A core gut microbiome in obese and lean twins
Peter J. Turnbaugh,Micah Hamady,Tanya Yatsunenko,Brandi L. Cantarel,Alexis E. Duncan,Ruth E. Ley,Mitchell L. Sogin,William J. Jones,Bruce A. Roe,Jason P. Affourtit,Michael Egholm,Bernard Henrissat,Andrew C. Heath,Rob Knight,Jeffrey I. Gordon +14 more
TLDR
The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.Abstract:
The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).read more
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Journal ArticleDOI
A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin,Ruiqiang Li,Jeroen Raes,Manimozhiyan Arumugam,Kristoffer Sølvsten Burgdorf,Chaysavanh Manichanh,Trine Nielsen,Nicolas Pons,Florence Levenez,Takuji Yamada,Daniel R. Mende,Junhua Li,Junming Xu,Shaochuan Li,Dongfang Li,Jianjun Cao,Bo Wang,Huiqing Liang,Huisong Zheng,Yinlong Xie,Julien Tap,Patricia Lepage,Marcelo Bertalan,Jean-Michel Batto,Torben Hansen,Denis Le Paslier,Allan Linneberg,H. Bjørn Nielsen,Eric Pelletier,Pierre Renault,Thomas Sicheritz-Pontén,Keith Turner,Hongmei Zhu,Chang Yu,Shengting Li,Min Jian,Yan Zhou,Yingrui Li,Xiuqing Zhang,Songgang Li,Nan Qin,Huanming Yang,Jian Wang,Søren Brunak,Joël Doré,Francisco Guarner,Karsten Kristiansen,Oluf Pedersen,Julian Parkhill,Jean Weissenbach,Peer Bork,S. Dusko Ehrlich,Jun Wang +52 more
TL;DR: The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species.
Journal ArticleDOI
Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the Global Burden of Disease Study 2013
Marie Ng,Tom P Fleming,Margaret Robinson,Blake Thomson,Nicholas Graetz,Christopher Margono,Erin C Mullany,Stan Biryukov,Cristiana Abbafati,Semaw Ferede Abera,Jerry Abraham,Niveen M E Abu-Rmeileh,Tom Achoki,Fadia AlBuhairan,Zewdie Aderaw Alemu,Rafael Alfonso,Mohammed K. Ali,Raghib Ali,Nelson Alvis Guzmán,Walid Ammar,Palwasha Anwari,Amitava Banerjee,Simón Barquera,Sanjay Basu,Derrick A Bennett,Zulfiqar A Bhutta,Jed D. Blore,N Cabral,Ismael Ricardo Campos Nonato,Jung-Chen Chang,Rajiv Chowdhury,Karen J. Courville,Michael H. Criqui,David K. Cundiff,Kaustubh Dabhadkar,Lalit Dandona,Lalit Dandona,Adrian Davis,Anand Dayama,Samath D Dharmaratne,Eric L. Ding,Adnan M. Durrani,Alireza Esteghamati,Farshad Farzadfar,Derek F J Fay,Valery L. Feigin,Abraham D. Flaxman,Mohammad H. Forouzanfar,Atsushi Goto,Mark A. Green,Rajeev Gupta,Nima Hafezi-Nejad,Graeme J. Hankey,Heather Harewood,Rasmus Havmoeller,Simon I. Hay,Lucia Hernandez,Abdullatif Husseini,Bulat Idrisov,Nayu Ikeda,Farhad Islami,Eiman Jahangir,Simerjot K. Jassal,Sun Ha Jee,Mona Jeffreys,Jost B. Jonas,Edmond K. Kabagambe,Shams Eldin Ali Hassan Khalifa,Andre Pascal Kengne,Yousef Khader,Young-Ho Khang,Daniel Kim,Ruth W Kimokoti,Jonas Minet Kinge,Yoshihiro Kokubo,Soewarta Kosen,Gene F. Kwan,Taavi Lai,Mall Leinsalu,Yichong Li,Xiaofeng Liang,Shiwei Liu,Giancarlo Logroscino,Paulo A. Lotufo,Yuan Qiang Lu,Jixiang Ma,Nana Kwaku Mainoo,George A. Mensah,Tony R. Merriman,Ali H. Mokdad,Joanna Moschandreas,Mohsen Naghavi,Aliya Naheed,Devina Nand,K.M. Venkat Narayan,Erica Leigh Nelson,Marian L. Neuhouser,Muhammad Imran Nisar,Takayoshi Ohkubo,Samuel Oti,Andrea Pedroza,Dorairaj Prabhakaran,Nobhojit Roy,Uchechukwu K.A. Sampson,Hyeyoung Seo,Sadaf G. Sepanlou,Kenji Shibuya,Rahman Shiri,Ivy Shiue,Gitanjali M Singh,Jasvinder A. Singh,Vegard Skirbekk,Nicolas J. C. Stapelberg,Lela Sturua,Bryan L. Sykes,Martin Tobias,Bach Xuan Tran,Leonardo Trasande,Hideaki Toyoshima,Steven van de Vijver,Tommi Vasankari,J. Lennert Veerman,Gustavo Velasquez-Melendez,Vasiliy Victorovich Vlassov,Stein Emil Vollset,Stein Emil Vollset,Theo Vos,Claire L. Wang,Xiao Rong Wang,Elisabete Weiderpass,Andrea Werdecker,Jonathan L. Wright,Y Claire Yang,Hiroshi Yatsuya,Jihyun Yoon,Seok Jun Yoon,Yong Zhao,Maigeng Zhou,Shankuan Zhu,Alan D. Lopez,Christopher J L Murray,Emmanuela Gakidou +141 more
TL;DR: The global, regional, and national prevalence of overweight and obesity in children and adults during 1980-2013 is estimated using a spatiotemporal Gaussian process regression model to estimate prevalence with 95% uncertainty intervals (UIs).
Journal ArticleDOI
Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
TL;DR: A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
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