 · Clinical and Translational Medicine
Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation
Fuyong Li, Anissa M. Armet, Katri Korpela, Junhong Liu, Rodrigo Margain Quevedo, Francesco Asnicar, Benjamin Seethaler, Tianna Rusnak, Janis L. Cole, Zhihong Zhang et al. · 2025 · Cell
Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis
Ammer-Herrmenau, Christoph, Antweiler, Kai L, Asendorf, Thomas, Beyer, Georg, Buchholz, Soeren M, Cameron, Silke, Capurso, Gabriele, Damm, Marko, Dang, Linh, Frost, Fabian et al. · 2024 · Gut
Disordered development of gut microbiome interferes with the establishment of the gut ecosystem during early childhood with atopic dermatitis
Min-Jung Lee, Yoon Mee Park, Byunghyun Kim, In Hwan Tae, Nam-Eun Kim, Marina Pranata, Taewon Kim, Sungho Won, Nam Joo Kang, Dong‐Woo Lee et al. · 2022 · Gut Microbes
The epithelial-specific ER stress sensor ERN2/IRE1β enables host-microbiota crosstalk to affect colon goblet cell development
Grey, Michael J., De Luca, Heidi, Ward, Doyle V., Kreulen, Irini A.M., Bugda Gwilt, Katlynn, Foley, Sage E., Thiagarajah, Jay R., McCormick, Beth A., Turner, Jerrold R., Lencer, Wayne I. · 2022 · Journal of Clinical Investigation
Old age and other factors associated with salivary microbiome variation
JOEL L. SCHWARTZ, Natalia Peña, Nadia I. Kawar, Andrew Zhang, Nicholas F. Callahan, Steven J. Robles, Andrew Griebel, Guy R. Adami · 2021 · BMC Oral Health
Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort
Süleyman Yıldırım, Özkan Ufuk Nalbantoğlu, Abdulahad Bayraktar, Fatma Betül Ercan, Aycan Gündoğdu, Halil Aziz Velioğlu, Mehmet Fatih Göl, Ayten Ekinci, Fatma Koç, Ezgi Aslan-Gülpınar et al. · 2022 · mSystems
Alterations of the Composition and Neurometabolic Profile of Human Gut Microbiota in Major Depressive Disorder
Alexey S. Kovtun, Olga V. Averina, Irina Y. Angelova, Roman А. Yunes, Yana Zorkina, Anna Y. Morozova, Alexey V. Pavlichenko, Timur Syunyakov, Olga Karpenko, Georgiy P. Kostyuk et al. · 2022 · Biomedicines
Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial
Suryang Kwak, JooHee Choi, Tiffany Hink, Kimberly A. Reske, Ken Blount, Courtney R. Jones, Margaret H. Bost, Xiaoqing Sun, Carey‐Ann D. Burnham, Erik R. Dubberke et al. · 2020 · Microbiome
Meta-analysis of shotgun sequencing of gut microbiota in Parkinson’s disease
Hiroshi Nishiwaki, Jun Ueyama, Mikako Ito, Tomonari Hamaguchi, Keiichi Takimoto, Tetsuya Maeda, Kenichi Kashihara, Yoshio Tsuboi, Hiroshi Mori, Ken Kurokawa et al. · 2024 · npj Parkinson s Disease
Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats
Kangpeng Xiao, Xianghui Liang, Haoran Lu, Xiaobing Li, Zhipeng Zhang, Xingbang Lu, Hai Wang, Yafei Meng, Ayan Roy, Wen Luo et al. · 2022 · The ISME Journal
Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition
Dena Ennis, Shimrit Shmorak, Evelyn Jantscher‐Krenn, Moran Yassour · 2024 · Nature Communications
Layer chicken microbiota: a comprehensive analysis of spatial and temporal dynamics across all major gut sections
Yadav Sharma Bajagai, Thi Thu Hao Van, Nitish Joat, Kapil K. Chousalkar, Robert J. Moore, Dragana Stanley · 2024 · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology
Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota
Shaqed Carasso, Rawan Zaatry, Haitham Hajjo, Dana Kadosh-Kariti, Nadav Ben-Assa, Rawi Naddaf, Noa Mandelbaum, Sigal Pressman, Yehuda Chowers, Tal Gefen et al. · 2024 · Cell Host & Microbe
Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation
Leonardo Mancabelli, Christian Milani, Rosita De Biase, Fabiana Bocchio, Federico Fontana, Gabriele Andrea Lugli, Giulia Alessandri, Chiara Tarracchini, Alice Viappiani, Flora De Conto et al. · 2024 · mSystems
Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer
Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu et al. · 2024 · Nature Communications
Protection of Alzheimer’s disease progression by a human-origin probiotics cocktail
Santosh Kumar Prajapati, Shaohua Wang, Sidharth Prasad Mishra, Shalini Jain, Hariom Yadav · 2025 · Scientific Reports
Cecal Microbiota Transfer Rescues Antibiotic-Induced Acceleration of Type 1 Diabetes and Alteration of Intestinal Gene Expression
Xue‐Song Zhang, Yue Sandra Yin, Jincheng Wang, Thomas Battaglia, Kimberly A. Krautkramer, Wei Vivian Li, Jackie Li, Mark Brown, Meifan Zhang, Michelle H. Badri et al. · 2021 · Cell Host & Microbe
Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes
Palacios, Natalia, Wilkinson, Jeremy, Bjornevik, Kjetil, Schwarzschild, Michael A., McIver, Lauren, Ascherio, Alberto, Huttenhower, Curtis · 2023 · Annals of Neurology
The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice
Zhirui Cao, Dejun Fan, Yang Sun, Ziyu Huang, Yue Li, Runping Su, Feng Zhang, Qing Li, Hongju Yang, Fen Zhang et al. · 2024 · Nature Communications
Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects
Orlando DeLeon, Mora Mocanu, Alan Tan, Ashley M. Sidebottom, Jason Koval, Hugo Dugolin Ceccato, Sarah E. Kralicek, John J Colgan, Marissa M. St. George, Joash Lake et al. · 2025 · Cell
The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome
Zhongyu Mou, Yi‐Yan Yang, Andrew Brantley Hall, Xiaofang Jiang · 2021 · BMC Genomics
A Low Glycemic Index Mediterranean Diet Combined with Aerobic Physical Activity Rearranges the Gut Microbiota Signature in NAFLD Patients
Francesco Maria Calabrese, Vittoria Disciglio, Isabella Franco, Paolo Sorino, Caterina Bonfiglio, Antonella Bianco, Angelo Campanella, Tamara Lippolis, Pasqua Letizia Pesole, Maurizio Gaetano Polignano et al. · 2022 · Nutrients
A metagenomic catalog of the early-life human gut virome
Shuqin Zeng, Alexandre Almeida, Shiping Li, Junjie Ying, Hua Wang, Yi Qu, R. Paul Ross, Catherine Stanton, Zhemin Zhou, Xiaoyu Niu et al. · 2024 · Nature Communications
Male‐Biased Gut Microbiome and Metabolites Aggravate Colorectal Cancer Development
Ling Wang, Yi‐Xuan Tu, Lu Chen, Yuan Zhang, Xue‐Ling Pan, Shu‐Qiao Yang, Shuai‐Jie Zhang, Shenghui Li, Ke‐Chun Yu, Shuo Song et al. · 2023 · Advanced Science
Lactobacillaceae differentially impact butyrate-producing gut microbiota to drive CNS autoimmunity
Theresa L. Montgomery, Lucinda C. Toppen, Korin M. Eckstrom, Eamonn R. Heney, Josephine J. Kennedy, Matthew Scarborough, Dimitry N. Krementsov · 2024 · Gut Microbes
Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins
Robin Mesnage, Ruth C. E. Bowyer, Souleiman El Balkhi, Franck Saint‐Marcoux, Arnaud Gardere, Quinten R. Ducarmon, Anoecim Robecca Geelen, Romy Daniëlle Zwittink, Dimitris Tsoukalas, Evangelia Sarandi et al. · 2022 · Environmental Health
Plasticity of the adult human small intestinal stoma microbiota
Bahtiyar Yılmaz, Tobias Fuhrer, Deborah Morgenthaler, Niklas Krupka, Daoming Wang, Daniel Spari, Daniel Candinas, Benjamin Misselwitz, Guido Beldi, Uwe Sauer et al. · 2022 · Cell Host & Microbe
Gut microbiota suppress feeding induced by palatable foods
James A. Ousey, Joseph C. Boktor, Sarkis K. Mazmanian · 2022 · Current Biology
Lifestyle patterns influence the composition of the gut microbiome in a healthy Chinese population
Yi Ren, Jiawei Wu, Yilin Wang, Lanying Zhang, Jing Ren, Zhiming Zhang, Binghan Chen, Kejian Zhang, Baoli Zhu, Wei Yong Liu et al. · 2023 · Scientific Reports
Gut microbiota produces biofilm-associated amyloids with potential for neurodegeneration
Ariadna Fernández-Calvet, Leticia Matilla-Cuenca, María Izco, Susanna Navarro, Miriam Serrano, Salvador Ventura, Javier Blesa, Maite Herráiz, Gorka Alkorta‐Aranburu, Sergio Galera et al. · 2024 · Nature Communications
Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants
Robert Thänert, Drew J. Schwartz, Eric C. Keen, Carla M. Hall-Moore, Bin Wang, Nurmohammad Shaikh, Jie Ning, L Colleen Rouggly-Nickless, Anna Thänert, Aura L. Ferreiro et al. · 2024 · Cell Host & Microbe
Development of the oral resistome during the first decade of life
Smitha Sukumar, Fang Wang, Carra A. Simpson, Cali E. Willet, Tracy Chew, Toby E Hughes, Michelle R. Bockmann, Rosemarie Sadsad, Fjelda Elizabeth Martin, Henry W. Lydecker et al. · 2023 · Nature Communications
Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans
Naama Lang‐Yona, J. Michel Flores, Rotem Haviv, Adriana Alberti, Julie Poulain, Caroline Belser, Miri Trainic, Daniella Gat, Hans‐Joachim Ruscheweyh, Patrick Wincker et al. · 2022 · Communications Earth & Environment
Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes
Santosh Lamichhane, Partho Sen, Alex M. Dickens, Marina Amaral Alves, Taina Härkönen, Jarno K. Honkanen, Tommi Vatanen, Ramnik J. Xavier, Tuulia Hyötyläinen, Mikael Knip et al. · 2022 · Cell Reports Medicine
Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes
Kelsey N. Thompson, Kevin Scott Bonham, Nicholas Edward Ilott, Graham J. Britton, Paula Colmenero, Samuel J. Bullers, Lauren J. McIver, Siyuan Ma, Long Hoang Nguyen, Andrew D. Filer et al. · 2023 · Science Translational Medicine
Convergent dysbiosis of gastric mucosa and fluid microbiome during stomach carcinogenesis
Cong He, Chao Peng, Xu Shu, Huan Wang, Zhenhua Zhu, Yaobin Ouyang, Xiaoyu Yang, Chuan Xie, Yi Hu, Nianshuang Li et al. · 2022 · Gastric Cancer
Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation
Sara Ricci, Cátia Pacífico, Ezequias Castillo‐Lopez, Raul Rivera‐Chacon, Heidi Schwartz, Nicole Reisinger, Franz Berthiller, Qendrim Zebeli, Renee Maxine Petri · 2022 · Frontiers in Microbiology
Delivery mechanism can enhance probiotic activity against honey bee pathogens
Brendan A. Daisley, Andrew P. Pitek, Christina Torres, Robin Lowery, Bethany A Adair, Kait F. Al, Bernardo D. Niño, Jeremy P. Burton, Emma Allen‐Vercoe, Graham Thompson et al. · 2023 · The ISME Journal
Fecal microbiota transplantation to prevent acute graft-versus-host disease: pre-planned interim analysis of donor effect
Swetha Reddi, Liliia Senyshyn, Maryam Ebadi, Daniel Podlesny, Samuel S. Minot, Ted Alan Gooley, Amanda J. Kabage, Geoffrey R. Hill, Stephanie Joi Lee, Alexander Khoruts et al. · 2025 · Nature Communications
Non-antibiotics disrupt colonization resistance against enteropathogens
Anne Grießhammer, Jacobo de la Cuesta‐Zuluaga, Patrick Müller, Cordula Gekeler, Jan Homolak, Hsuan Chang, Katharina Schmitt, Chiara Planker, Verena Schmidtchen, Suchira Gallage et al. · 2025 · Nature
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers
Alaric W. D’Souza, Manish Boolchandani, Sanket Patel, Gianluca Galazzo, Jarne M. van Hattem, Maris S. Arcilla, Damian C. Melles∗, Menno D. de Jong, Constance Schultsz, Martin Bootsma et al. · 2021 · Genome Medicine
Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture
Andrea Quagliariello, Alessandra Modi, Gabriel Innocenti, Valentina Zaro, Cecilia Conati Barbaro, Annamaria Ronchitelli, Francesco Boschin, Claudio Cavazzuti, Elena Dellù, Francesca Radina et al. · 2022 · Nature Communications
Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity
Xinliang Hu, Chong Ho Alex Yu, Yuting He, Songling Zhu, Shuang Wang, Ziqiong Xu, Shaohui You, Yanlei Jiao, Shu‐Lin Liu, Hongxia Bao · 2024 · BMC Microbiology
The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation
Samat Amat, Devin B. Holman, Kaycie N. Schmidt, Ana Clara B Menezes, Friederike Baumgaertner, Thomas Winders, James D Kirsch, Tingting Liu, Timothy Damian Schwinghamer, Kevin K K Sedivec et al. · 2021 · Microorganisms
Associations between maternal obesity and offspring gut microbiome in the first year of life
Stephanie P. Gilley, Meghan Lynne Ruebel, Clark R. Sims, Ying Zhong, Donald Turner, Renny Shang-Lun Lan, Lindsay Pack, Brian D. Piccolo, Sree Vamsee Chintapalli, Ann Abraham et al. · 2022 · Pediatric Obesity
Impact of international travel and diarrhea on gut microbiome and resistome dynamics
Manish Boolchandani, Kevin S. Blake, Drake Hamilton Tilley, Miguel M. Cabada, Drew J. Schwartz, Sanket Patel, Maria Luisa Morales, Rina A. Meza, Giselle M. Soto, Sandra D. Isidean et al. · 2022 · Nature Communications
Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis
Jianjun Liu, Qiulong Yan, Shenghui Li, Juying Jiao, Yiming Hao, Guixin Zhang, Qingkai Zhang, Fei Luo, Yue Zhang, Qingbo Lv et al. · 2024 · npj Biofilms and Microbiomes
G ut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine
Henok Ayalew Tegegne, Tor Savidge · 2025 · Gut Microbes
Changes in Gut Microbiota after a Four-Week Intervention with Vegan vs. Meat-Rich Diets in Healthy Participants: A Randomized Controlled Trial
Eva Kohnert, Clemens Kreutz, Nadine Binder, Luciana Hannibal, Gregor Gorkiewicz, Alexander Müller, Maximilian Andreas Storz, Roman Huber, Ann‐Kathrin Lederer · 2021 · Microorganisms
Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes
Devin B. Holman, Arun Kommadath, Jeffrey P. Tingley, D. Wade Abbott · 2022 · Microbiology Spectrum
Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion
Jennifer A. Fulcher, Fan Li, Nicole H. Tobin, Sara Zabih, Julie E. Elliott, Jesse L. Clark, Richard T. D’Aquila, Brian S. Mustanski, Michele D. Kipke, STEVEN J. SHOPTAW et al. · 2022 · EBioMedicine
Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?
Robert M. Hechler, Matthew C. Yates, Frédéric J. J. Chain, Melania E. Cristescu · 2023 · Molecular Ecology
Microbial and metabolic profiles unveil mutualistic microbe-microbe interaction in obesity-related colorectal cancer
Jinming Li, Ziying Chen, Qinying Wang, Lutao Du, Yongzhi Peter Yang, Fanying Guo, Xinxiang Li, Yanjie Chao, Yanlei Ma · 2024 · Cell Reports Medicine
Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach
Tomás Clive Barker‐Tejeda, Elisa Zubeldia‐Varela, Andrea Macías‐Camero, Lola Alonso, Isabel Adoración Martín‐Antoniano, Fernanda Rey-Stolle, Leticia Mera‐Berriatua, Raphaëlle Bazire, Paula Cabrera‐Freitag, Meera Shanmuganathan et al. · 2024 · Nature Communications
Human Gut Microbiota for Diagnosis and Treatment of Depression
Olga V. Averina, Elena U. Poluektova, Yana Zorkina, Alexey S. Kovtun, В. Н. Даниленко · 2024 · International Journal of Molecular Sciences
A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies
Jakob Wirbel, Morgan Essex, Sofia Kirke Forslund, Georg Zeller · 2024 · Genome biology
A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide
S. Emil Ruff, Isabella Hrabě de Angelis, Megan M. Mullis, Jérôme P. Payet, Cara Magnabosco, Karen G. Lloyd, Cody S. Sheik, Andrew D. Steen, Anna Shipunova, Aleksey Morozov et al. · 2024 · Science Advances
Diversity and biogeography of the bacterial microbiome in glacier-fed streams
Leïla Ezzat, Hannes Peter, Massimo Bourquin, Susheel Bhanu Busi, Grégoire Michoud, Stilianos Fodelianakis, Tyler J. Kohler, Thomas Lamy, Aileen Ute Geers, Paraskevi V. Pramateftaki et al. · 2025 · Nature
The Influence of an AI-Driven Personalized Nutrition Program on the Human Gut Microbiome and Its Health Implications
Konstantinos Rouskas, Mary Guela, Marianna Pantoura, Ioannis G. Pagkalos, Maria N. Hassapidou, Elena Lalama, Andreas F. H. Pfeiffer, Elise Decorte, Véronique Cornelissen, Saskia Wilson-Barnes et al. · 2025 · Nutrients
Sex-specific relationships of the infant microbiome and early-childhood behavioral outcomes
Hannah E. Laue, Margaret Rita Karagas, Modupe Oluseun Coker, David C. Bellinger, Emily Baker, Susan Korrick, Juliette C. Madan · 2021 · Pediatric Research
Association between gut microbiome-related metabolites and symptomatic hand osteoarthritis in two independent cohorts
Jie Wei, Zidan Yang, Jiatian Li, Yuqing Zhang, Weiya Zhang, Michael Doherty, Tuo Yang, Yuanheng Yang, Hui Li, Yilun Wang et al. · 2023 · EBioMedicine
Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation
Elkrief, Arielle, Waters, Nicholas R., Smith, Natalie, Dai, Angel, Slingerland, John, Aleynick, Nathan, Febles, Binita, Gogia, Pooja, Socci, Nicholas D., Lumish, Melissa et al. · 2024 · Cancer Immunology Research
Transmission and dynamics of mother-infant gut viruses during pregnancy and early life
Sanzhima Garmaeva, Trishla Sinha, Anastasia A. Gulyaeva, Nataliia Kuzub, Johanne E. Spreckels, Sergio Andreu‐Sánchez, Ranko Gaćeša, Arnau Vich Vila, Siobhan Brushett, Marloes Kruk et al. · 2024 · Nature Communications
Interaction effect between NAFLD severity and high carbohydrate diet on gut microbiome alteration and hepatic de novo lipogenesis
Hyena Kang, Hyun Ju You, Giljae Lee, Seung Hyun Lee, Taekyeong Yoo, Murim Choi, Sae Kyung Joo, Jeong Hwan Park, Mee Soo Chang, Dong Hyeon Lee et al. · 2022 · Gut Microbes
Conditioning Regimens are Associated with Distinct Patterns of Microbiota Injury in Allogeneic Hematopoietic Cell Transplantation
Roni Shouval, Nicholas R. Waters, Antonio L. C. Gomes, Corrado Zuanelli Brambilla, Teng Fei, Sean M. Devlin, Chi L. Nguyen, Kate Ann Markey, Anqi Dai, John B. Slingerland et al. · 2022 · Clinical Cancer Research
Candida albicans accelerates atherosclerosis by activating intestinal hypoxia-inducible factor2α signaling
Xuemei Wang, Shuang Zhou, Xiaomin Hu, Chuan Ye, Qixing Nie, Kai Wang, Sen Yan, Jun Lin, Feng Xu, Meng Li et al. · 2024 · Cell Host & Microbe
Chlorhexidine digluconate mouthwash alters the oral microbial composition and affects the prevalence of antimicrobial resistance genes
Sibylle Bartsch, Eva Kohnert, Clemens Kreutz, Johan Peter Woelber, Annette Carola Anderson, Ann-Sophie Burkhardt, Elmar Hellwig, Wolfgang Buchalla, Karl‐Anton Hiller, Petra Ratka‐Krueger et al. · 2024 · Frontiers in Microbiology
Identification of commensal gut microbiota signatures as predictors of clinical severity and disease progression in multiple sclerosis
Theresa L. Montgomery, Qin Wang, Ali Mirza, Deanna Dwyer, Qi Wu, Catherine A. Dowling, Jacob William Shelton Martens, Jennifer Yang, Dimitry N. Krementsov, Yang Mao‐Draayer · 2024 · Scientific Reports
Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer’s disease
Longhao Jia, Yize Ke, Shuo Zhao, Jinxin Liu, Xiaohui Luo, Jixin Cao, Yujia Liu, Qihao Guo, Wei‐Hua Chen, Feng Chen et al. · 2025 · Molecular Psychiatry
SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition
Tzipi Braun, Shiraz Halevi, Rotem Hadar, Gilat Efroni, Efrat G. Saar, Natahan Keller, Amnon Amir, Sharon Amit, Yael Haberman · 2021 · Scientific Reports
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
Source of human milk (mother or donor) is more important than fortifier type (human or bovine) in shaping the preterm infant microbiome
Shreyas V. Kumbhare, William-Diehl Jones, Sharla Fast, Christine Bonner, Geert W. ‘t Jong, Gary Van Domselaar, Morag Graham, Michael R Narvey, Meghan B. Azad · 2022 · Cell Reports Medicine
Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets
Yanxian Li, Karina Gajardo, Alexander Jaramillo-Torres, Trond M. Kortner, Åshild Krogdahl · 2022 · Animal Microbiome
Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population
Xiaowu Bai, Yang Sun, Yue Li, Maojuan Li, Zhirui Cao, Ziyu Huang, Feng Zhang, Ping Yan, Lan Wang, Juan Luo et al. · 2022 · Microbiome
Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study
David J. M. Barnett, Martha F. Endika, Cynthia E. Klostermann, Fangjie Gu, Carel T. Thijs, Arjen Nauta, Henk Arie Schols, Hauke Smidt, Ilja C.W. Arts, John Penders · 2023 · Gut Microbes
Intratumoral microbiome is driven by metastatic site and associated with immune histopathological parameters: An ancillary study of the SHIVA clinical trial
Marc Hilmi, Maud T Kamal, Sophie Vacher, Célia Dupain, Sabrina Ibadioune, Maral Halladjian, Marie Paule Sablin, Grégoire Marret, Zahra Castel Ajgal, Michèle Nijnikoff et al. · 2023 · European Journal of Cancer
Multigenerational adversity impacts on human gut microbiome composition and socioemotional functioning in early childhood
Francesca R. Querdasi, Craig K. Enders, Neerja Karnani, Birit F. P. Broekman, Chong Yap Seng, Peter David Gluckman, Lourdes Mary Daniel, Fabian K. P. Yap, Johan Gunnar Eriksson, Shirong Cai et al. · 2023 · Proceedings of the National Academy of Sciences
Antibiotics taken within the first year of life are linked to infant gut microbiome disruption and elevated atopic dermatitis risk
Courtney Hoskinson, Maria Medeleanu, Myrtha E. Reyna, Darlene Liying Dai, Biswajit Chowdhury, Theo J. Moraes, Piush J. Mandhane, Elinor Simons, Anita Luba Kozyrskyj, Meghan B. Azad et al. · 2024 · Journal of Allergy and Clinical Immunology
A yeast-based oral therapeutic delivers immune checkpoint inhibitors to reduce intestinal tumor burden
Olivia N. Rebeck, Miranda J. Wallace, Jerome Prusa, Jie Ning, Esse M. Evbuomwan, Sunaina Rengarajan, LeMoyne Habimana-Griffin, Suryang Kwak, David Zahrah, Jason Tung et al. · 2024 · Cell chemical biology
Associations between Maternal Diet, Body Composition and Gut Microbial Ecology in Pregnancy
Meghan Lynne Ruebel, Stephanie P. Gilley, Clark R. Sims, Ying Zhong, Donald Turner, Sree Vamsee Chintapalli, Brian D. Piccolo, Aline Andres, Kartik Shankar · 2021 · Nutrients
Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth
Todd Testerman, Zhongyao Li, Brittany Galuppo, Joerg Graf, Nicola Santoro · 2022 · Hepatology Communications
Rural environment reduces allergic inflammation by modulating the gut microbiota
Zhaowei Yang, Zhong Chen, Xinliu Lin, Siyang Yao, Mo Xian, Xiaoping Ning, Wanyi Fu, Mei Jiang, Naijian Li, Xiaojun Xiao et al. · 2022 · Gut Microbes
Ecology of the respiratory tract microbiome
Ana Elena Pérez‐Cobas, Jerónimo Rodríguez-Beltrán, Fernando Baquero, Teresa M. Coque · 2023 · Trends in Microbiology
Short- and long-term effects of continuous compost amendment on soil microbiome community
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