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https://www.readbyqxmd.com/read/29138485/evaluating-the-impact-of-domestication-and-captivity-on-the-horse-gut-microbiome
#1
Jessica L Metcalf, Se Jin Song, James T Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie, Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly modified...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29116004/reproductive-profiles-and-risk-of-breast-cancer-subtypes-a-multi-center-case-only-study
#2
Olivier Brouckaert, Anja Rudolph, Annouschka Laenen, Renske Keeman, Manjeet K Bolla, Qin Wang, Adelheid Soubry, Hans Wildiers, Irene L Andrulis, Volker Arndt, Matthias W Beckmann, Javier Benitez, Carl Blomqvist, Stig E Bojesen, Hiltrud Brauch, Paul Brennan, Hermann Brenner, Georgia Chenevix-Trench, Ji-Yeob Choi, Sten Cornelissen, Fergus J Couch, Angela Cox, Simon S Cross, Kamila Czene, Mikael Eriksson, Peter A Fasching, Jonine Figueroa, Henrik Flyger, Graham G Giles, Anna González-Neira, Pascal Guénel, Per Hall, Antoinette Hollestelle, John L Hopper, Hidemi Ito, Michael Jones, Daehee Kang, Julia A Knight, Veli-Matti Kosma, Jingmei Li, Annika Lindblom, Jenna Lilyquist, Artitaya Lophatananon, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, Keitaro Matsuo, Kenneth Muir, Heli Nevanlinna, Paolo Peterlongo, Katri Pylkäs, Suleeporn Saajrang, Caroline Seynaeve, Chen-Yang Shen, Xiao-Ou Shu, Melissa C Southey, Anthony Swerdlow, Soo-Hwang Teo, Rob A E M Tollenaar, Thérèse Truong, Chiu-Chen Tseng, Alexandra J van den Broek, Carolien H M van Deurzen, Robert Winqvist, Anna H Wu, Cheng Har Yip, Jyh-Cherng Yu, Wei Zheng, Roger L Milne, Paul D P Pharoah, Douglas F Easton, Marjanka K Schmidt, Montserrat Garcia-Closas, Jenny Chang-Claude, Diether Lambrechts, Patrick Neven
BACKGROUND: Previous studies have shown that reproductive factors are differentially associated with breast cancer (BC) risk by subtypes. The aim of this study was to investigate associations between reproductive factors and BC subtypes, and whether these vary by age at diagnosis. METHODS: We used pooled data on tumor markers (estrogen and progesterone receptor, human epidermal growth factor receptor-2 (HER2)) and reproductive risk factors (parity, age at first full-time pregnancy (FFTP) and age at menarche) from 28,095 patients with invasive BC from 34 studies participating in the Breast Cancer Association Consortium (BCAC)...
November 7, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29069100/gut-microbiome-of-mothers-delivering-prematurely-shows-reduced-diversity-and-lower-relative-abundance-of-bifidobacterium-and-streptococcus
#3
Cecilie Dahl, Maggie Stanislawski, Nina Iszatt, Siddhartha Mandal, Catherine Lozupone, Jose C Clemente, Rob Knight, Hein Stigum, Merete Eggesbø
OBJECTIVE: Preterm birth is the main reason for neonatal deaths worldwide. We investigate whether maternal gut microbiota may play a previously overlooked role. METHODS: The Norwegian Microbiota Study (NoMIC) is a case control study on preterm birth (<259 days of gestation, calculated primarily based on the last menstrual period), including two consecutively born term infants per infant born prematurely. Eligible mothers were fluent in Norwegian and recruited from the maternity ward at a county hospital in Eastern Norway in the period 2002-2005...
2017: PloS One
https://www.readbyqxmd.com/read/29059683/association-analysis-identifies-65-new-breast-cancer-risk-loci
#4
Kyriaki Michailidou, Sara Lindström, Joe Dennis, Jonathan Beesley, Shirley Hui, Siddhartha Kar, Audrey Lemaçon, Penny Soucy, Dylan Glubb, Asha Rostamianfar, Manjeet K Bolla, Qin Wang, Jonathan Tyrer, Ed Dicks, Andrew Lee, Zhaoming Wang, Jamie Allen, Renske Keeman, Ursula Eilber, Juliet D French, Xiao Qing Chen, Laura Fachal, Karen McCue, Amy E McCart Reed, Maya Ghoussaini, Jason S Carroll, Xia Jiang, Hilary Finucane, Marcia Adams, Muriel A Adank, Habibul Ahsan, Kristiina Aittomäki, Hoda Anton-Culver, Natalia N Antonenkova, Volker Arndt, Kristan J Aronson, Banu Arun, Paul L Auer, François Bacot, Myrto Barrdahl, Caroline Baynes, Matthias W Beckmann, Sabine Behrens, Javier Benitez, Marina Bermisheva, Leslie Bernstein, Carl Blomqvist, Natalia V Bogdanova, Stig E Bojesen, Bernardo Bonanni, Anne-Lise Børresen-Dale, Judith S Brand, Hiltrud Brauch, Paul Brennan, Hermann Brenner, Louise Brinton, Per Broberg, Ian W Brock, Annegien Broeks, Angela Brooks-Wilson, Sara Y Brucker, Thomas Brüning, Barbara Burwinkel, Katja Butterbach, Qiuyin Cai, Hui Cai, Trinidad Caldés, Federico Canzian, Angel Carracedo, Brian D Carter, Jose E Castelao, Tsun L Chan, Ting-Yuan David Cheng, Kee Seng Chia, Ji-Yeob Choi, Hans Christiansen, Christine L Clarke, Margriet Collée, Don M Conroy, Emilie Cordina-Duverger, Sten Cornelissen, David G Cox, Angela Cox, Simon S Cross, Julie M Cunningham, Kamila Czene, Mary B Daly, Peter Devilee, Kimberly F Doheny, Thilo Dörk, Isabel Dos-Santos-Silva, Martine Dumont, Lorraine Durcan, Miriam Dwek, Diana M Eccles, Arif B Ekici, A Heather Eliassen, Carolina Ellberg, Mingajeva Elvira, Christoph Engel, Mikael Eriksson, Peter A Fasching, Jonine Figueroa, Dieter Flesch-Janys, Olivia Fletcher, Henrik Flyger, Lin Fritschi, Valerie Gaborieau, Marike Gabrielson, Manuela Gago-Dominguez, Yu-Tang Gao, Susan M Gapstur, José A García-Sáenz, Mia M Gaudet, Vassilios Georgoulias, Graham G Giles, Gord Glendon, Mark S Goldberg, David E Goldgar, Anna González-Neira, Grethe I Grenaker Alnæs, Mervi Grip, Jacek Gronwald, Anne Grundy, Pascal Guénel, Lothar Haeberle, Eric Hahnen, Christopher A Haiman, Niclas Håkansson, Ute Hamann, Nathalie Hamel, Susan Hankinson, Patricia Harrington, Steven N Hart, Jaana M Hartikainen, Mikael Hartman, Alexander Hein, Jane Heyworth, Belynda Hicks, Peter Hillemanns, Dona N Ho, Antoinette Hollestelle, Maartje J Hooning, Robert N Hoover, John L Hopper, Ming-Feng Hou, Chia-Ni Hsiung, Guanmengqian Huang, Keith Humphreys, Junko Ishiguro, Hidemi Ito, Motoki Iwasaki, Hiroji Iwata, Anna Jakubowska, Wolfgang Janni, Esther M John, Nichola Johnson, Kristine Jones, Michael Jones, Arja Jukkola-Vuorinen, Rudolf Kaaks, Maria Kabisch, Katarzyna Kaczmarek, Daehee Kang, Yoshio Kasuga, Michael J Kerin, Sofia Khan, Elza Khusnutdinova, Johanna I Kiiski, Sung-Won Kim, Julia A Knight, Veli-Matti Kosma, Vessela N Kristensen, Ute Krüger, Ava Kwong, Diether Lambrechts, Loic Le Marchand, Eunjung Lee, Min Hyuk Lee, Jong Won Lee, Chuen Neng Lee, Flavio Lejbkowicz, Jingmei Li, Jenna Lilyquist, Annika Lindblom, Jolanta Lissowska, Wing-Yee Lo, Sibylle Loibl, Jirong Long, Artitaya Lophatananon, Jan Lubinski, Craig Luccarini, Michael P Lux, Edmond S K Ma, Robert J MacInnis, Tom Maishman, Enes Makalic, Kathleen E Malone, Ivana Maleva Kostovska, Arto Mannermaa, Siranoush Manoukian, JoAnn E Manson, Sara Margolin, Shivaani Mariapun, Maria Elena Martinez, Keitaro Matsuo, Dimitrios Mavroudis, James McKay, Catriona McLean, Hanne Meijers-Heijboer, Alfons Meindl, Primitiva Menéndez, Usha Menon, Jeffery Meyer, Hui Miao, Nicola Miller, Nur Aishah Mohd Taib, Kenneth Muir, Anna Marie Mulligan, Claire Mulot, Susan L Neuhausen, Heli Nevanlinna, Patrick Neven, Sune F Nielsen, Dong-Young Noh, Børge G Nordestgaard, Aaron Norman, Olufunmilayo I Olopade, Janet E Olson, Håkan Olsson, Curtis Olswold, Nick Orr, V Shane Pankratz, Sue K Park, Tjoung-Won Park-Simon, Rachel Lloyd, Jose I A Perez, Paolo Peterlongo, Julian Peto, Kelly-Anne Phillips, Mila Pinchev, Dijana Plaseska-Karanfilska, Ross Prentice, Nadege Presneau, Darya Prokofyeva, Elizabeth Pugh, Katri Pylkäs, Brigitte Rack, Paolo Radice, Nazneen Rahman, Gadi Rennert, Hedy S Rennert, Valerie Rhenius, Atocha Romero, Jane Romm, Kathryn J Ruddy, Thomas Rüdiger, Anja Rudolph, Matthias Ruebner, Emiel J T Rutgers, Emmanouil Saloustros, Dale P Sandler, Suleeporn Sangrajrang, Elinor J Sawyer, Daniel F Schmidt, Rita K Schmutzler, Andreas Schneeweiss, Minouk J Schoemaker, Fredrick Schumacher, Peter Schürmann, Rodney J Scott, Christopher Scott, Sheila Seal, Caroline Seynaeve, Mitul Shah, Priyanka Sharma, Chen-Yang Shen, Grace Sheng, Mark E Sherman, Martha J Shrubsole, Xiao-Ou Shu, Ann Smeets, Christof Sohn, Melissa C Southey, John J Spinelli, Christa Stegmaier, Sarah Stewart-Brown, Jennifer Stone, Daniel O Stram, Harald Surowy, Anthony Swerdlow, Rulla Tamimi, Jack A Taylor, Maria Tengström, Soo H Teo, Mary Beth Terry, Daniel C Tessier, Somchai Thanasitthichai, Kathrin Thöne, Rob A E M Tollenaar, Ian Tomlinson, Ling Tong, Diana Torres, Thérèse Truong, Chiu-Chen Tseng, Shoichiro Tsugane, Hans-Ulrich Ulmer, Giske Ursin, Michael Untch, Celine Vachon, Christi J van Asperen, David Van Den Berg, Ans M W van den Ouweland, Lizet van der Kolk, Rob B van der Luijt, Daniel Vincent, Jason Vollenweider, Quinten Waisfisz, Shan Wang-Gohrke, Clarice R Weinberg, Camilla Wendt, Alice S Whittemore, Hans Wildiers, Walter Willett, Robert Winqvist, Alicja Wolk, Anna H Wu, Lucy Xia, Taiki Yamaji, Xiaohong R Yang, Cheng Har Yip, Keun-Young Yoo, Jyh-Cherng Yu, Wei Zheng, Ying Zheng, Bin Zhu, Argyrios Ziogas, Elad Ziv, Sunil R Lakhani, Antonis C Antoniou, Arnaud Droit, Irene L Andrulis, Christopher I Amos, Fergus J Couch, Paul D P Pharoah, Jenny Chang-Claude, Per Hall, David J Hunter, Roger L Milne, Montserrat García-Closas, Marjanka K Schmidt, Stephen J Chanock, Alison M Dunning, Stacey L Edwards, Gary D Bader, Georgia Chenevix-Trench, Jacques Simard, Peter Kraft, Douglas F Easton
Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry. We identified 65 new loci that are associated with overall breast cancer risk at P < 5 × 10(-8)...
November 2, 2017: Nature
https://www.readbyqxmd.com/read/29058716/identification-of-ten-variants-associated-with-risk-of-estrogen-receptor-negative-breast-cancer
#5
Roger L Milne, Karoline B Kuchenbaecker, Kyriaki Michailidou, Jonathan Beesley, Siddhartha Kar, Sara Lindström, Shirley Hui, Audrey Lemaçon, Penny Soucy, Joe Dennis, Xia Jiang, Asha Rostamianfar, Hilary Finucane, Manjeet K Bolla, Lesley McGuffog, Qin Wang, Cora M Aalfs, Marcia Adams, Julian Adlard, Simona Agata, Shahana Ahmed, Habibul Ahsan, Kristiina Aittomäki, Fares Al-Ejeh, Jamie Allen, Christine B Ambrosone, Christopher I Amos, Irene L Andrulis, Hoda Anton-Culver, Natalia N Antonenkova, Volker Arndt, Norbert Arnold, Kristan J Aronson, Bernd Auber, Paul L Auer, Margreet G E M Ausems, Jacopo Azzollini, François Bacot, Judith Balmaña, Monica Barile, Laure Barjhoux, Rosa B Barkardottir, Myrto Barrdahl, Daniel Barnes, Daniel Barrowdale, Caroline Baynes, Matthias W Beckmann, Javier Benitez, Marina Bermisheva, Leslie Bernstein, Yves-Jean Bignon, Kathleen R Blazer, Marinus J Blok, Carl Blomqvist, William Blot, Kristie Bobolis, Bram Boeckx, Natalia V Bogdanova, Anders Bojesen, Stig E Bojesen, Bernardo Bonanni, Anne-Lise Børresen-Dale, Aniko Bozsik, Angela R Bradbury, Judith S Brand, Hiltrud Brauch, Hermann Brenner, Brigitte Bressac-de Paillerets, Carole Brewer, Louise Brinton, Per Broberg, Angela Brooks-Wilson, Joan Brunet, Thomas Brüning, Barbara Burwinkel, Saundra S Buys, Jinyoung Byun, Qiuyin Cai, Trinidad Caldés, Maria A Caligo, Ian Campbell, Federico Canzian, Olivier Caron, Angel Carracedo, Brian D Carter, J Esteban Castelao, Laurent Castera, Virginie Caux-Moncoutier, Salina B Chan, Jenny Chang-Claude, Stephen J Chanock, Xiaoqing Chen, Ting-Yuan David Cheng, Jocelyne Chiquette, Hans Christiansen, Kathleen B M Claes, Christine L Clarke, Thomas Conner, Don M Conroy, Jackie Cook, Emilie Cordina-Duverger, Sten Cornelissen, Isabelle Coupier, Angela Cox, David G Cox, Simon S Cross, Katarina Cuk, Julie M Cunningham, Kamila Czene, Mary B Daly, Francesca Damiola, Hatef Darabi, Rosemarie Davidson, Kim De Leeneer, Peter Devilee, Ed Dicks, Orland Diez, Yuan Chun Ding, Nina Ditsch, Kimberly F Doheny, Susan M Domchek, Cecilia M Dorfling, Thilo Dörk, Isabel Dos-Santos-Silva, Stéphane Dubois, Pierre-Antoine Dugué, Martine Dumont, Alison M Dunning, Lorraine Durcan, Miriam Dwek, Bernd Dworniczak, Diana Eccles, Ros Eeles, Hans Ehrencrona, Ursula Eilber, Bent Ejlertsen, Arif B Ekici, A Heather Eliassen, Christoph Engel, Mikael Eriksson, Laura Fachal, Laurence Faivre, Peter A Fasching, Ulrike Faust, Jonine Figueroa, Dieter Flesch-Janys, Olivia Fletcher, Henrik Flyger, William D Foulkes, Eitan Friedman, Lin Fritschi, Debra Frost, Marike Gabrielson, Pragna Gaddam, Marilie D Gammon, Patricia A Ganz, Susan M Gapstur, Judy Garber, Vanesa Garcia-Barberan, José A García-Sáenz, Mia M Gaudet, Marion Gauthier-Villars, Andrea Gehrig, Vassilios Georgoulias, Anne-Marie Gerdes, Graham G Giles, Gord Glendon, Andrew K Godwin, Mark S Goldberg, David E Goldgar, Anna González-Neira, Paul Goodfellow, Mark H Greene, Grethe I Grenaker Alnæs, Mervi Grip, Jacek Gronwald, Anne Grundy, Daphne Gschwantler-Kaulich, Pascal Guénel, Qi Guo, Lothar Haeberle, Eric Hahnen, Christopher A Haiman, Niclas Håkansson, Emily Hallberg, Ute Hamann, Nathalie Hamel, Susan Hankinson, Thomas V O Hansen, Patricia Harrington, Steven N Hart, Jaana M Hartikainen, Catherine S Healey, Alexander Hein, Sonja Helbig, Alex Henderson, Jane Heyworth, Belynda Hicks, Peter Hillemanns, Shirley Hodgson, Frans B Hogervorst, Antoinette Hollestelle, Maartje J Hooning, Bob Hoover, John L Hopper, Chunling Hu, Guanmengqian Huang, Peter J Hulick, Keith Humphreys, David J Hunter, Evgeny N Imyanitov, Claudine Isaacs, Motoki Iwasaki, Louise Izatt, Anna Jakubowska, Paul James, Ramunas Janavicius, Wolfgang Janni, Uffe Birk Jensen, Esther M John, Nichola Johnson, Kristine Jones, Michael Jones, Arja Jukkola-Vuorinen, Rudolf Kaaks, Maria Kabisch, Katarzyna Kaczmarek, Daehee Kang, Karin Kast, Renske Keeman, Michael J Kerin, Carolien M Kets, Machteld Keupers, Sofia Khan, Elza Khusnutdinova, Johanna I Kiiski, Sung-Won Kim, Julia A Knight, Irene Konstantopoulou, Veli-Matti Kosma, Vessela N Kristensen, Torben A Kruse, Ava Kwong, Anne-Vibeke Lænkholm, Yael Laitman, Fiona Lalloo, Diether Lambrechts, Keren Landsman, Christine Lasset, Conxi Lazaro, Loic Le Marchand, Julie Lecarpentier, Andrew Lee, Eunjung Lee, Jong Won Lee, Min Hyuk Lee, Flavio Lejbkowicz, Fabienne Lesueur, Jingmei Li, Jenna Lilyquist, Anne Lincoln, Annika Lindblom, Jolanta Lissowska, Wing-Yee Lo, Sibylle Loibl, Jirong Long, Jennifer T Loud, Jan Lubinski, Craig Luccarini, Michael Lush, Robert J MacInnis, Tom Maishman, Enes Makalic, Ivana Maleva Kostovska, Kathleen E Malone, Siranoush Manoukian, JoAnn E Manson, Sara Margolin, John W M Martens, Maria Elena Martinez, Keitaro Matsuo, Dimitrios Mavroudis, Sylvie Mazoyer, Catriona McLean, Hanne Meijers-Heijboer, Primitiva Menéndez, Jeffery Meyer, Hui Miao, Austin Miller, Nicola Miller, Gillian Mitchell, Marco Montagna, Kenneth Muir, Anna Marie Mulligan, Claire Mulot, Sue Nadesan, Katherine L Nathanson, Susan L Neuhausen, Heli Nevanlinna, Ines Nevelsteen, Dieter Niederacher, Sune F Nielsen, Børge G Nordestgaard, Aaron Norman, Robert L Nussbaum, Edith Olah, Olufunmilayo I Olopade, Janet E Olson, Curtis Olswold, Kai-Ren Ong, Jan C Oosterwijk, Nick Orr, Ana Osorio, V Shane Pankratz, Laura Papi, Tjoung-Won Park-Simon, Ylva Paulsson-Karlsson, Rachel Lloyd, Inge Søkilde Pedersen, Bernard Peissel, Ana Peixoto, Jose I A Perez, Paolo Peterlongo, Julian Peto, Georg Pfeiler, Catherine M Phelan, Mila Pinchev, Dijana Plaseska-Karanfilska, Bruce Poppe, Mary E Porteous, Ross Prentice, Nadege Presneau, Darya Prokofieva, Elizabeth Pugh, Miquel Angel Pujana, Katri Pylkäs, Brigitte Rack, Paolo Radice, Nazneen Rahman, Johanna Rantala, Christine Rappaport-Fuerhauser, Gad Rennert, Hedy S Rennert, Valerie Rhenius, Kerstin Rhiem, Andrea Richardson, Gustavo C Rodriguez, Atocha Romero, Jane Romm, Matti A Rookus, Anja Rudolph, Thomas Ruediger, Emmanouil Saloustros, Joyce Sanders, Dale P Sandler, Suleeporn Sangrajrang, Elinor J Sawyer, Daniel F Schmidt, Minouk J Schoemaker, Fredrick Schumacher, Peter Schürmann, Lukas Schwentner, Christopher Scott, Rodney J Scott, Sheila Seal, Leigha Senter, Caroline Seynaeve, Mitul Shah, Priyanka Sharma, Chen-Yang Shen, Xin Sheng, Hermela Shimelis, Martha J Shrubsole, Xiao-Ou Shu, Lucy E Side, Christian F Singer, Christof Sohn, Melissa C Southey, John J Spinelli, Amanda B Spurdle, Christa Stegmaier, Dominique Stoppa-Lyonnet, Grzegorz Sukiennicki, Harald Surowy, Christian Sutter, Anthony Swerdlow, Csilla I Szabo, Rulla M Tamimi, Yen Y Tan, Jack A Taylor, Maria-Isabel Tejada, Maria Tengström, Soo H Teo, Mary B Terry, Daniel C Tessier, Alex Teulé, Kathrin Thöne, Darcy L Thull, Maria Grazia Tibiletti, Laima Tihomirova, Marc Tischkowitz, Amanda E Toland, Rob A E M Tollenaar, Ian Tomlinson, Ling Tong, Diana Torres, Martine Tranchant, Thérèse Truong, Kathy Tucker, Nadine Tung, Jonathan Tyrer, Hans-Ulrich Ulmer, Celine Vachon, Christi J van Asperen, David Van Den Berg, Ans M W van den Ouweland, Elizabeth J van Rensburg, Liliana Varesco, Raymonda Varon-Mateeva, Ana Vega, Alessandra Viel, Joseph Vijai, Daniel Vincent, Jason Vollenweider, Lisa Walker, Zhaoming Wang, Shan Wang-Gohrke, Barbara Wappenschmidt, Clarice R Weinberg, Jeffrey N Weitzel, Camilla Wendt, Jelle Wesseling, Alice S Whittemore, Juul T Wijnen, Walter Willett, Robert Winqvist, Alicja Wolk, Anna H Wu, Lucy Xia, Xiaohong R Yang, Drakoulis Yannoukakos, Daniela Zaffaroni, Wei Zheng, Bin Zhu, Argyrios Ziogas, Elad Ziv, Kristin K Zorn, Manuela Gago-Dominguez, Arto Mannermaa, Håkan Olsson, Manuel R Teixeira, Jennifer Stone, Kenneth Offit, Laura Ottini, Sue K Park, Mads Thomassen, Per Hall, Alfons Meindl, Rita K Schmutzler, Arnaud Droit, Gary D Bader, Paul D P Pharoah, Fergus J Couch, Douglas F Easton, Peter Kraft, Georgia Chenevix-Trench, Montserrat García-Closas, Marjanka K Schmidt, Antonis C Antoniou, Jacques Simard
Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10(-8) with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies...
October 23, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29056429/three-dimensional-microbiome-and-metabolome-cartography-of-a-diseased-human-lung
#6
Neha Garg, Mingxun Wang, Embriette Hyde, Ricardo R da Silva, Alexey V Melnik, Ivan Protsyuk, Amina Bouslimani, Yan Wei Lim, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S Brouha, Nuno Bandeira, Grace Y Lin, Forest Rohwer, Douglas J Conrad, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein
Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient...
November 8, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/29042495/impact-of-dietary-resistant-starch-on-the-human-gut-microbiome-metaproteome-and-metabolome
#7
Tanja V Maier, Marianna Lucio, Lang Ho Lee, Nathan C VerBerkmoes, Colin J Brislawn, Jörg Bernhardt, Regina Lamendella, Jason E McDermott, Nathalie Bergeron, Silke S Heinzmann, James T Morton, Antonio González, Gail Ackermann, Rob Knight, Katharina Riedel, Ronald M Krauss, Philippe Schmitt-Kopplin, Janet K Jansson
Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS. We determined the impact of RS on the gut microbiome and metabolic pathways in the gut, using a combination of "omics" approaches, including 16S rRNA gene sequencing, metaproteomics, and metabolomics...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29034330/perinatal-bisphenol-a-exposure-induces-chronic-inflammation-in-rabbit-offspring-via-modulation-of-gut-bacteria-and-their-metabolites
#8
Lavanya Reddivari, D N Rao Veeramachaneni, William A Walters, Catherine Lozupone, Jennifer Palmer, M K Kurundu Hewage, Rohil Bhatnagar, Amnon Amir, Mary J Kennett, Rob Knight, Jairam K P Vanamala
Bisphenol A (BPA) accumulates in the maturing gut and liver in utero and is known to alter gut bacterial profiles in offspring. Gut bacterial dysbiosis may contribute to chronic colonic and systemic inflammation. We hypothesized that perinatal BPA exposure-induced intestinal (and liver) inflammation in offspring is due to alterations in the microbiome and colonic metabolome. The 16S rRNA amplicon sequencing analysis revealed differences in beta diversity with a significant reduction in the relative abundances of short-chain fatty acid (SCFA) producers such as Oscillospira and Ruminococcaceae due to BPA exposure...
September 2017: MSystems
https://www.readbyqxmd.com/read/29022944/erratum-strains-functions-and-dynamics-in-the-expanded-human-microbiome-project
#9
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A Brantley Hall, Arthur Brady, Heather H Creasy, Carrie McCracken, Michelle G Giglio, Daniel McDonald, Eric A Franzosa, Rob Knight, Owen White, Curtis Huttenhower
This corrects the article DOI: 10.1038/nature23889.
October 12, 2017: Nature
https://www.readbyqxmd.com/read/29020741/the-sponge-microbiome-project
#10
Lucas Moitinho-Silva, Shaun Nielsen, Amnon Amir, Antonio Gonzalez, Gail L Ackermann, Carlo Cerrano, Carmen Astudillo-Garcia, Cole Easson, Detmer Sipkema, Fang Liu, Georg Steinert, Giorgos Kotoulas, Grace P McCormack, Guofang Feng, James J Bell, Jan Vicente, Johannes R Björk, Jose M Montoya, Julie B Olson, Julie Reveillaud, Laura Steindler, Mari-Carmen Pineda, Maria V Marra, Micha Ilan, Michael W Taylor, Paraskevi Polymenakou, Patrick M Erwin, Peter J Schupp, Rachel L Simister, Rob Knight, Robert W Thacker, Rodrigo Costa, Russell T Hill, Susanna Lopez-Legentil, Thanos Dailianis, Timothy Ravasi, Ute Hentschel, Zhiyong Li, Nicole S Webster, Torsten Thomas
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28985400/dramatic-differences-in-gut-bacterial-densities-correlate-with-diet-and-habitat-in-rainforest-ants
#11
Jon G Sanders, Piotr Lukasik, Megan E Frederickson, Jacob A Russell, Ryuichi Koga, Rob Knight, Naomi E Pierce
Abundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative polymerase chain reaction as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing...
July 27, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28985326/the-effects-of-captivity-on-the-mammalian-gut-microbiome
#12
Valerie J McKenzie, Se Jin Song, Frédéric Delsuc, Tiffany L Prest, Angela M Oliverio, Timothy M Korpita, Alexandra Alexiev, Katherine R Amato, Jessica L Metcalf, Martin Kowalewski, Nico L Avenant, Andres Link, Anthony Di Fiore, Andaine Seguin-Orlando, Claudia Feh, Ludovic Orlando, Joseph R Mendelson, Jon Sanders, Rob Knight
Recent studies increasingly note the effect of captivity or the built environment on the microbiome of humans and other animals. As symbiotic microbes are essential to many aspects of biology (e.g., digestive and immune functions), it is important to understand how lifestyle differences can impact the microbiome, and, consequently, the health of hosts. Animals living in captivity experience a range of changes that may influence the gut bacteria, such as diet changes, treatments, and reduced contact with other individuals, species and variable environmental substrates that act as sources of bacterial diversity...
August 7, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28968189/impacts-of-the-human-gut-microbiome-on-therapeutics
#13
Yoshiki Vázquez-Baeza, Chris Callewaert, Justine Debelius, Embriette Hyde, Clarisse Marotz, James T Morton, Austin Swafford, Alison Vrbanac, Pieter C Dorrestein, Rob Knight
The human microbiome contains a vast source of genetic and biochemical variation, and its impacts on therapeutic responses are just beginning to be understood. This expanded understanding is especially important because the human microbiome differs far more among different people than does the human genome, and it is also dramatically easier to change. Here, we describe some of the major factors driving differences in the human microbiome among individuals and populations. We then describe some of the many ways in which gut microbes modify the action of specific chemotherapeutic agents, including nonsteroidal anti-inflammatory drugs and cardiac glycosides, and outline the potential of fecal microbiota transplant as a therapeutic...
October 2, 2017: Annual Review of Pharmacology and Toxicology
https://www.readbyqxmd.com/read/28967885/assessment-of-variation-in-microbial-community-amplicon-sequencing-by-the-microbiome-quality-control-mbqc-project-consortium
#14
Rashmi Sinha, Galeb Abu-Ali, Emily Vogtmann, Anthony A Fodor, Boyu Ren, Amnon Amir, Emma Schwager, Jonathan Crabtree, Siyuan Ma, Christian C Abnet, Rob Knight, Owen White, Curtis Huttenhower
In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols...
November 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28953883/strains-functions-and-dynamics-in-the-expanded-human-microbiome-project
#15
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A Brantley Hall, Arthur Brady, Heather H Creasy, Carrie McCracken, Michelle G Giglio, Daniel McDonald, Eric A Franzosa, Rob Knight, Owen White, Curtis Huttenhower
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization...
October 5, 2017: Nature
https://www.readbyqxmd.com/read/28894881/erratum-to-diet-versus-phylogeny-a-comparison-of-gut-microbiota-in-captive-colobine-monkey-species
#16
Vanessa L Hale, Chia L Tan, Kefeng Niu, Yeqin Yang, Rob Knight, Qikun Zhang, Duoying Cui, Katherine R Amato
No abstract text is available yet for this article.
September 11, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28893978/gut-bacteria-from-multiple-sclerosis-patients-modulate-human-t-cells-and-exacerbate-symptoms-in-mouse-models
#17
Egle Cekanaviciute, Bryan B Yoo, Tessel F Runia, Justine W Debelius, Sneha Singh, Charlotte A Nelson, Rachel Kanner, Yadira Bencosme, Yun Kyung Lee, Stephen L Hauser, Elizabeth Crabtree-Hartman, Ilana Katz Sand, Mar Gacias, Yunjiao Zhu, Patrizia Casaccia, Bruce A C Cree, Rob Knight, Sarkis K Mazmanian, Sergio E Baranzini
The gut microbiota regulates T cell functions throughout the body. We hypothesized that intestinal bacteria impact the pathogenesis of multiple sclerosis (MS), an autoimmune disorder of the CNS and thus analyzed the microbiomes of 71 MS patients not undergoing treatment and 71 healthy controls. Although no major shifts in microbial community structure were found, we identified specific bacterial taxa that were significantly associated with MS. Akkermansia muciniphila and Acinetobacter calcoaceticus, both increased in MS patients, induced proinflammatory responses in human peripheral blood mononuclear cells and in monocolonized mice...
October 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28892370/mass-spectrometry-based-chemical-cartography-of-a-cardiac-parasitic-infection
#18
Laura-Isobel McCall, James T Morton, Jean A Bernatchez, Jair Lage de Siqueira-Neto, Rob Knight, Pieter C Dorrestein, James H McKerrow
Trypanosoma cruzi parasites are the causative agents of Chagas disease, a leading infectious form of heart failure whose pathogenesis is still not fully characterized. In this work, we applied untargeted liquid chromatography-tandem mass spectrometry to heart sections from T. cruzi-infected and uninfected mice. We combined molecular networking and three-dimensional modeling to generate chemical cartographical heart models. This approach revealed for the first time preferential parasite localization to the base of the heart and regiospecific distributions of nucleoside derivatives and eicosanoids, which we correlated to tissue-damaging immune responses...
September 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28839072/seasonal-cycling-in-the-gut-microbiome-of-the-hadza-hunter-gatherers-of-tanzania
#19
Samuel A Smits, Jeff Leach, Erica D Sonnenburg, Carlos G Gonzalez, Joshua S Lichtman, Gregor Reid, Rob Knight, Alphaxard Manjurano, John Changalucha, Joshua E Elias, Maria Gloria Dominguez-Bello, Justin L Sonnenburg
Although humans have cospeciated with their gut-resident microbes, it is difficult to infer features of our ancestral microbiome. Here, we examine the microbiome profile of 350 stool samples collected longitudinally for more than a year from the Hadza hunter-gatherers of Tanzania. The data reveal annual cyclic reconfiguration of the microbiome, in which some taxa become undetectable only to reappear in a subsequent season. Comparison of the Hadza data set with data collected from 18 populations in 16 countries with varying lifestyles reveals that gut community membership corresponds to modernization: Notably, the taxa within the Hadza that are the most seasonally volatile similarly differentiate industrialized and traditional populations...
August 25, 2017: Science
https://www.readbyqxmd.com/read/28836939/genetic-influences-on-the-human-oral-microbiome
#20
Brittany A Demmitt, Robin P Corley, Brooke M Huibregtse, Matthew C Keller, John K Hewitt, Matthew B McQueen, Rob Knight, Ivy McDermott, Kenneth S Krauter
BACKGROUND: The human oral microbiome is formed early in development. Its composition is influenced by environmental factors including diet, substance use, oral health, and overall health and disease. The influence of human genes on the composition and stability of the oral microbiome is still poorly understood. We studied both environmental and genetic characteristics on the oral microbiome in a large twin sample as well as in a large cohort of unrelated individuals. We identify several significantly heritable features of the oral microbiome...
August 24, 2017: BMC Genomics
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