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A core gut microbiome in obese and lean twins

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Cited by:

  1. Li, Jie & Shen, Xuzhu & Li, YaoTang, 2021. "Modeling the temporal dynamics of gut microbiota from a local community perspective," Ecological Modelling, Elsevier, vol. 460(C).
  2. Xingqing Zhao & Jian Huang & Xuyan Zhu & Jinchun Chai & Xiaoli Ji, 2020. "Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area," IJERPH, MDPI, vol. 17(16), pages 1-18, August.
  3. Baoxing Song & Xiaoquan Su & Jian Xu & Kang Ning, 2012. "MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-10, November.
  4. Wei Chen & Clarence K Zhang & Yongmei Cheng & Shaowu Zhang & Hongyu Zhao, 2013. "A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs," PLOS ONE, Public Library of Science, vol. 8(8), pages 1-10, August.
  5. Chihiro Morita & Hirokazu Tsuji & Tomokazu Hata & Motoharu Gondo & Shu Takakura & Keisuke Kawai & Kazufumi Yoshihara & Kiyohito Ogata & Koji Nomoto & Kouji Miyazaki & Nobuyuki Sudo, 2015. "Gut Dysbiosis in Patients with Anorexia Nervosa," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-13, December.
  6. Huang Lin & Merete Eggesbø & Shyamal Das Peddada, 2022. "Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  7. Patrick D Schloss, 2009. "A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-9, December.
  8. John Molloy & Katrina Allen & Fiona Collier & Mimi L. K. Tang & Alister C. Ward & Peter Vuillermin, 2013. "The Potential Link between Gut Microbiota and IgE-Mediated Food Allergy in Early Life," IJERPH, MDPI, vol. 10(12), pages 1-22, December.
  9. Toby Kenney & Hong Gu & Tianshu Huang, 2021. "Poisson PCA: Poisson measurement error corrected PCA, with application to microbiome data," Biometrics, The International Biometric Society, vol. 77(4), pages 1369-1384, December.
  10. Alessandra N. Bazzano & Kaitlin S. Potts & Lydia A. Bazzano & John B. Mason, 2017. "The Life Course Implications of Ready to Use Therapeutic Food for Children in Low-Income Countries," IJERPH, MDPI, vol. 14(4), pages 1-19, April.
  11. Bharati Patel & Kadamb Patel & Shabbir Moochhala, 2020. "Diet-Derived Post-Biotic Metabolites to Promote Microbiota Function and Human Health," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 28(2), pages 21520-21524, June.
  12. Georg K Gerber & Andrew B Onderdonk & Lynn Bry, 2012. "Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems," PLOS Computational Biology, Public Library of Science, vol. 8(8), pages 1-14, August.
  13. Xinhui Wang & Marinus J C Eijkemans & Jacco Wallinga & Giske Biesbroek & Krzysztof Trzciński & Elisabeth A M Sanders & Debby Bogaert, 2012. "Multivariate Approach for Studying Interactions between Environmental Variables and Microbial Communities," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-7, November.
  14. Mark Reppell & John Novembre, 2018. "Using pseudoalignment and base quality to accurately quantify microbial community composition," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-23, April.
  15. Lena Takayasu & Wataru Suda & Eiichiro Watanabe & Shinji Fukuda & Kageyasu Takanashi & Hiroshi Ohno & Misako Takayasu & Hideki Takayasu & Masahira Hattori, 2017. "A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-20, August.
  16. Xiaolin Hao & Ting Chen, 2012. "OTU Analysis Using Metagenomic Shotgun Sequencing Data," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-10, November.
  17. Małgorzata Moszak & Monika Szulińska & Marta Walczak-Gałęzewska & Paweł Bogdański, 2021. "Nutritional Approach Targeting Gut Microbiota in NAFLD—To Date," IJERPH, MDPI, vol. 18(4), pages 1-32, February.
  18. Claudia Sala & Enrico Giampieri & Silvia Vitali & Paolo Garagnani & Daniel Remondini & Armando Bazzani & Claudio Franceschi & Gastone C Castellani, 2020. "Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging," PLOS ONE, Public Library of Science, vol. 15(10), pages 1-23, October.
  19. Ahmed A Metwally & Philip S Yu & Derek Reiman & Yang Dai & Patricia W Finn & David L Perkins, 2019. "Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks," PLOS Computational Biology, Public Library of Science, vol. 15(2), pages 1-16, February.
  20. Sean M Gibbons & Claire Duvallet & Eric J Alm, 2018. "Correcting for batch effects in case-control microbiome studies," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-17, April.
  21. Liat Shenhav & Ori Furman & Leah Briscoe & Mike Thompson & Justin D Silverman & Itzhak Mizrahi & Eran Halperin, 2019. "Modeling the temporal dynamics of the gut microbial community in adults and infants," PLOS Computational Biology, Public Library of Science, vol. 15(6), pages 1-21, June.
  22. Doris Vandeputte & Lindsey Commer & Raul Y. Tito & Gunter Kathagen & João Sabino & Séverine Vermeire & Karoline Faust & Jeroen Raes, 2021. "Temporal variability in quantitative human gut microbiome profiles and implications for clinical research," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  23. Aisling J. Daly & Jan M. Baetens & Bernard De Baets, 2018. "Ecological Diversity: Measuring the Unmeasurable," Mathematics, MDPI, vol. 6(7), pages 1-28, July.
  24. Patricia L Hibberd & Lauren Kleimola & Anne-Maria Fiorino & Christine Botelho & Miriam Haverkamp & Irina Andreyeva & Debra Poutsiaka & Claire Fraser & Gloria Solano-Aguilar & David R Snydman, 2014. "No Evidence of Harms of Probiotic Lactobacillus rhamnosus GG ATCC 53103 in Healthy Elderly—A Phase I Open Label Study to Assess Safety, Tolerability and Cytokine Responses," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-21, December.
  25. Fiona B. Tamburini & Dylan Maghini & Ovokeraye H. Oduaran & Ryan Brewster & Michaella R. Hulley & Venesa Sahibdeen & Shane A. Norris & Stephen Tollman & Kathleen Kahn & Ryan G. Wagner & Alisha N. Wade, 2022. "Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  26. Kai Markus Schneider & Antje Mohs & Wenfang Gui & Eric J. C. Galvez & Lena Susanna Candels & Lisa Hoenicke & Uthayakumar Muthukumarasamy & Christian H. Holland & Carsten Elfers & Konrad Kilic & Caroli, 2022. "Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  27. Xiao-Tao Jiang & Hai Zhang & Hua-Fang Sheng & Yu Wang & Yan He & Fei Zou & Hong-Wei Zhou, 2012. "Two-Stage Clustering (TSC): A Pipeline for Selecting Operational Taxonomic Units for the High-Throughput Sequencing of PCR Amplicons," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-8, January.
  28. Pirjo Wacklin & Harri Mäkivuokko & Noora Alakulppi & Janne Nikkilä & Heli Tenkanen & Jarkko Räbinä & Jukka Partanen & Kari Aranko & Jaana Mättö, 2011. "Secretor Genotype (FUT2 gene) Is Strongly Associated with the Composition of Bifidobacteria in the Human Intestine," PLOS ONE, Public Library of Science, vol. 6(5), pages 1-10, May.
  29. Yunxi Liu & R. A. Leo Elworth & Michael D. Jochum & Kjersti M. Aagaard & Todd J. Treangen, 2022. "De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  30. Andrea Fontana & Concetta Panebianco & Andrea Picchianti-Diamanti & Bruno Laganà & Duccio Cavalieri & Adele Potenza & Riccardo Pracella & Elena Binda & Massimiliano Copetti & Valerio Pazienza, 2019. "Gut Microbiota Profiles Differ among Individuals Depending on Their Region of Origin: An Italian Pilot Study," IJERPH, MDPI, vol. 16(21), pages 1-20, October.
  31. C. E. Dubé & M. Ziegler & A. Mercière & E. Boissin & S. Planes & C. A. -F. Bourmaud & C. R. Voolstra, 2021. "Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
  32. Koji Hosomi & Mayu Saito & Jonguk Park & Haruka Murakami & Naoko Shibata & Masahiro Ando & Takahiro Nagatake & Kana Konishi & Harumi Ohno & Kumpei Tanisawa & Attayeb Mohsen & Yi-An Chen & Hitoshi Kawa, 2022. "Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  33. Marina Sanchez & Shirin Panahi & Angelo Tremblay, 2014. "Childhood Obesity: A Role for Gut Microbiota?," IJERPH, MDPI, vol. 12(1), pages 1-14, December.
  34. Dongyang Yang & Wei Xu, 2023. "Estimation of Mediation Effect on Zero-Inflated Microbiome Mediators," Mathematics, MDPI, vol. 11(13), pages 1-16, June.
  35. Taylor Priest & Ellen Oldenburg & Ovidiu Popa & Bledina Dede & Katja Metfies & Wilken-Jon Appen & Sinhué Torres-Valdés & Christina Bienhold & Bernhard M. Fuchs & Rudolf Amann & Antje Boetius & Matthia, 2025. "Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  36. Mariana F. Fernández & Iris Reina-Pérez & Juan Manuel Astorga & Andrea Rodríguez-Carrillo & Julio Plaza-Díaz & Luis Fontana, 2018. "Breast Cancer and Its Relationship with the Microbiota," IJERPH, MDPI, vol. 15(8), pages 1-20, August.
  37. Agnieszka Mika & Will Van Treuren & Antonio González & Jonathan J Herrera & Rob Knight & Monika Fleshner, 2015. "Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-20, May.
  38. Thomas J Sharpton & Samantha J Riesenfeld & Steven W Kembel & Joshua Ladau & James P O'Dwyer & Jessica L Green & Jonathan A Eisen & Katherine S Pollard, 2011. "PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data," PLOS Computational Biology, Public Library of Science, vol. 7(1), pages 1-13, January.
  39. Alba Ordoñez-Rodriguez & Pablo Roman & Lola Rueda-Ruzafa & Ana Campos-Rios & Diana Cardona, 2023. "Changes in Gut Microbiota and Multiple Sclerosis: A Systematic Review," IJERPH, MDPI, vol. 20(5), pages 1-16, March.
  40. Sanjeena Subedi & Drew Neish & Stephen Bak & Zeny Feng, 2020. "Cluster analysis of microbiome data by using mixtures of Dirichlet–multinomial regression models," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 69(5), pages 1163-1187, November.
  41. Gertrude Ecklu-Mensah & Candice Choo-Kang & Maria Gjerstad Maseng & Sonya Donato & Pascal Bovet & Bharathi Viswanathan & Kweku Bedu-Addo & Jacob Plange-Rhule & Prince Oti Boateng & Terrence E. Forrest, 2023. "Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  42. Lai Jiang & Kathryn L Penney & Edward Giovannucci & Peter Kraft & Kathryn M Wilson, 2018. "A genome-wide association study of energy intake and expenditure," PLOS ONE, Public Library of Science, vol. 13(8), pages 1-18, August.
  43. Wodan Ling & Jiuyao Lu & Ni Zhao & Anju Lulla & Anna M. Plantinga & Weijia Fu & Angela Zhang & Hongjiao Liu & Hoseung Song & Zhigang Li & Jun Chen & Timothy W. Randolph & Wei Li A. Koay & James R. Whi, 2022. "Batch effects removal for microbiome data via conditional quantile regression," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  44. Li, Huimin & Wang, Jinru, 2024. "Sparse basis covariance matrix estimation for high dimensional compositional data via hard thresholding," Statistics & Probability Letters, Elsevier, vol. 209(C).
  45. Daniela Langfeldt & Sven C Neulinger & Wieland Heuer & Ingmar Staufenbiel & Sven Künzel & John F Baines & Jörg Eberhard & Ruth A Schmitz, 2014. "Composition of Microbial Oral Biofilms during Maturation in Young Healthy Adults," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-8, February.
  46. Silvia Rodrigues Jardim & Lucila Marieta Perrotta de Souza & Heitor Siffert Pereira de Souza, 2023. "The Rise of Gastrointestinal Cancers as a Global Phenomenon: Unhealthy Behavior or Progress?," IJERPH, MDPI, vol. 20(4), pages 1-23, February.
  47. Jeffrey D Galley & Michael Bailey & Claire Kamp Dush & Sarah Schoppe-Sullivan & Lisa M Christian, 2014. "Maternal Obesity Is Associated with Alterations in the Gut Microbiome in Toddlers," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-13, November.
  48. Shinji Fukuda & Yumiko Nakanishi & Eisuke Chikayama & Hiroshi Ohno & Tsuneo Hino & Jun Kikuchi, 2009. "Evaluation and Characterization of Bacterial Metabolic Dynamics with a Novel Profiling Technique, Real-Time Metabolotyping," PLOS ONE, Public Library of Science, vol. 4(3), pages 1-10, March.
  49. Liangwu Qiu & Fuhong Gong & Jiang Wu & Dingyun You & Yinzhou Zhao & Lianwu Xu & Xue Cao & Fukai Bao, 2022. "Exercise Interventions Improved Sleep Quality through Regulating Intestinal Microbiota Composition," IJERPH, MDPI, vol. 19(19), pages 1-14, September.
  50. Hannah Lees & Jonathan Swann & Simon M Poucher & Jeremy K Nicholson & Elaine Holmes & Ian D Wilson & Julian R Marchesi, 2014. "Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
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