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 401–500 of 1,002

  1. DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate
    Yuqing Yan, Jiayao Zhang, Lili Tian, Xuejun Yan, Lin Xue Du, Aaron Leininger, Mou Zhang, Nan Li, Zhiyong Jason Ren, Xin Wang · 2023 · Water Research
  2. Understanding the microbial basis of body odor in pre-pubescent children and teenagers
    Tze Hau Lam, Davide Verzotto, Purbita Brahma, Amanda Hui Qi Ng, Ping Hu, Dan J. Schnell, Jay P. Tiesman, Rong Kong, Thi My Uyen Ton, Jianjun Li et al. · 2018 · Microbiome
  3. Streaming algorithms for identification pathogens and antibiotic resistance potential from real-time MinION™ sequencing
    Minh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott, Huihui Zhang, Matthew A. Cooper, Lachlan Coin · 2016 · GigaScience
  4. The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness
    Alok Madan, Daisy G.Y. Thompson-Lake, J.C. Fowler, Nadim J. Ajami, Ramiro Salas, Bartley Christopher Frueh, Major R. Bradshaw, Benjamin L. Weinstein, John M. Oldham, Joseph F. Petrosino · 2019 · Journal of Affective Disorders
  5. Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Alexander S. F. Berry, Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, Kevin M. O’Brien, Ying Chen, Samuel J. Murray, Lydia A. Ramharack, Robert N. Baldassano, Thomas D. Parsons et al. · 2021 · Microbiome
  6. Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota
    Thomas J. Vogl, Shelley Klompus, Sigal Leviatan, Iris N. Kalka, Adina Weinberger, Cisca Wijmenga, Jingyuan Fu, Alexandra Zhernakova, Rinse Karel Weersma, Eran Segal · 2021 · Nature Medicine
  7. Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates
    Javad Gharechahi, Sajjad Sarikhan, Jianlin Han, Xuezhi Ding, Ghasem Hosseini Salekdeh · 2022 · npj Biofilms and Microbiomes
  8. Strain/species identification in metagenomes using genome-specific markers
    Qichao Tu, Zhili He, Jizhong Z. Zhou · 2014 · Nucleic Acids Research
  9. Isolation and Identification of the Follicular Microbiome: Implications for Acne Research
    Jacob B. Hall, Zhaoyuan Cong, Yuka Imamura Kawasawa, Brian A. Kidd, Joel T. Dudley, Diane M. Thiboutot, Amanda M. Nelson · 2018 · Journal of Investigative Dermatology
  10. Impact of plants on the diversity and activity of methylotrophs in soil
    Michael Christopher Macey, Jennifer Pratscher, Andrew T. Crombie, J. Colin Murrell · 2020 · Microbiome
  11. Soil type shapes the antibiotic resistome profiles of long-term manured soil
    Yu Zhang, Dengmiao Cheng, Yuting Zhang, Jun Xie, Huaye Xiong, Yu Wan, Yueqiang Zhang, Xinping Chen, Xiaojun Shi · 2021 · The Science of The Total Environment
  12. The Contribution of the Human Oral Microbiome to Oral Disease: A Review
    Austin Gregory Morrison, Soumyadev Sarkar, Shahid Umar, Sonny T. M. Lee, Sufi Mary Thomas · 2023 · Microorganisms
  13. Long-term impact of fecal transplantation in healthy volunteers
    Oleg Valerievich Goloshchapov, Evgenii I. Olekhnovich, Sidorenko Sv, Ivan Moiseev, М. A. Kucher, Dmitry E. Fedorov, Alexander Vladimirovich Pavlenko, Alexander I. Manolov, Гостев Владимир Валерьевич, Vladimir A. Veselovsky et al. · 2019 · BMC Microbiology
  14. Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth
    Alastair M. McKee, Benjamin M. Kirkup, Matthew Madgwick, Wesley J. Fowler, Christopher A. Price, Sally A. Dreger, Rebecca Ansorge, Kate A. Makin, Shabhonam Caim, Gwénaëlle Le Gall et al. · 2021 · iScience
  15. Metabolic capability and in situ activity of microorganisms in an oil reservoir
    Yi-Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia Soares Zaramela, Ji‐Dong Gu, Bo‐Zhong Mu, Karsten Zengler · 2018 · Microbiome
  16. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling
    Brian W. Ji, Ravi U. Sheth, Purushottam D. Dixit, Yiming Huang, Andrew Kaufman, Harris H. Wang, Dennis Vitkup · 2019 · Nature Methods
  17. METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses
    Christian Milani, Gabriele Andrea Lugli, Federico Fontana, Leonardo Mancabelli, Giulia Alessandri, Giulia Longhi, Rosaria Anzalone, Alice Viappiani, Francesca Turroni, Douwe van Sinderen et al. · 2021 · mSystems
  18. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock
    Alexandre Maciel-Guerra, Michelle Baker, Yue Hu, Wei Wang, Xibin Zhang, Jia Rong, Yimin Zhang, Jing Zhang, Jasmeet Kaler, David Renney et al. · 2022 · The ISME Journal
  19. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course
    Melanie Schirmer, Martin Stražar, Julián Ávila-Pacheco, Daniel F. Rojas‐Tapias, Eric Brown, Emily R. Temple, Amy Deik, Kevin H. Bullock, Sarah Jeanfavre, Kerry A. Pierce et al. · 2024 · Cell Host & Microbe
  20. Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici
    Xin Mei Zhou, Jin-Ting Wang, Wei-Hua Wang, Clement K. M. Tsui, Lei Cai · 2020 · Microbial Ecology
  21. Assessing taxonomic metagenome profilers with OPAL
    Meyer, Fernando, Bremges, Andreas, Belmann, Peter, Janssen, Stefan, McHardy, Alice C., Koslicki, David · 2019 · Genome Biology
  22. Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing
    Hui‐Yu Sui, Ana A. Weil, Edwin Nuwagira, Firdausi Qadri, Edward Thomas Ryan, Melissa Paola Mezzari, Wanda Phipatanakul, Peggy S. Lai · 2020 · Frontiers in Microbiology
  23. Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis
    Veronika B. Dubinkina, Dmitry S. Ischenko, Ульянцев Владимир Игоревич, Alexander Tyakht, Dmitry G. Alexeev · 2016 · BMC Bioinformatics
  24. High‐Throughput DNA sequencing of ancient wood
    Stefanie Wagner, Frédéric Lagane, Andaine Seguin‐Orlando, Mikkel Schubert, Thibault Leroy, Erwan Guichoux, Émilie Chancerel, Inger Bech-Hebelstrup, Vincent Bernard, Cyrille Billard et al. · 2018 · Molecular Ecology
  25. Maltitol: Analytical Determination Methods, Applications in the Food Industry, Metabolism and Health Impacts
    Ariana Saraiva, Conrado Carrascosa, Dele Raheem, Fernando Ramos, António Raposo · 2020 · International Journal of Environmental Research and Public Health
  26. Randomized trial assessing impact of probiotic supplementation on gut microbiome and clinical outcome from targeted therapy in metastatic renal cell carcinoma
    Dizman, Nazli, Hsu, JoAnn, Bergerot, Paulo G., Gillece, John D., Folkerts, Megan, Reining, Lauren, Trent, Jeffrey, Highlander, Sarah K., Pal, Sumanta K. · 2021 · Cancer Medicine
  27. One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density
    Peishun Li, Boyang Ji, Hao Luo, Daniel Sundh, Mattias Lorentzon, Jens Nielsen · 2022 · npj Biofilms and Microbiomes
  28. Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions
    Yvonne Jean Huang, John R. Erb‐Downward, Robert P. Dickson, Jeffrey L. Curtis, Gary B. Huffnagle, MeiLan King Han · 2016 · Translational research
  29. Environment dominates over host genetics in shaping human gut microbiota
    Daphna Rothschild, Omer Weissbrod, Elad Barkan, Alexander Kurilshikov, Tal Korem, David Zeevi, Paul Igor Costea, Anastasia Godneva, Kalka IN, Bar N · 2018 · Yearbook of pediatric endocrinology
  30. Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China
    Michelle Baker, Xibin Zhang, Alexandre Maciel-Guerra, Yinping Dong, Wei Wang, Yujie Hu, David Renney, Yue Hu, Longhai Liu, Hui Li et al. · 2023 · Nature Food
  31. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
    Emilie E. L. Muller, Nicolás Pinel, Cedric Christian Laczny, Michael R. Hoopmann, Shaman Narayanasamy, Laura Lebrun, Hugo Roume, Jake Lin, Patrick May, Nathan D. Hicks et al. · 2014 · Nature Communications
  32. MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures
    Samuele Girotto, Cinzia Pizzi, Matteo Comin · 2016 · Bioinformatics
  33. Identifying strains that contribute to complex diseases through the study of microbial inheritance
    Jeremiah J. Faith, Jean‐Frédéric Colombel, Jeffrey I. Gordon · 2015 · Proceedings of the National Academy of Sciences
  34. Gastrointestinal Pathology in Juvenile and Adult CFTR-Knockout Ferrets
    Xingshen Sun, Alicia K. Olivier, Yaling Yi, Christopher E. Pope, Hillary S. Hayden, Bo Liang, Hongshu Sui, Weihong Zhou, Kyle R. Hager, Yulong Zhang et al. · 2014 · American Journal Of Pathology
  35. Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages
    George V. Tetz, Stuart M. Brown, Yuhan Hao, Victor Tetz · 2019 · Scientific Reports
  36. Chronic liver disease enables gut Enterococcus faecalis colonization to promote liver carcinogenesis
    Noriho Iida, Eishiro Mizukoshi, Tatsuya Yamashita, Masahiro Yutani, Jun Seishima, Ziyu Wang, Kuniaki Arai, Hikari Okada, Taro Yamashita, Yoshio Sakai et al. · 2021 · Nature Cancer
  37. The transcriptional profile of coronary arteritis in Kawasaki disease
    Anne Heitzman Rowley, Kristine M. Wylie, Kwang‐Youn A. Kim, Adam J Pink, Amy Yang, Rebecca Reindel, Susan C. Baker, Stanford T. Shulman, Jan Marc Orenstein, Mark William Lingen et al. · 2015 · BMC Genomics
  38. Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods
    Andrew D. Huang, Chengwei Luo, Ángela Peña, Michael R. Weigand, Cheryl L. Tarr, Konstantinos T. Konstantinidis · 2016 · Applied and Environmental Microbiology
  39. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
    Alexandra M. Linz, Shaomei He, Sarah L. R. Stevens, Karthik Anantharaman, Robin R. Rohwer, Rex R. Malmstrom, Stefan Bertilsson, Katherine D. McMahon · 2018 · PeerJ
  40. Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
    Jihoon Jo, Jooseong Oh, Chungoo Park · 2020 · The Journal of Microbiology
  41. The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces
    Ivan Vujkovic-Cvijin, Hugh C. Welles, Connie W. Y. Ha, Lutfi Huq, Shreni Mistry, Jason M. Brenchley, Giorgio Trinchieri, Suzanne Devkota, Yasmine Belkaid · 2022 · Science Translational Medicine
  42. From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
    Robyn Wright, A. Comeau, Morgan G. I. Langille · 2023 · Microbial Genomics
  43. Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants
    Diana Hazard Taft, Namasivayam Ambalavanan, Kurt R. Schibler, Zhuoteng Yu, David S. Newburg, Hitesh S. Deshmukh, Doyle V. Ward, Ardythe Luxion Morrow · 2015 · PLoS ONE
  44. Learning about who we are
    David A. Relman · 2012 · Nature
  45. Research Techniques Made Simple: Profiling the Skin Microbiota
    Max D. Grogan, Casey Bartow‐McKenney, Laurice J. Flowers, Simon A.B. Knight, Aayushi Uberoi, Elizabeth A. Grice · 2019 · Journal of Investigative Dermatology
  46. Next-Generation Metagenomics: Methodological Challenges and Opportunities
    Ilaria Laudadio, Valerio Fulci, Laura Stronati, Claudia Carissimi · 2019 · OMICS A Journal of Integrative Biology
  47. Antibiotic Cocktail for Pediatric Acute Severe Colitis and the Microbiome: The PRASCO Randomized Controlled Trial
    Dan Turner, Jason D. Bishai, Leah Reshef, Guila Abitbol, Gili Focht, Dana Marcus, Oren Ledder, Raffi Lev‐Tzion, Esther Orlanski‐Meyer, Baruch Yerushalmi et al. · 2019 · Inflammatory Bowel Diseases
  48. Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
    Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu, Kang Ning · 2014 · PLoS ONE
  49. STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies
    Tehmina Bharucha, Clarissa Oeser, François Balloux, Julianne Rose Brown, Ellen C. Carbo, André Charlett, Charles Y. Chiu, Eric C. J. Claas, Marcus Christofoor de Goffau, Jutte J.C. de Vries et al. · 2020 · The Lancet Infectious Diseases
  50. Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering
    Leonor García-Bayona, Michael J. Coyne, Laurie E. Comstock · 2021 · PLoS Genetics
  51. Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry
    Tapan Behl, Ishnoor Kaur, Aayush Sehgal, Sukhbir Singh, Saurabh Bhatia, Ahmed Al‐Harrasi, Gökhan Zengin, Elena Emilia Babeş, Ciprian Brisc, Manuela Stoicescu et al. · 2021 · International Journal of Molecular Sciences
  52. Alterations in microbiota and their metabolites are associated with beneficial effects of bile acid sequestrant on icteric primary biliary Cholangitis
    Bo Li, Jun Zhang, Yong Chen, Qixia Wang, Yan Li, Rui Wang, Yiran Wei, Zhengrui You, Yikang Li, Qi Miao et al. · 2021 · Gut Microbes
  53. Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis
    Christopher J. Damman, M. Brittnacher, Maria A. Westerhoff, Hillary S. Hayden, Matthew C. Radey, Kyle R. Hager, Sara R. Marquis, Samuel I. Miller, Timothy L. Zisman · 2015 · PLoS ONE
  54. Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing
    Karen G. Jarvis, James Robert White, Christopher J. Grim, Laura Ewing, Andrea Ottesen, Junia Jean-Gilles Beaubrun, James Pettengill, Eric W. Brown, Darcy E. Hanes · 2015 · BMC Microbiology
  55. FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
    Saima Sultana Tithi, Frank O. Aylward, Roderick V. Jensen, Liqing Zhang · 2018 · PeerJ
  56. Genomic Analysis of Viral Outbreaks
    Shirlee Wohl, Stephen F. Schaffner, Pardis C. Sabeti · 2016 · Annual Review of Virology
  57. Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis
    Jiwon Huh, Tae‐Young Roh · 2020 · BMC Microbiology
  58. Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma
    Mykhaylo Usyk, Abhishek Pandey, Richard B. Hayes, Una Moran, Anna C. Pavlick, Iman Osman, Jeffrey S. Weber, Jiyoung Ahn · 2021 · Genome Medicine
  59. Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation
    Daniel Podlesny, Cesar Arze, Elisabeth Dörner, Sandeep Verma, Sudhir Dutta, Jens Walter, W. Florian Fricke · 2022 · Microbiome
  60. Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
    Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen · 2014 · PLoS Computational Biology
  61. Impact of Immunosuppression on the Metagenomic Composition of the Intestinal Microbiome: a Systems Biology Approach to Post-Transplant Diabetes
    Mamatha Bhat, Elisa Pasini, J. Copeland, Marc Angeli, Shahid Husain, Deepali Kumar, Eberhard L. Renner, Anastasia A. Teterina, Johane P. Allard, David S. Guttman et al. · 2017 · Scientific Reports
  62. Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile
    Ranjit Kumar, Nengjun Yi, Degui Zhi, Peter G. Eipers, Kelly T. Goldsmith, Paula B. Dixon, David K. Crossman, Michael R. Crowley, Elliot J. Lefkowitz, J. Martin Rodriguez et al. · 2017 · npj Biofilms and Microbiomes
  63. Microbial bioinformatics for food safety and production
    Wynand B. L. Alkema, Jos Boekhorst, Michiel Wels, Sacha A. F. T. van Hijum · 2015 · Briefings in Bioinformatics
  64. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past
    Clio S. I. Der Sarkissian, Vianney Pichereau, Catherine Dupont, Peter Ilsøe, Mickael Perrigault, Paul Butler, Laurent Chauvaud A, Jón Eiríksson, James David Scourse, Christine Paillard A et al. · 2017 · Molecular Ecology Resources
  65. Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads
    Rogan Carr, Elhanan Borenstein · 2014 · PLoS ONE
  66. Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults
    Xuanji Li, Asker Brejnrod, Jonathan Thorsen, Trine Zachariasen, Urvish Trivedi, Jakob Russel, Gisle Vestergaard, Jakob Stokholm, Morten Arendt Rasmussen, Søren Johannes Sørensen · 2023 · Nature Communications
  67. Validation of high throughput sequencing and microbial forensics applications
    Bruce Budowle, Nancy D Connell, Anna Bielecka-Oder, Rita R. Colwell, Cindi R. Corbett, Jacqueline Fletcher, Mats Forsman, Dana R. Kadavy, Alemka Markotić, Stephen Morse et al. · 2014 · Investigative Genetics
  68. Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection
    Victor C. M. Leung, Caroline Vincent, Thaddeus J. Edens, Mark A. Miller, Amee R. Manges · 2017 · Clinical Infectious Diseases
  69. Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination
    Blaise Pascal Bougnom, Cheikna Zongo, Alan McNally, Vito Ricci, François Xavier Etoa, Sören Thiele‐Bruhn, Laura J. V. Piddock · 2018 · Environmental Research
  70. Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
    Yuhao Chen, Thomas C. Brook, Cho Zin Soe, Ian J. O’Neill, Cristina Alcon-Giner, Onnicha Leelastwattanagul, Sarah Phillips, Shabhonam Caim, Paul Clarke, Lindsay J. Hall et al. · 2020 · Microbial Genomics
  71. A metagenome-wide association study of gut microbiome and visceral fat accumulation
    Xiaomin Nie, Jiarui Chen, Xiaojing Ma, Yueqiong Ni, Yun Shen, Haoyong Yu, Gianni Panagiotou, Yuqian Bao · 2020 · Computational and Structural Biotechnology Journal
  72. Exposure to environmental toxicants is associated with gut microbiome dysbiosis, insulin resistance and obesity
    Partho Sen, Yong Fan, Jennifer J. Schlezinger, Stanislav Dusko Ehrlich, Thomas F. Webster, Tuulia Hyötyläinen, Oluf Borbye Pedersen, Matej Orešič · 2024 · Environment International
  73. Microbes as forensic indicators.
    G. Hinnebusch Alan, Jood Mudar Sarah · 2012 · PubMed
  74. Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn’s disease
    Kong, Lingjia, Lloyd-Price, Jason, Vatanen, Tommi, Seksik, Philippe, Beaugerie, Laurent, Simon, Tabassome, Vlamakis, Hera, Sokol, Harry, Xavier, Ramnik J. · 2020 · Gastroenterology
  75. Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research
    Irina M. Velsko, Laurent Frantz, Alexander Herbig, Greger Larson, Christina Warinner · 2018 · mSystems
  76. Microbiome and antibiotic resistome in household dust from Beijing, China
    Long‐Jun Ding, Xinyuan Zhou, Yong‐Guan Zhu · 2020 · Environment International
  77. Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China
    Yiming Li, Weiwei Cao, Shuli Liang, Shinji Yamasaki, Xun Chen, Lei Shi, Lei Ye · 2020 · Scientific Reports
  78. Metagenome association study of the gut microbiome revealed biomarkers linked to chemotherapy outcomes in locally advanced and advanced lung cancer
    Zhe Zhao, Kailun Fei, Hua Bai, Zhijie Wang, Jianchun Duan, Jie Wang · 2020 · Thoracic Cancer
  79. 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
  80. 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
  81. Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens
    Natacha Couto, Leonard Schuele, Erwin C. Raangs, Miguel P. Machado, Catarina Inês Mendes, Tiago F. Jesus, Monika A. Chlebowicz, Sigrid Rosema, Mário Ramirez, João André Carriço et al. · 2018 · Scientific Reports
  82. Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants
    Bing Ma, Elias J. McComb, Pawel Gajer, Hongqiu Yang, Mike S. Humphrys, Adora C. Okogbule-Wonodi, Alessio Fasano, Jacques Ravel, Rose Marie Viscardi · 2018 · Frontiers in Microbiology
  83. Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease
    Nicholas S. Rhoades, Tasha Barr, Sara M. Hendrickson, Kamm Prongay, Andrew J. Haertel, Leanne Gill, Laura M. Garzel, Katrine Whiteson, Mark K. Slifka, Ilhem Messaoudi · 2019 · Genome biology
  84. Microbial Dark Matter: From Discovery to Applications
    Yuguo Zha, Hui Chong, Pengshuo Yang, Kang Ning · 2022 · Genomics Proteomics & Bioinformatics
  85. Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers
    Min Li, Jinxin Liu, Jiaying Zhu, Huarui Wang, Chuqing Sun, Na Gao, Xing‐Ming Zhao, Wei‐Hua Chen · 2023 · Gut Microbes
  86. A Perspective Study of Koumiss Microbiome by Metagenomics Analysis Based on Single-Cell Amplification Technique
    Yao, Guoqiang, Yu, Jie, Hou, Qiangchuan, Hui, Wenyan, Liu, Wenjun, Kwok, Lai-Yu, Menghe, Bilige, Sun, Tiansong, Zhang, Heping, Zhang, Wenyi · 2017 · Frontiers in Microbiology
  87. All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing
    Ripp, Fabian, Krombholz, Christopher Felix, Liu, Yongchao, Weber, Mathias, Schäfer, Anne, Schmidt, Bertil, Köppel, Rene, Hankeln, Thomas · 2014 · BMC Genomics
  88. Gut microbial changes of patients with psychotic and affective disorders: A systematic review
    Vindegaard, Nina, Speyer, Helene, Nordentoft, Merete, Rasmussen, Simon, Benros, Michael Eriksen · 2021 · Schizophrenia Research
  89. Pros and cons of methylation-based enrichment methods for ancient DNA
    Andaine Seguin‐Orlando, Cristina Gamba, Clio S. I. Der Sarkissian, Luca Ermini, G. Louvel, Eugenia Boulygina, Alexey Sokolov, Artem Nedoluzhko, Eline D. Lorenzen, Patricio Lopez et al. · 2015 · Scientific Reports
  90. 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
  91. Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments
    Xuexia Jin, Sizhen Liu, Zhenting Zhang, Tong Liu, Na Li, Yunxiang Liang, Jinshui Zheng, Nan Peng · 2022 · Journal of Hazardous Materials
  92. Omics in gut microbiome analysis
    Tae Woong Whon, Na‐Ri Shin, Joon Yong Kim, Seong Woon Roh · 2021 · The Journal of Microbiology
  93. Pan-genome analysis of Bacillus for microbiome profiling
    Yihwan Kim, InSong Koh, Mi Young Lim, Won‐Hyong Chung, Mina Rho · 2017 · Scientific Reports
  94. Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease
    Tarini Shankar Ghosh, Jérôme Arnoux, Paul William O’Toole · 2020 · Gut Microbes
  95. Respiratory tract infections and gut microbiome modifications: A systematic review
    Claire A. Woodall, Luke J. McGeoch, Alastair D Hay, Ashley Hammond · 2022 · PLoS ONE
  96. Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions
    Elisa Salvetti, Stefano Campanaro, Ilenia Campedelli, Fabio Fracchetti, Alex Gobbi, Giovanni Battista Tornielli, Sandra Torriani, Giovanna E. Felis · 2016 · Frontiers in Microbiology
  97. Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in Spinach Using Metagenomic Sequencing
    S. Leonard, M. Mammel, D. Lacher, C. Elkins · 2016 · PLoS ONE
  98. The gut virome in Irritable Bowel Syndrome differs from that of controls
    Simone Coughlan, Anubhav Das, Eileen A. O’Herlihy, Fergus Shanahan, Paul William O’Toole, Ian B. Jeffery · 2021 · Gut Microbes
  99. mBodyMap: a curated database for microbes across human body and their associations with health and diseases
    Hanbo Jin, Guoru Hu, Chuqing Sun, Yiqian Duan, Zhenmo Zhang, Zhi Liu, Xing‐Ming Zhao, Wei‐Hua Chen · 2021 · Nucleic Acids Research
  100. Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
    Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera · 2022 · Frontiers in Bioinformatics