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 101–200 of 1,002

  1. Ancient and modern environmental DNA
    Mikkel Winther Pedersen, Søren Overballe‐Petersen, Luca Ermini, Clio S. I. Der Sarkissian, James Haile, Micaela Hellström, Johan Spens, Philip Francis Thomsen, Kristine Bohmann, Enrico Cappellini et al. · 2014 · Philosophical Transactions of the Royal Society B Biological Sciences
  2. Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer
    Arthur, Janelle C., Gharaibeh, Raad Z., Mühlbauer, Marcus, Perez-Chanona, Ernesto, Uronis, Joshua M., McCafferty, Jonathan, Fodor, Anthony A., Jobin, Christian · 2014 · Nature Communications
  3. The landscape of viral associations in human cancers
    Marc Zapatka, Ivan Borozan, Daniel S. Brewer, Murat Iskar, Adam T. Grundhoff, Malik Alawi, Nikita Desai, Holger Sültmann, Holger Moch, PCAWG Pathogens et al. · 2020 · Nature Genetics
  4. Antibiotic resistance genes and human bacterial pathogens: Co-occurrence, removal, and enrichment in municipal sewage sludge digesters
    Feng Ju, Bing Jhang Li, Liping Ma, Yübo Wang, Danping Huang, Tong Zhang · 2015 · Water Research
  5. Strain-level microbial epidemiology and population genomics from shotgun metagenomics
    Matthias Scholz, Doyle V. Ward, Edoardo Pasolli, T. Tolio, Moreno Zolfo, Francesco Asnicar, Duy Tin Truong, Adrian Tett, Ardythe Luxion Morrow, Nicola Segata · 2016 · Nature Methods
  6. Functional metagenomic profiling of intestinal microbiome in extreme ageing
    Rampelli, Simone, Candela, Marco, Turroni, Silvia, Biagi, Elena, Collino, Sebastiano, Franceschi, Claudio, O'Toole, Paul W, Brigidi, Patrizia · 2013 · Aging
  7. Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain
    Parker, Aimée, Romano, Stefano, Ansorge, Rebecca, Aboelnour, Asmaa, Le Gall, Gwenaelle, Savva, George M., Pontifex, Matthew G., Telatin, Andrea, Baker, David, Jones, Emily et al. · 2022 · Microbiome
  8. Critical Assessment of Metagenome Interpretation: the second round of challenges
    Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey A. Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini et al. · 2022 · Nature Methods
  9. phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
    Harald R. Gruber‐Vodicka, Brandon Kwee Boon Seah, Elmar Pruesse · 2020 · mSystems
  10. Bacterial colonization and succession in a newly opened hospital
    Simon M. Lax, Naseer Sangwan, Daniel P. Smith, Peter Emil Larsen, Kim M. Handley, Miles Richardson, Kristina L. Guyton, Monika A. Krezalek, Benjamin D. Shogan, Jennifer R. DeFazio et al. · 2017 · Science Translational Medicine
  11. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
    Nandita R. Garud, Benjamin H. Good, Oskar Hallatschek, Katherine S. Pollard · 2019 · PLoS Biology
  12. bioBakery: a meta’omic analysis environment
    Lauren J. McIver, Galeb Abu-Ali, Eric A. Franzosa, Randall Schwager, Xochitl C. Morgan, Levi Waldron, Nicola Segata, Curtis Huttenhower · 2017 · Bioinformatics
  13. Biogas Upgrading via Hydrogenotrophic Methanogenesis in Two-Stage Continuous Stirred Tank Reactors at Mesophilic and Thermophilic Conditions
    Ilaria Bassani, Panagiotis Kougias, Laura Treu, İrini Angelidaki · 2015 · Environmental Science & Technology
  14. Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
    Ryan J. Williams, Adina Howe, Kirsten Hofmockel · 2014 · Frontiers in Microbiology
  15. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
    Stephen Nayfach, Katherine S. Pollard · 2015 · Genome biology
  16. Noninvasive monitoring of infection and rejection after lung transplantation
    Iwijn De Vlaminck, Lance Martin, Michael Kertesz, K. Patel, Mark Kowarsky, Calvin Strehl, Garrett Cohen, Helen I. Luikart, Norma F Neff, Jennifer Okamoto et al. · 2015 · Proceedings of the National Academy of Sciences
  17. Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial
    Marta Reyman, Marlies A. van Houten, Rebecca L. Watson, Mei Ling J. N. Chu, Kayleigh Arp, Wouter J. de Waal, Irene Schiering, Frans Berend Plötz, Rob J. L. Willems, Willem van Schaik et al. · 2022 · Nature Communications
  18. Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir
    Aaron M. Walsh, Fiona Crispie, Kieran Noel Kilcawley, Órla O’Sullivan, Maurice G. O’Sullivan, Marcus Joakim Claesson, Paul D. Cotter · 2016 · mSystems
  19. A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter
    Finucane, Mariel M., Sharpton, Thomas J., Laurent, Timothy J., Pollard, Katherine S. · 2014 · PLoS ONE
  20. Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition
    Cheng Wang, Da Dong, Haoshu Wang, Karin Müller, Yong Qin, Hailong Wang, Weixiang Wu · 2016 · Biotechnology for Biofuels
  21. <scp>GABA</scp> ‐producing <i>Bifidobacterium dentium</i> modulates visceral sensitivity in the intestine
    Pokusaeva, K., Johnson, C., Luk, B., Uribe, G., Fu, Y., Oezguen, N., Matsunami, R. K., Lugo, M., Major, A., Mori‐Akiyama, Y. et al. · 2017 · Neurogastroenterology &amp; Motility
  22. A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4
    Nicholas James Loman, Chrystala Constantinidou, Martin Christner, Holger Rohde, Jacqueline Z.-M. Chan, Joshua Quick, Jacqueline Weir, Christopher Quince, Geoffrey P. Smith, Jason R. Betley et al. · 2013 · JAMA
  23. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
    Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge A. Gandara, Sagar Chhangawala et al. · 2015 · Cell Systems
  24. A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis
    Tae Gyu Oh, Susy M. Kim, Cyrielle Caussy, Ting Fu, Jian Ping Guo, Shirin Bassirian, Seema Singh, Egbert V. Madamba, Ricki Bettencourt, Lisa Richards et al. · 2020 · Cell Metabolism
  25. Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice
    Lee, Se-Hoon, Cho, Sung-Yup, Yoon, Youngmin, Park, Changho, Sohn, Jinyoung, Jeong, Jin-Ju, Jeon, Bu-Nam, Jang, Mongjoo, An, Choa, Lee, Suro et al. · 2021 · Nature Microbiology
  26. High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
    James Kaminski, Molly K. Gibson, Eric A. Franzosa, Nicola Segata, Gautam A. Dantas, Curtis Huttenhower · 2015 · PLoS Computational Biology
  27. Metagenomics: The Next Culture-Independent Game Changer
    J. Forbes, N. Knox, J. Ronholm, F. Pagotto, A. Reimer · 2017 · Frontiers in Microbiology
  28. An evaluation of the accuracy and speed of metagenome analysis tools
    Stinus Lindgreen, Karen L. Adair, Paul P. Gardner · 2016 · Scientific Reports
  29. Skin Microbiome Surveys Are Strongly Influenced by Experimental Design
    Jacquelyn S. Meisel, Geoffrey D. Hannigan, Amanda S. Tyldsley, Adam J. SanMiguel, Brendan Paul Hodkinson, Qi Zheng, Elizabeth A. Grice · 2016 · Journal of Investigative Dermatology
  30. Computational meta'omics for microbial community studies
    Nicola Segata, Daniela Boernigen, Timothy L. Tickle, Xochitl C. Morgan, Wendy S. Garrett, Curtis Huttenhower · 2013 · Molecular Systems Biology
  31. The intestinal microbiome of fish under starvation
    Jun Xia, Grace Lin, Gui Hong Fu, Zi Yi Wan, May Lee, Le Wang, Xiaojun Liu, Gen Hua Yue · 2014 · BMC Genomics
  32. Prehistoric genomes reveal the genetic foundation and cost of horse domestication
    Schubert, Mikkel, Jónsson, Hákon, Chang, Dan, Der Sarkissian, Clio, Ermini, Luca, Ginolhac, Aurélien, Albrechtsen, Anders, Dupanloup, Isabelle, Foucal, Adrien, Petersen, Bent et al. · 2014 · Proceedings of the National Academy of Sciences
  33. Ancient pathogen genomics as an emerging tool for infectious disease research
    Maria A. Spyrou, Kirsten I. Bos, Alexander Herbig, Johannes Krause · 2019 · Nature Reviews Genetics
  34. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico
    Åshild J. Vågene‬, Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna J. Sabin, Maria A. Spyrou, Aida Andrades Valtueña, Daniel H. Huson, Noreen Tuross et al. · 2018 · Nature Ecology & Evolution
  35. Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities.
    Na Jia, Jin-Feng Wang, Wen-Qiang Shi, Li-Feng Du, Yi Sun, Wei Zhan, Jia-Fu Jiang, Qian Wang, Bing Zhang, Pei-Feng Ji et al. · 2020 · Cell
  36. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
    Pérez-Cobas, Ana Elena, Gomez-Valero, Laura, Buchrieser, Carmen · 2020 · Microbial Genomics
  37. MicrobiotaProcess: A comprehensive R package for deep mining microbiome
    Shuangbin Xu, Li Zhan, Wenli Tang, Zehan Dai, Lang Zhou, Tingze Feng, Meijun Chen, Shanshan Liu, Tianzhi Wu, Erqiang Hu et al. · 2023 · The Innovation
  38. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
    Joshua Quick, Philip Ashton, Szymon Calus, Carol Chatt, Savita Gossain, Jeremy I Hawker, Satheesh Nair, Keith R Neal, Kathy Nye, Tansy M. Peters et al. · 2015 · Genome biology
  39. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome
    Ceylan Tanes, Kyle L. Bittinger, Yuan Gao, Elliot S. Friedman, Lisa A. Nessel, Unmesha Roy Paladhi, Lillian Chau, Erika Panfen, Michael Andrew Fischbach, Jonathan G. Braun et al. · 2021 · Cell Host & Microbe
  40. The gut microbiota and metabolic disease: current understanding and future perspectives
    Tulika Arora, Fredrik Bäckhed · 2016 · Journal of Internal Medicine
  41. Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy
    Serrano, Myrna G., Parikh, Hardik I., Brooks, J. Paul, Edwards, David J., Arodz, Tom J., Edupuganti, Laahirie, Huang, Bernice, Girerd, Philippe H., Bokhari, Yahya A., Bradley, Steven P. et al. · 2019 · Nature Medicine
  42. Toward Accurate and Quantitative Comparative Metagenomics
    Stephen Nayfach, Katherine S. Pollard · 2016 · Cell
  43. Whole-Genome Sequencing in Outbreak Analysis
    Carol A. Gilchrist, Stephen Turner, Margaret Foster Riley, William A. Petri, Erik L. Hewlett · 2015 · Clinical Microbiology Reviews
  44. The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
    Geoffrey D. Hannigan, Jacquelyn S. Meisel, Amanda S. Tyldsley, Qi Zheng, Brendan Paul Hodkinson, Adam J. SanMiguel, Samuel S. Minot, Frederic D. Bushman, Elizabeth A. Grice · 2015 · mBio
  45. Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients
    Peters, Brandilyn A., Wilson, Melissa, Moran, Una, Pavlick, Anna, Izsak, Allison, Wechter, Todd, Weber, Jeffrey S., Osman, Iman, Ahn, Jiyoung · 2019 · Genome Medicine
  46. Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis
    Hongzhe Li · 2015 · Annual Review of Statistics and Its Application
  47. Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition
    Christopher Quince, Umer Zeeshan Ijaz, Nicholas James Loman, A. Murat Eren, Delphine M. A. Saulnier, Julie A. Russell, Sarah–Jane Haig, Szymon Calus, Joshua Quick, Andrew Robert Barclay et al. · 2015 · The American Journal of Gastroenterology
  48. Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes
    Moran Yassour, Mi Young Lim, Hyun Sun Yun, Timothy L. Tickle, Joohon Sung, Yun‐Mi Song, Kayoung Lee, Eric A. Franzosa, Xochitl C. Morgan, Dirk Gevers et al. · 2016 · Genome Medicine
  49. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
    Milani, Christian, Lugli, Gabriele Andrea, Duranti, Sabrina, Turroni, Francesca, Mancabelli, Leonardo, Ferrario, Chiara, Mangifesta, Marta, Hevia, Arancha, Viappiani, Alice, Scholz, Matthias et al. · 2015 · Scientific Reports
  50. Human gut microbiota community structures in urban and rural populations in Russia
    Alexander Tyakht, Elena Kostryukova, Anna Popenko, Maxim S. Belenikin, Alexander Vladimirovich Pavlenko, Andrey K. Larin, Irina Yuryevna Karpova, Oksana V. Selezneva, Tatyana A. Semashko, Elena A. Ospanova et al. · 2013 · Nature Communications
  51. Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes
    Sandra Reitmeier, Silke Kießling, Thomas Clavel, Markus List, Eduardo L. Almeida, Tarini Shankar Ghosh, Klaus Neuhaus, Harald Grallert, Jakob Linseisen, Thomas Skurk et al. · 2020 · Cell Host & Microbe
  52. Reconstructing ancient genomes and epigenomes
    Ludovic Orlando, Marcus Thomas P. Gilbert, Eske Willerslev · 2015 · Nature Reviews Genetics
  53. Ancient plant DNA in lake sediments
    Laura Parducci, Keith David Bennett, Gentile Francesco Ficetola, Inger Greve Alsos, Yoshihisa Suyama, Jamie R. Wood, Mikkel Winther Pedersen · 2017 · New Phytologist
  54. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences
    Himel Mallick, Eric A. Franzosa, Lauren J. Mclver, Soumya Banerjee, Alexandra Sirota‐Madi, Aleksandar David Kostic, Clary B. Clish, Hera C. Vlamakis, Ramnik J. Xavier, Curtis Huttenhower · 2019 · Nature Communications
  55. Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis
    Hyde, Embriette R., Andrade, Fernando, Vaksman, Zalman, Parthasarathy, Kavitha, Jiang, Hong, Parthasarathy, Deepa K., Torregrossa, Ashley C., Tribble, Gena, Kaplan, Heidi B., Petrosino, Joseph F. et al. · 2014 · PLoS ONE
  56. Structure, function and diversity of the healthy human microbiome
    The Human Microbiome Project Consortium · 2012 · Nature
  57. Identifying biases and their potential solutions in human microbiome studies
    Nearing, Jacob T., Comeau, André M., Langille, Morgan G. I. · 2021 · Microbiome
  58. MMseqs software suite for fast and deep clustering and searching of large protein sequence sets
    Maria Hauser, Martin Steinegger, J. Söding · 2016 · Bioinform.
  59. Gut microbiota dysbiosis and altered tryptophan catabolism contribute to autoimmunity in lupus-susceptible mice
    Choi, Seung-Chul, Brown, Josephine, Gong, Minghao, Ge, Yong, Zadeh, Mojgan, Li, Wei, Croker, Byron P., Michailidis, George, Garrett, Timothy J., Mohamadzadeh, Mansour et al. · 2020 · Science Translational Medicine
  60. Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
    Clooney, Adam G., Fouhy, Fiona, Sleator, Roy D., O’ Driscoll, Aisling, Stanton, Catherine, Cotter, Paul D., Claesson, Marcus J. · 2016 · PLOS ONE
  61. Accounting for reciprocal host–microbiome interactions in experimental science
    Thaddeus S. Stappenbeck, Herbert W. Virgin · 2016 · Nature
  62. ConStrains identifies microbial strains in metagenomic datasets
    Chengwei Luo, Rob D. Knight, Heli Siljander, Mikael Knip, Ramnik J. Xavier, Dirk Gevers · 2015 · Nature Biotechnology
  63. A two-part mixed-effects model for analyzing longitudinal microbiome compositional data
    Chen, Eric Z., Li, Hongzhe · 2016 · Bioinformatics
  64. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome
    Bikel, Shirley, Valdez-Lara, Alejandra, Cornejo-Granados, Fernanda, Rico, Karina, Canizales-Quinteros, Samuel, Soberón, Xavier, Del Pozo-Yauner, Luis, Ochoa-Leyva, Adrián · 2015 · Computational and Structural Biotechnology Journal
  65. Biodiversity and functional genomics in the human microbiome
    Xochitl C. Morgan, Nicola Segata, Curtis Huttenhower · 2012 · Trends in Genetics
  66. Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis
    Joana Pereira‐Marques, A. van der Hout, Rui M. Ferreira, Michiel Weber, Inês Pinto-Ribeiro, Leen‐Jan van Doorn, Cornelis W. Knetsch, Céu Figueiredo · 2019 · Frontiers in Microbiology
  67. Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model
    McCafferty, Jonathan, Mühlbauer, Marcus, Gharaibeh, Raad Z, Arthur, Janelle C, Perez-Chanona, Ernesto, Sha, Wei, Jobin, Christian, Fodor, Anthony A · 2013 · The ISME Journal
  68. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples
    Changjin Hong, Solaiappan Manimaran, Ying Shen, Joseph F. Perez-Rogers, Allyson L. Byrd, Eduardo Castro‐Nallar, Keith A. Crandall, William Evan Johnson · 2014 · Microbiome
  69. Identification of microbial markers across populations in early detection of colorectal cancer
    Yuanqi Wu, Na Jiao, Ruixin Zhu, Yida Zhang, Dingfeng Wu, An-Jun Wang, Sa Fang, Liwen Tao, Yichen Li, Sijing Cheng et al. · 2021 · Nature Communications
  70. Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers
    Olabisi Oluwabukola Coker, Changan Liu, William Ka Kei Wu, Sunny Hei Wong, Wei Ping Jia, Joseph J.�Y. Sung, Jun Qing Yu · 2022 · Microbiome
  71. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome
    Christina Warinner, Camilla Speller, Matthew J. Collins · 2014 · Philosophical Transactions of the Royal Society B Biological Sciences
  72. Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota
    Huating Li, Lei Zhang, Jun Li, Qian Wu, Lingling Qian, Junsheng He, Yueqiong Ni, Petia Kovatcheva‐Datchary, Rui Rong Yuan, Shuangbo Liu et al. · 2024 · Nature Metabolism
  73. Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis
    Jaeyun Sung, Seunghyeon Kim, Josephine Jill T. Cabatbat, Sungho Jang, Yong‐Su Jin, Gyoo Yeol Jung, Nicholas Chia, Pan‐Jun Kim · 2017 · Nature Communications
  74. Detecting Human Bacterial Pathogens in Wastewater Treatment Plants by a High-Throughput Shotgun Sequencing Technique
    Lin Cai, Tong Zhang · 2013 · Environmental Science & Technology
  75. Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohnʼs Disease
    Suskind, David L., Brittnacher, Mitchell J., Wahbeh, Ghassan, Shaffer, Michele L., Hayden, Hillary S., Qin, Xuan, Singh, Namita, Damman, Christopher J., Hager, Kyle R., Nielson, Heather et al. · 2015 · Inflammatory Bowel Diseases
  76. Microbiota-mediated inflammation and antimicrobial defense in the intestine
    Caballero, Silvia, Pamer, Eric G. · 2015 · Annual Review of Immunology
  77. Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
    Michael Tessler, Johannes S. Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe Machado Velho, Bianca Trevizan Segóvia, Fábio Amodêo Lansac‐Tôha, Michael Lemke, Rob DeSalle et al. · 2017 · Scientific Reports
  78. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers
    Melissa K. Takahashi, Xiao Tan, Aaron J. Dy, Dana Braff, Reid Akana, Yoshikazu Furuta, Nina M. Donghia, Ashwin N. Ananthakrishnan, James J. Collins · 2018 · Nature Communications
  79. Microbial genome-enabled insights into plant–microorganism interactions
    David S. Guttman, Alice Carolyn McHardy, Paul Schulze‐Lefert · 2014 · Nature Reviews Genetics
  80. Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration
    Zinkernagel, Martin S., Zysset-Burri, Denise C., Keller, Irene, Berger, Lieselotte E., Leichtle, Alexander B., Largiadèr, Carlo R., Fiedler, Georg M., Wolf, Sebastian · 2017 · Scientific Reports
  81. A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Feehery, George R., Yigit, Erbay, Oyola, Samuel O., Langhorst, Bradley W., Schmidt, Victor T., Stewart, Fiona J., Dimalanta, Eileen T., Amaral-Zettler, Linda A., Davis, Theodore, Quail, Michael A. et al. · 2013 · PLoS ONE
  82. The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn’s Disease–Like Ileitis
    Rodriguez-Palacios, Alexander, Harding, Andrew, Menghini, Paola, Himmelman, Catherine, Retuerto, Mauricio, Nickerson, Kourtney P, Lam, Minh, Croniger, Colleen M, McLean, Mairi H, Durum, Scott K et al. · 2018 · Inflammatory Bowel Diseases
  83. Antibiotic resistance: turning evolutionary principles into clinical reality
    Andersson, Dan I, Balaban, Nathalie Q, Baquero, Fernando, Courvalin, Patrice, Glaser, Philippe, Gophna, Uri, Kishony, Roy, Molin, Søren, Tønjum, Tone · 2020 · FEMS Microbiology Reviews
  84. Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohnʼs Disease
    Byron P. Vaughn, Tommi Vatanen, Jessica Ravikoff Allegretti, Aiping Bai, Ramnik J. Xavier, Joshua R. Korzenik, Dirk Gevers, Amanda Ting, Simon Christopher Robson, Alan C. Moss · 2016 · Inflammatory Bowel Diseases
  85. Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India
    Ankit Gupta, Darshan B. Dhakan, Abhijit Maji, Rituja Saxena, V. K., Shruti Mahajan, Joby Pulikkan, Jacob Kurian, Andres M. Gomez, Joy Scaria et al. · 2019 · mSystems
  86. Altered microbiome composition in individuals with fibromyalgia
    Minerbi, Amir, Gonzalez, Emmanuel, Brereton, Nicholas J.B., Anjarkouchian, Abraham, Dewar, Ken, Fitzcharles, Mary-Ann, Chevalier, Stéphanie, Shir, Yoram · 2019 · Pain
  87. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults
    Winston Anthony, Bin Wang, Kimberley V. Sukhum, Alaric W. D’Souza, Tiffany Hink, Candice Cass, Sondra M. Seiler, Kimberly A. Reske, Christopher Coon, Erik R. Dubberke et al. · 2022 · Cell Reports
  88. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life
    Tommi Vatanen, Damian Rafal Plichta, Juhi Somani, Philipp C. Münch, Timothy D. Arthur, Andrew Brantley Hall, Sabine Rudolf, Edward J. Oakeley, Xiaobo Ke, Rachel A Young et al. · 2018 · Nature Microbiology
  89. An Autoimmunogenic and Proinflammatory Profile Defined by the Gut Microbiota of Patients With Untreated Systemic Lupus Erythematosus
    Bei-di Chen, Xinmiao Jia, Jia‐yue Xu, Lidan Zhao, Junyi Ji, Bingxuan Wu, Fei Yun-yun, Hua-xia Yang, Hua Chen, Xiaoxia Zuo et al. · 2020 · Arthritis & Rheumatology
  90. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
    Erik Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Jesse Connell, Jung‐Jin Lee, Bryton Fett, Frederic D. Bushman, Kyle L. Bittinger · 2019 · Microbiome
  91. Profile and Fate of Bacterial Pathogens in Sewage Treatment Plants Revealed by High-Throughput Metagenomic Approach
    Bing Jhang Li, Feng Ju, Lin Cai, Tong Zhang · 2015 · Environmental Science & Technology
  92. The preterm placental microbiome varies in association with excess maternal gestational weight gain
    Kathleen M. Antony, Jun Ma, Kristen B. Mitchell, Diana Racusin, James A. Versalovic, Kjersti Marie Aagaard · 2015 · American Journal of Obstetrics and Gynecology
  93. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss
    Brian Piening, Wenyu Zhou, Kévin Contrepois, Hannes Luc Röst, Gucci Jijuan Gu, Tejaswini Mishra, Blake Hanson, Eddy J. Bautista, Shana R. Leopold, Christine Y. Yeh et al. · 2018 · Cell Systems
  94. One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review
    Pauline Trinh, Jesse Zaneveld, Sarah M Safranek, Peter MacGarr Rabinowitz · 2018 · Frontiers in Public Health
  95. Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis
    Adrian Tett, Edoardo Pasolli, Stefania Farina, Duy Tin Truong, Francesco Asnicar, Moreno Zolfo, Francesco Beghini, Federica Armanini, Olivier Jousson, Veronica De Sanctis et al. · 2017 · npj Biofilms and Microbiomes
  96. Species abundance information improves sequence taxonomy classification accuracy
    Benjamin D. Kaehler, Nicholas A. Bokulich, Daniel T. McDonald, Rob D. Knight, J. Gregory Caporaso, Gavin A. Huttley · 2019 · Nature Communications
  97. Pyrosequencing Reveals the Influence of Organic and Conventional Farming Systems on Bacterial Communities
    Ru Li, Ehsan Khafipour, Denis O. Krause, Martin H. Entz, Teresa R. de Kievit, W. G. Dilantha Fernando · 2012 · PLoS ONE
  98. A human gut phage catalog correlates the gut phageome with type 2 diabetes
    Yingfei Ma, Xiaoyan You, Guoqin Mai, Taku A. Tokuyasu, Chenli Liu · 2018 · Microbiome
  99. MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
    Daniel H. Huson, Benjamin Albrecht, Caner Bağcı, Irina N. Bessarab, Anna Górska, Dino Jolić, Rohan B. H. Williams · 2018 · Biology Direct
  100. A Robust Framework for Microbial Archaeology
    Christina Warinner, Alexander Herbig, Allison E. Mann, James A. Fellows Yates, Clemens L. Weiß, Hernán A. Burbano, Ludovic Orlando, Johannes Krause · 2017 · Annual Review of Genomics and Human Genetics