Metagenomic microbial community profiling using unique clade-specific marker genes

Segata, Nicola, Waldron, Levi, Ballarini, Annalisa, Narasimhan, Vagheesh, Jousson, Olivier, Huttenhower, Curtis·2012·Nature Methods

Cited by (1,002)

Items 501–600 of 1,002

  1. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods
    Meghana Srinivas, Órla O’Sullivan, Paul D. Cotter, Douwe van Sinderen, John G. Kenny · 2022 · Foods
  2. A deep learning approach to pattern recognition for short DNA sequences
    Akosua Busia, George E. Dahl, Clara Fannjiang, David H. Alexander, Elizabeth H. Dorfman, Ryan E. Poplin, Cory Y. McLean, Pi-Chuan Chang, Mark A. DePristo · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  3. Metagenomic and metabolomic analysis of the toxic effects of trichloroacetamide-induced gut microbiome and urine metabolome perturbations in mice
    Zhang, Yan, Zhao, Fuzheng, Deng, Yongfeng, Zhao, Yanping, Ren, Hongqiang · 2015 · Journal of Proteome Research
  4. Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans
    B. Anne Neville, Paul O. Sheridan, Hugh M. B. Harris, Simone Coughlan, Harry James Flint, Sylvia H. Duncan, Ian B. Jeffery, Marcus Joakim Claesson, R. Paul Ross, Karen P. Scott et al. · 2013 · PLoS ONE
  5. 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
  6. Prospects for multi-omics in the microbial ecology of water engineering
    Elizabeth McDaniel, A. Wahl, Shun’ichi Ishii, Ameet J. Pinto, Ryan M. Ziels, Per Halkjær Nielsen, Katherine D. McMahon, Rohan B. H. Williams · 2021 · Water Research
  7. Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring
    Emily Garner, Ayella Maile-Moskowitz, Luisa F. Angeles, Carl‐Fredrik Flach, Diana S. Aga, Indumathi Manivannan Nambi, D. G. Joakim Larsson, Helmut Bürgmann, Tong Zhang, Peter J. Vikesland et al. · 2024 · Environmental Science & Technology
  8. Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches
    Cervin Guyomar, Fabrice Legeai, Emmanuelle Jousselin, Christophe Mougel, Claire Lemaitre, Jean‐Christophe Simon · 2018 · Microbiome
  9. Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
    Min Yap, Conor Feehily, Calum J. Walsh, Mark A. Fenelon, Eileen F. Murphy, Fionnuala Mary McAuliffe, Douwe van Sinderen, Paul William O’Toole, Órla O’Sullivan, Paul D. Cotter · 2020 · Scientific Reports
  10. 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
  11. Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities
    Fabien Cottier, Kandhadayar Gopalan Srinivasan, Marina Yurieva, Webber W. P. Liao, Michael Poidinger, Francesca Zolezzi, Norman Pavelka · 2018 · npj Biofilms and Microbiomes
  12. The Gut Microbiome Dynamically Associates with Host Glucose Metabolism throughout Pregnancy: Longitudinal Findings from a Matched Case‐Control Study of Gestational Diabetes Mellitus
    Zhonghan Sun, Xiong‐Fei Pan, Xiao Li, Limiao Jiang, Ping Hu, Yi Wang, Yi Ye, Ping Wu, Bin Zhao, Jianguo Xu et al. · 2023 · Advanced Science
  13. Metatranscriptomic Evidence for Co-Occurring Top-Down and Bottom-Up Controls on Toxic Cyanobacterial Communities
    Morgan M. Steffen, B. Shafer Belisle, Sue B. Watson, Gregory L. Boyer, Richard A. Bourbonniere, Steven W. Wilhelm · 2015 · Applied and Environmental Microbiology
  14. Shotgun microbial profiling of fossil remains
    Clio S. I. Der Sarkissian, Luca Ermini, Hákon Jónsson, Anatoly Nikoyevich Alekseev, Éric Crubézy, Beth Shapiro, Ludovic Orlando · 2014 · Molecular Ecology
  15. Functional analysis of gut microbiota and immunoinflammation in children with autism spectrum disorders
    Claudia Carissimi, Ilaria Laudadio, Francesca Palone, Valerio Fulci, Vincenzo Cesi, Francesco Cardona, Chiara Alfonsi, Salvatore Cucchiara, Sara Isoldi, Laura Stronati · 2019 · Digestive and Liver Disease
  16. Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis)
    Fábio Augusto Vannucci, Douglas N. Foster, Connie Jane Gebhart · 2013 · BMC Genomics
  17. Clinical metagenomic analysis of bacterial communities in breast abscesses of granulomatous mastitis
    Haijing Yu, Hua Deng, Jian Ma, Shujun Huang, Jianmin Yang, Yan-fen Huang, Xiaoping Mu, Liang Zhang, Qi Wang · 2016 · International Journal of Infectious Diseases
  18. MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes
    Pierre Péricard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet · 2017 · Bioinformatics
  19. Effect of implant cleaning on titanium particle dissolution and cytocompatibility
    Georgios A. Kotsakis, Rachel M. Black, Jason Kum, Larissa Oliveira Berbel, Ali Sadr, Ioannis K. Karoussis, Mara Simopoulou, Diane M. Daubert · 2020 · Journal of Periodontology
  20. Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution
    Rogan Carr, Shai S. Shen-Orr, Elhanan Borenstein · 2013 · PLoS Computational Biology
  21. Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)
    Adina Howe, Patrick Chain · 2015 · Frontiers in Microbiology
  22. The influence of the gut microbiome on BCG-induced trained immunity
    Martin Stražar, Vera P. Mourits, Valerie A. C. M. Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A. B. Joosten, Reinout van Crevel, Hera C. Vlamakis, Mihai Gheorghe Netea, Ramnik J. Xavier · 2021 · Genome biology
  23. Role of Probiotics in the Management of COVID-19: A Computational Perspective
    Quang Vo Nguyen, Li Chuin Chong, Yan-Yan Hor, Lee-Ching Lew, Irfan Ahmad Rather, Sy-Bing Choi · 2022 · Nutrients
  24. An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents
    Daphna Rothschild, Sigal Leviatan, Ariel Hanemann, Yossi Cohen, Omer Weissbrod, Eran Segal · 2022 · PLoS ONE
  25. Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma
    Anita Yvonne Voigt, Akintunde Emiola, Jethro S. Johnson, Elizabeth S. Fleming, Hoan Thi Nguyen, Wei Lan Zhou, Kenneth Yee Tsai, Christine Fink, Julia Oh · 2022 · Journal of Investigative Dermatology
  26. Successful Dietary Therapy in Paediatric Crohn’s Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls
    Charlotte M. Verburgt, Katherine A. Dunn, Mohammed Ghiboub, James D. Lewis, Eytan Wine, Rotem Sigall Boneh, Konstantinos Gerasimidis, Raanan Shamir, Susanne L. Penny, Devanand M. Pinto et al. · 2022 · Journal of Crohn s and Colitis
  27. Entropy-Scaling Search of Massive Biological Data
    Yun William Yu, Noah M. Daniels, David Danko, Bonnie Berger · 2015 · Cell Systems
  28. A genomic and historical synthesis of plague in 18th century Eurasia
    Meriam Guellil, Oliver Kersten, Amine Namouchi, Stefania Luciani, Isolina Marota, Caroline Arcini, Elisabeth Iregren, Robert A. Lindemann, Gunnar Warfvinge, Lela G. Bakanidze et al. · 2020 · Proceedings of the National Academy of Sciences
  29. Multi ‘Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway
    Adam J. Berlinberg, Emilie H. Regner, Andrew Stahly, Ana Brar, Julie A. Reisz, Mark E. Gerich, Blair P. Fennimore, Frank I. Scott, Alison E. Freeman, Kristine A. Kuhn · 2021 · Frontiers in Immunology
  30. Phage-inclusive profiling of human gut microbiomes with Phanta
    Yishay Pinto, Meenakshi Chakraborty, Navami Jain, Ami Siddharth Bhatt · 2023 · Nature Biotechnology
  31. High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
    Vahan V. Simonyan, Raja Mazumder · 2014 · Genes
  32. MetaRef: a pan-genomic database for comparative and community microbial genomics
    Katherine H Huang, Arthur Brady, Anup Mahurkar, Owen R. White, Dirk Gevers, Curtis Huttenhower, Nicola Segata · 2013 · Nucleic Acids Research
  33. Carbohydrate Staple Food Modulates Gut Microbiota of Mongolians in China
    Jing Li, Qiangchuan Hou, Jiachao Zhang, Haiyan Xu, Zhihong Sun, Bilige Menghe, Heping Zhang · 2017 · Frontiers in Microbiology
  34. A Comparative Study of the Bacterial Community in Denitrifying and Traditional Enhanced Biological Phosphorus Removal Processes
    Xiaomei Lv, Ming-Fei Shao, Chaolin Li, Ji Li, Xin-lei Gao, Feiyun Sun · 2014 · Microbes and Environments
  35. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda
    René Dommain, Morgan Andama, Molly M. McDonough, Natalia A. Prado, Tobias Goldhammer, Richard Potts, Jesús Eduardo Maldonado, John Bosco Nkurunungi, Michael G. Campana · 2020 · Frontiers in Ecology and Evolution
  36. Strain inheritance and neonatal gut microbiota development: A meta-analysis
    Daniel Podlesny, W. Florian Fricke · 2021 · International Journal of Medical Microbiology
  37. β-Glucuronidase Pattern Predicted From Gut Metagenomes Indicates Potentially Diversified Pharmacomicrobiomics
    Francesco Candeliere, Stefano Raimondi, Raffaella Ranieri, Eliana Musmeci, Alfonso Zambon, Alberto Amaretti, Maddalena Rossi · 2022 · Frontiers in Microbiology
  38. The microbiota-gut-brain-immune interface in the pathogenesis of neuroinflammatory diseases: a narrative review of the emerging literature
    Alison Warren, Yvonne Nyavor, Nikkia Zarabian, Aidan Mahoney, Leigh A. Frame · 2024 · Frontiers in Immunology
  39. Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes
    Ryan Joynson, Leighton Pritchard, Ekenakema Osemwekha, N. Ferry · 2017 · Frontiers in Microbiology
  40. MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome
    Stephen Nayfach, Michael Andrew Fischbach, Katherine S. Pollard · 2015 · Bioinformatics
  41. The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults
    Clea R. Barnett, Lama Nazzal, David S. Goldfarb, Martin J. Blaser · 2015 · The Journal of Urology
  42. The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data
    Eria Alaide Rebollar, Ana Gutiérrez‐Preciado, Cecilia A. Noecker, Alexander Eng, Myra C. Hughey, Daniel Medina, Jenifer B. Walke, Elhanan Borenstein, Roderick V. Jensen, Lisa K. Belden et al. · 2018 · Frontiers in Microbiology
  43. System performance and microbial community in ethanol-fed anaerobic reactors acclimated with different organic carbon to sulfate ratios
    Danfei Zeng, Qidong Yin, Qing Du, Guangxue Wu · 2019 · Bioresource Technology
  44. Mitochondrial perturbation in the intestine causes microbiota-dependent injury and gene signatures discriminative of inflammatory disease
    Elisabeth Urbauer, Doriane Aguanno, Nora Mindermann, Hélène Omer, Amira Metwaly, Tina Krammel, Tim Faro, Marianne Remke, Sandra Reitmeier, Stefanie Bärthel et al. · 2024 · Cell Host & Microbe
  45. Screening and Expression of Genes from Metagenomes
    Benedikt Leis, Angel Angelov, Wolfgang Liebl · 2013 · Advances in applied microbiology
  46. Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation
    Jin‐Ming Cui, Guoqin Mai, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma, Chenli Liu · 2019 · Frontiers in Microbiology
  47. Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies
    Janus Borner, Thorsten Burmester · 2017 · BMC Genomics
  48. DUDes: a top-down taxonomic profiler for metagenomics
    Vitor C. Piro, Martin S. Lindner, Bernhard Y. Renard · 2016 · Bioinformatics
  49. The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes
    Alise Jany Ponsero, Bonnie L. Hurwitz · 2019 · Frontiers in Microbiology
  50. Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics
    Reilly O. Cooper, Clayton E. Cressler · 2020 · Scientific Reports
  51. Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study
    Rojelio Mejía, Ashish V. Damania, Rebecca Jeun, Patricia E. Bryan, Paola A. Vargas, Marisa Juaréz, Pamela S. Cajal, Julio R. Nasser, Alejandro Javier Krolewiecki, Emilie Lefoulon et al. · 2020 · Parasites & Vectors
  52. Whole exome sequencing analyses reveal gene–microbiota interactions in the context of IBD
    Shixian Hu, Arnau Vich Vila, Ranko Gaćeša, Valerie Collij, Christine R. Stevens, Jack M. Fu, Isaac Wong, Michael E. Talkowski, Manuel A. Rivas, Floris Imhann et al. · 2020 · Gut
  53. Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years
    Hannah E. Laue, Susan Korrick, Emily Baker, Margaret Rita Karagas, Juliette C. Madan · 2020 · Scientific Reports
  54. Atopic dermatitis microbiomes stratify into ecologic dermotypes enabling microbial virulence and disease severity
    Angeline Su Ling Tay, Chenhao Li, Tannistha Nandi, Kern Rei Chng, Anand Kumar Andiappan, Vijaya Saradhi Mettu, Camille de Cevins, Aarthi Ravikrishnan, Charles‐Antoine Dutertre, X.F. Colin C. Wong et al. · 2020 · Journal of Allergy and Clinical Immunology
  55. Comparing Circadian Rhythmicity in the Human Gut Microbiome
    Sandra Reitmeier, Silke Kießling, Klaus Neuhaus, Dirk Haller · 2020 · STAR Protocols
  56. 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
  57. Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur
    Andre L. A. Neves, Fuyong Li, Bibaswan Ghoshal, Tim Angus McAllister, Le Luo Guan · 2017 · Frontiers in Microbiology
  58. Genome-resolved metagenomics of sugarcane vinasse bacteria
    Noriko A. Cassman, Késia Silva Lourenço, Janaína Braga do Carmo, Heitor Cantarella, Eiko E. Kuramae · 2018 · Biotechnology for Biofuels
  59. Maximal viral information recovery from sequence data using VirMAP
    Nadim J. Ajami, Matthew C. Wong, Matthew Clayton Ross, Richard E. Lloyd, Joseph F. Petrosino · 2018 · Nature Communications
  60. The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries
    Caroline Young, Henry M. Wood, Ramakrishnan Ayloor Seshadri, Pham Van Nang, Carlos Alberto Vaccaro, L Contreras, Mayilvahanan Bose, Mai Van Doi, Tamara Alejandra Piñero, Camilo Tapia Valladares et al. · 2021 · Genome Medicine
  61. Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome
    Donovan H. Parks, Fabio Rigato, Patricia Vera-Wolf, Lutz Krause, Philip Hugenholtz, Gene W. Tyson, David Wood · 2021 · Frontiers in Microbiology
  62. Critical perspectives on advancing antibiotic resistant gene (ARG) detection technologies in aquatic ecosystems
    Zainab Nassereddine, Somie Opara, Oliver Coutinho, Florent Qyteti, Reeghan Book, Matthew P. Heinicke, Jacob A. Napieralski, Sonia M. Tiquia-Arashiro · 2024 · The Science of The Total Environment
  63. Genomic Microdiversity ofBifidobacterium pseudocatenulatumUnderlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
    Guojun Gary Wu, Chenhong Zhang, Huan Wu, Ruirui Wang, Jian Shen, Linghua Wang, Yufeng Zhao, Xiaoyan Pang, Xiaojun Zhang, Liping Zhao et al. · 2017 · mBio
  64. Abundance estimation and differential testing on strain level in metagenomics data
    Martina Fischer, Benjamin Strauch, Bernhard Y. Renard · 2017 · Bioinformatics
  65. Studying microbial functionality within the gut ecosystem by systems biology
    Bastian Hornung, Vítor A. P. Martins dos Santos, Hauke Smidt, Peter J. Schaap · 2018 · Genes & Nutrition
  66. Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol
    Lara Ruth Dugas, Louise Lie, Jacob Plange‐Rhule, Kweku Bedu-Addo, Pascal Bovet, Estelle Victoria Lambert, Terrence Forrester, Amy H. Luke, Jack A. Gilbert, Brian Thomas Layden · 2018 · BMC Public Health
  67. Separating the signal from the noise in metagenomic cell-free DNA sequencing
    Philip Burnham, Nardhy Gomez‐Lopez, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz, Darshana M. Dadhania, John R. Lee, Manikkam Suthanthiran, Roberto J. Romero, Iwijn De Vlaminck · 2020 · Microbiome
  68. Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment
    Will P. M. Rowe, David W. Verner–Jeffreys, Craig Baker‐Austin, Jim J. Ryan, Duncan J. Maskell, GR Pearce · 2015 · Water Science & Technology
  69. Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures
    Shaopu Wang, Shuqin Zeng, Muireann Egan, Paul Cherry, Conall Strain, Emilene da Silva Morais, Patrick Boyaval, C. Anthony Ryan, Eugene Michael Dempsey, R. Paul Ross et al. · 2021 · Gut Microbes
  70. Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes
    Carlos Eduardo Posada-Perlaza, Adán Andrés Ramírez Rojas, Paola Porras, Boahemaa Adu‐Oppong, Ana M. Botero-Coy, Felix J. Hernández, Juan Manuel Anzola, Lorena Díaz, Gautam A. Dantas, Alejandro Reyes et al. · 2019 · Scientific Reports
  71. Implications of Gut Microbiota in Complex Human Diseases
    Dahai Yu, Xin Meng, Willem M. de Vos, Hao Wu, Xuexun Fang, Amit K. Maiti · 2021 · International Journal of Molecular Sciences
  72. Multimodal deep learning applied to classify healthy and disease states of human microbiome
    Seung Jae Lee, Mina Rho · 2022 · Scientific Reports
  73. Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial
    Xiaotao Zhang, Ehsan Irajizad, Kristi Louise Hoffman, Johannes Francois Fahrmann, Fangyu Li, Yongwoo David Seo, Gladys J. Browman, Jennifer B. Dennison, Jody V. Vykoukal, Pamela N. Luna et al. · 2023 · EBioMedicine
  74. Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data
    Allyson L. Byrd, Joseph F. Perez-Rogers, Solaiappan Manimaran, Eduardo Castro‐Nallar, Ian Toma, Timothy A. McCaffrey, Marc Siegel, Gary Benson, Keith A. Crandall, William Evan Johnson · 2014 · BMC Bioinformatics
  75. Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
    Stefano Léo, Nadia Gaïa, Étienne Ruppé, Stéphane Emonet, Myriam Girard, Vladimir Lazarević, Jacques Schrenzel · 2017 · International Journal of Molecular Sciences
  76. MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage
    Yu Xia, An-Dong Li, Yu Deng, Xiao-Tao Jiang, Li-Guan Li, Tong Zhang · 2017 · Frontiers in Microbiology
  77. Selective colonization ability of human fecal microbes in different mouse gut environments
    Wei Lan Zhou, Kin-Hoe Chow, Elizabeth S. Fleming, Julia Oh · 2018 · The ISME Journal
  78. Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks
    Baiba Vilne, Irēna Meistere, Lelde Grantiņa-Ieviņa, Juris Ķibilds · 2019 · Frontiers in Microbiology
  79. Does Quorum Sensing play a role in microbial shifts along spontaneous fermentation of cocoa beans? An in silico perspective
    Otávio Guilherme Gonçalves de Almeida, Uelinton Manoel Pinto, Claudia Matos, Diego Araújo Frazilio, V.F. Braga, Márcia Regina von Zeska Kress, Elaine Cristina Pereira De Martinis · 2020 · Food Research International
  80. Autoimmune Hepatitis: Shifts in Gut Microbiota and Metabolic Pathways among Egyptian Patients
    Nahla M. Elsherbiny, mohammed ramadan, Elham Ahmed Hassan, Mohamed E. Ali, Abeer Sharaf El‐Din Abd El‐Rehim, Wael A. Abbas, Mohamed A. A. Abozaid, Ebtisam Shawky Ahmed Hassanin, ‏Helal F. Hetta · 2020 · Microorganisms
  81. MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes
    Guocai Yao, Wenliang Zhang, Minglei Yang, Huan Yang, Jianbo Wang, Haiyue Zhang, Lai Wei, Zhi Xie, Weizhong Li · 2020 · Genomics Proteomics & Bioinformatics
  82. Indoor microbiome, microbial and plant metabolites, chemical compounds, and asthma symptoms in junior high school students: a multicentre association study in Malaysia
    Yu Sun, Mei Zhang, Zheyuan Ou, Yi Meng, Yang Chen, Ruqin Lin, Jamal Hisham Hashim, Zailina Binti Hashim, Gunilla Wieslander, Qingsong Chen et al. · 2022 · European Respiratory Journal
  83. The tumor microbiome in cancer progression: mechanisms and therapeutic potential
    Wanting Zhang, Yuhang Xiang, He Ren, Yilin Liu, Qi Wang, Mengdi Ran, Wanting Zhou, Tian Lu, Xianhui Zheng, Cong Qiao et al. · 2025 · Molecular Cancer
  84. Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator–prey genotypes
    Naseer Sangwan, Carey Lambert, Anukriti Sharma, Vipin Gupta, Paramjit Khurana, Jitendra Paul Khurana, Renee Elizabeth Sockett, Jack A. Gilbert, Rup Lal · 2015 · Environmental Microbiology Reports
  85. k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets
    David Ainsworth, Michael J.E. Sternberg, Come Raczy, Sarah Butcher · 2016 · Nucleic Acids Research
  86. MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
    Nathan LaPierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C. Wu, David Koslicki, Eleazar Eskin · 2019 · BMC Genomics
  87. Interaction of bacterial communities and indicators of water quality in shoreline sand, sediment, and water of Lake Michigan
    Meredith Becker Nevers, Muruleedhara N. Byappanahalli, Cindy H. Nakatsu, Julie L. Kinzelman, Mantha S. Phanikumar, Dawn A. Shively, Ashley M. Spoljaric · 2020 · Water Research
  88. Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea
    Mario López‐Pérez, Nikole E. Kimes, Jose Manuel Haro-Moreno, Francisco Rodríguez‐Valera · 2016 · Frontiers in Microbiology
  89. Metagenomic characterization of ambulances across the USA
    Niamh B. O’Hara, Harry Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, GAIL L. ROSEN, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy et al. · 2017 · Microbiome
  90. Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing
    Yanfen Cheng, Ying Wang, Yuanfei Li, Yipeng Zhang, Tianyi Liu, Yu Wang, Thomas J. Sharpton, Weiyun Zhu · 2017 · Frontiers in Microbiology
  91. Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications
    Jonathan Asante, John Osei Sekyere · 2019 · Environmental Microbiology Reports
  92. A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors
    Shaikh, Fyza Y., White, James R., Gills, Joell J., Hakozaki, Taiki, Richard, Corentin, Routy, Bertrand, Okuma, Yusuke, Usyk, Mykhaylo, Pandey, Abhishek, Weber, Jeffrey S. et al. · 2021 · Clinical Cancer Research
  93. Altered Gut Microbiome and Fecal Immune Phenotype in Early Preterm Infants With Leaky Gut
    Jose M. Lemme‐Dumit, Yang Song, Hnin Wai Lwin, Claudia Hernandez-Chavez, Sripriya Sundararajan, Rose Marie Viscardi, Jacques Ravel, Marcela F. Pasetti, Bing Ma · 2022 · Frontiers in Immunology
  94. Microbiota Present in Cystic Fibrosis Lungs as Revealed by Whole Genome Sequencing
    Philippe M. Hauser, Thomas Bernard, Gilbert Greub, Katia Jaton, Marco Pagni, Gaudenz Hafen · 2014 · PLoS ONE
  95. Transcriptomic Responses in the Bloom-Forming Cyanobacterium Microcystis Induced during Exposure to Zooplankton
    Matthew J. Harke, Jennifer G. Jankowiak, Brooke K. Morrell, Christopher J. Gobler · 2016 · Applied and Environmental Microbiology
  96. A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis
    Fiona Fouhy, Nicola J. Ronan, Órla O’Sullivan, Yvonne McCarthy, Aaron M. Walsh, Desmond M. Murphy, M. Daly, Evelyn Flanagan, C. Fleming, Melissa M. McCarthy et al. · 2017 · Scientific Reports
  97. Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study)
    Marc Oliva, Pierre H. H. Schneeberger, Victor Rey, Matthew Cho, Rachel Taylor, Aaron Richard Hansen, Kirsty Taylor, Ali Hosni, Andrew Bayley, Andrew J. Hope et al. · 2021 · British Journal of Cancer
  98. Characterization of carbapenem resistance in environmental samples and Acinetobacter spp. isolates from wastewater and river water in Poland
    Jakub Hubeny, Ewa Korzeniewska, Martyna Buta, Wiktor Zieliński, Damian Rolbiecki, Monika Harnisz · 2022 · The Science of The Total Environment
  99. FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets
    Anna Shcherbina · 2014 · BMC Research Notes
  100. Experimental metagenomics and ribosomal profiling of the human skin microbiome
    Pamela Ferretti, Stefania Farina, Mario Cristofolini, Giampiero Girolomoni, Adrian Tett, Nicola Segata · 2016 · Experimental Dermatology