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  1. Content type: Research

    Major risk factors for necrotizing enterocolitis (NEC) include premature birth and formula feeding in the context of microbial colonization of the gastrointestinal tract. We previously showed that feeding form...

    Authors: Lee Call, Barbara Stoll, Berthe Oosterloo, Nadim Ajami, Fariha Sheikh, Anja Wittke, Rosaline Waworuntu, Brian Berg, Joseph Petrosino, Oluyinka Olutoye and Douglas Burrin

    Citation: Microbiome 2018 6:111

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  2. Content type: Research

    In social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short- and long-lived host phenotypes are polari...

    Authors: Kirk E. Anderson, Vincent A. Ricigliano, Brendon M. Mott, Duan C. Copeland, Amy S. Floyd and Patrick Maes

    Citation: Microbiome 2018 6:108

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  3. Content type: Research

    The gut microbiota is closely associated with gastrointestinal (GI) motility disorder, but the mechanism(s) by which bacteria interact with and affect host GI motility remains unclear. In this study, through u...

    Authors: Ling Zhao, Yufen Huang, Lin Lu, Wei Yang, Tao Huang, Zesi Lin, Chengyuan Lin, Hiuyee Kwan, Hoi Leong Xavier Wong, Yang Chen, Silong Sun, Xuefeng Xie, Xiaodong Fang, Huanming Yang, Jian Wang, Lixin Zhu…

    Citation: Microbiome 2018 6:107

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  4. Content type: Research

    pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to “spillover effects” on other chemical parameters (e.g., availability of Al, Fe,...

    Authors: Daniel R. Lammel, Gabriel Barth, Otso Ovaskainen, Leonardo M. Cruz, Josileia A. Zanatta, Masahiro Ryo, Emanuel M. de Souza and Fábio O. Pedrosa

    Citation: Microbiome 2018 6:106

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  5. Content type: Research

    Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the seque...

    Authors: Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, Corinne Da Silva, Patrick Wincker, Eric Pelletier, Ian Probert, Johan Decelle, Stéphane Le Crom, Fabrice Not and Lucie Bittner

    Citation: Microbiome 2018 6:105

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  6. Content type: Research

    Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma. Unraveling the nature and mechanisms of these complex associations will r...

    Authors: Juliana Durack, Yvonne J. Huang, Snehal Nariya, Laura S. Christian, K. Mark Ansel, Avraham Beigelman, Mario Castro, Anne-Marie Dyer, Elliot Israel, Monica Kraft, Richard J. Martin, David T. Mauger, Sharon R. Rosenberg, Tonya S. King, Steven R. White, Loren C. Denlinger…

    Citation: Microbiome 2018 6:104

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  7. Content type: Research

    Huddling is highly evolved as a cooperative behavioral strategy for social mammals to maximize their fitness in harsh environments. Huddling behavior can change psychological and physiological responses. The c...

    Authors: Xue-Ying Zhang, Gansukh Sukhchuluun, Ting-Bei Bo, Qing-Sheng Chi, Jun-Jie Yang, Bin Chen, Lei Zhang and De-Hua Wang

    Citation: Microbiome 2018 6:103

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    The Correction to this article has been published in Microbiome 2018 6:126

  8. Content type: Research

    As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown.

    Authors: Xiaobo Liu, Meng Li, Cindy J. Castelle, Alexander J. Probst, Zhichao Zhou, Jie Pan, Yang Liu, Jillian F. Banfield and Ji-Dong Gu

    Citation: Microbiome 2018 6:102

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  9. Content type: Microbiome Announcement

    In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces un...

    Authors: Jun Wang, Alexander Kurilshikov, Djawad Radjabzadeh, Williams Turpin, Kenneth Croitoru, Marc Jan Bonder, Matthew A. Jackson, Carolina Medina-Gomez, Fabian Frost, Georg Homuth, Malte Rühlemann, David Hughes, Han-na Kim, Tim D. Spector, Jordana T. Bell, Claire J. Steves…

    Citation: Microbiome 2018 6:101

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  10. Content type: Research

    Microbially mediated oral diseases can signal underlying HIV/AIDS progression in HIV-infected adults. The role of the oral microbiota in HIV-infected youth is not known. The Adolescent Master Protocol of the P...

    Authors: Jacqueline R. Starr, Yanmei Huang, Kyu Ha Lee, C. M. Murphy, Anna-Barbara Moscicki, Caroline H. Shiboski, Mark I. Ryder, Tzy-Jyun Yao, Lina L. Faller, Russell B. Van Dyke and Bruce J. Paster

    Citation: Microbiome 2018 6:100

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  11. Content type: Research

    Variation in induced models of autoimmunity has been attributed to the housing environment and its effect on the gut microbiota. In Graves’ disease (GD), autoantibodies to the thyrotropin receptor (TSHR) cause...

    Authors: Giulia Masetti, Sajad Moshkelgosha, Hedda-Luise Köhling, Danila Covelli, Jasvinder Paul Banga, Utta Berchner-Pfannschmidt, Mareike Horstmann, Salvador Diaz-Cano, Gina-Eva Goertz, Sue Plummer, Anja Eckstein, Marian Ludgate, Filippo Biscarini and Julian Roberto Marchesi

    Citation: Microbiome 2018 6:97

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  12. Content type: Research

    The early-life gut microbiota plays a critical role in host metabolism in later life. However, little is known about how the fatty acid profile of the maternal diet during gestation and lactation influences th...

    Authors: Ruairi C. Robertson, Kanakaraju Kaliannan, Conall R. Strain, R. Paul Ross, Catherine Stanton and Jing X. Kang

    Citation: Microbiome 2018 6:95

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  13. Content type: Review

    After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in de...

    Authors: Melhem Bilen, Jean-Charles Dufour, Jean-Christophe Lagier, Fréderic Cadoret, Ziad Daoud, Grégory Dubourg and Didier Raoult

    Citation: Microbiome 2018 6:94

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  14. Content type: Methodology

    Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their ...

    Authors: Kymberleigh A. Romano, Kimberly A. Dill-McFarland, Kazuyuki Kasahara, Robert L. Kerby, Eugenio I. Vivas, Daniel Amador-Noguez, Pamela Herd and Federico E. Rey

    Citation: Microbiome 2018 6:91

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  15. Content type: Research

    Imbalances of gut microbiota composition are linked to a range of metabolic perturbations. In the present study, we examined the gut microbiota of women with gestational diabetes mellitus (GDM) and normoglycae...

    Authors: Mie Korslund Wiinblad Crusell, Tue Haldor Hansen, Trine Nielsen, Kristine Højgaard Allin, Malte C. Rühlemann, Peter Damm, Henrik Vestergaard, Christina Rørbye, Niklas Rye Jørgensen, Ole Bjarne Christiansen, Femke-Anouska Heinsen, Andre Franke, Torben Hansen, Jeannet Lauenborg and Oluf Pedersen

    Citation: Microbiome 2018 6:89

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  16. Content type: Research

    Campylobacters are an unwelcome member of the poultry gut microbiota in terms of food safety. The objective of this study was to compare the microbiota, inflammatory responses, and zootechnical parameters of b...

    Authors: Phillippa L. Connerton, Philip J. Richards, Geraldine M. Lafontaine, Peter M. O’Kane, Nacheervan Ghaffar, Nicola J. Cummings, Darren L. Smith, Neville M. Fish and Ian F. Connerton

    Citation: Microbiome 2018 6:88

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  17. Content type: Short report

    Recent studies have conflicting data regarding the presence of intra-amniotic microbiota. Viral communities are increasingly recognized as important although overlooked components of the human microbiota. It i...

    Authors: Efrem S. Lim, Cynthia Rodriguez and Lori R. Holtz

    Citation: Microbiome 2018 6:87

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    The Correction to this article has been published in Microbiome 2019 7:22

  18. Content type: Research

    All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the inter...

    Authors: Michal Sorek, Yisrael Schnytzer, Hiba Waldman Ben-Asher, Vered Chalifa Caspi, Chii-Shiarng Chen, David J. Miller and Oren Levy

    Citation: Microbiome 2018 6:83

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  19. Content type: Research

    Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainabl...

    Authors: Ania T. Deutscher, Catherine M. Burke, Aaron E. Darling, Markus Riegler, Olivia L. Reynolds and Toni A. Chapman

    Citation: Microbiome 2018 6:85

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  20. Content type: Research

    The gelada monkey (Theropithecus gelada), endemic to the Ethiopian highlands, is the only graminivorous primate, i.e., it feeds mainly on grasses and sedges. In spite of known dental, manual, and locomotor adapta...

    Authors: Pål Trosvik, Eric J. de Muinck, Eli K. Rueness, Peter J. Fashing, Evan C. Beierschmitt, Kadie R. Callingham, Jacob B. Kraus, Thomas H. Trew, Amera Moges, Addisu Mekonnen, Vivek V. Venkataraman and Nga Nguyen

    Citation: Microbiome 2018 6:84

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  21. Content type: Research

    Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ...

    Authors: Katharina Fietz, Christian Olaf Rye Hintze, Mikkel Skovrind, Tue Kjærgaard Nielsen, Morten T. Limborg, Marcus A. Krag, Per J. Palsbøll, Lars Hestbjerg Hansen, Peter Rask Møller and M. Thomas P. Gilbert

    Citation: Microbiome 2018 6:82

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  22. Content type: Commentary

    The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relat...

    Authors: Maarten van de Guchte, Hervé M. Blottière and Joël Doré

    Citation: Microbiome 2018 6:81

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  23. Content type: Research

    Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer l...

    Authors: Nathan Vannier, Cendrine Mony, Anne-Kristel Bittebiere, Sophie Michon-Coudouel, Marine Biget and Philippe Vandenkoornhuyse

    Citation: Microbiome 2018 6:79

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  24. Content type: Review

    The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selectio...

    Authors: Eugene Rosenberg and Ilana Zilber-Rosenberg

    Citation: Microbiome 2018 6:78

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  25. Content type: Research

    Environmental factors have a large influence on the composition of the human gut microbiota. One of the most influential and well-studied is host diet. To assess and interpret the impact of non-dietary factors...

    Authors: Ruth C. E. Bowyer, Matthew A. Jackson, Tess Pallister, Jane Skinner, Tim D. Spector, Ailsa A. Welch and Claire J. Steves

    Citation: Microbiome 2018 6:77

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  26. Content type: Software

    The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in...

    Authors: Sebastian Jaenicke, Stefan P. Albaum, Patrick Blumenkamp, Burkhard Linke, Jens Stoye and Alexander Goesmann

    Citation: Microbiome 2018 6:76

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  27. Content type: Review

    Chronic rhinosinusitis (CRS) is a chronic inflammation of the mucosa of the nose and paranasal sinuses affecting approximately 11% of the adult population in Europe. Inadequate immune responses, as well as a d...

    Authors: Charlotte De Rudder, Marta Calatayud Arroyo, Sarah Lebeer and Tom Van de Wiele

    Citation: Microbiome 2018 6:75

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  28. Content type: Correction

    Following publication of the original article [1], the authors reported that while the ordination graphs are all correct, the symbols in the legend are wrong.

    Authors: Kyle Hartman, Marcel G. A. van der Heijden, Raphaël A. Wittwer, Samiran Banerjee, Jean-Claude Walser and Klaus Schlaeppi

    Citation: Microbiome 2018 6:74

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    The original article was published in Microbiome 2018 6:14

  29. Content type: Research

    Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such micr...

    Authors: Xiaozhou Fan, Brandilyn A. Peters, Eric J. Jacobs, Susan M. Gapstur, Mark P. Purdue, Neal D. Freedman, Alexander V. Alekseyenko, Jing Wu, Liying Yang, Zhiheng Pei, Richard B. Hayes and Jiyoung Ahn

    Citation: Microbiome 2018 6:59

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  30. Content type: Research

    The dietary methylamines choline, carnitine, and phosphatidylcholine are used by the gut microbiota to produce a range of metabolites, including trimethylamine (TMA). However, little is known about the use of ...

    Authors: Lesley Hoyles, Maria L. Jiménez-Pranteda, Julien Chilloux, Francois Brial, Antonis Myridakis, Thomas Aranias, Christophe Magnan, Glenn R. Gibson, Jeremy D. Sanderson, Jeremy K. Nicholson, Dominique Gauguier, Anne L. McCartney and Marc-Emmanuel Dumas

    Citation: Microbiome 2018 6:73

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  31. Content type: Research

    Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metageno...

    Authors: Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Robert Hayward, Sofia K. Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R. Jackson, Qinghong Li and Peer Bork

    Citation: Microbiome 2018 6:72

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  32. Content type: Research

    A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based m...

    Authors: Cinta Gomez-Silvan, Marcus H. Y. Leung, Katherine A. Grue, Randeep Kaur, Xinzhao Tong, Patrick K. H. Lee and Gary L. Andersen

    Citation: Microbiome 2018 6:71

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  33. Content type: Research

    Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes...

    Authors: Zhenwei Dai, Olabisi Oluwabukola Coker, Geicho Nakatsu, William K. K. Wu, Liuyang Zhao, Zigui Chen, Francis K. L. Chan, Karsten Kristiansen, Joseph J. Y. Sung, Sunny Hei Wong and Jun Yu

    Citation: Microbiome 2018 6:70

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  34. Content type: Research

    Tetrapods do not express hydrolases for cellulose and hemicellulose assimilation, and hence, the independent acquisition of herbivory required the establishment of new endosymbiotic relationships between tetra...

    Authors: Patricia Campos, Miriam Guivernau, Francesc X. Prenafeta-Boldú and Luis Cardona

    Citation: Microbiome 2018 6:69

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  35. Content type: Research

    Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in...

    Authors: Andrey N. Shkoporov, Feargal J. Ryan, Lorraine A. Draper, Amanda Forde, Stephen R. Stockdale, Karen M. Daly, Siobhan A. McDonnell, James A. Nolan, Thomas D.S. Sutton, Marion Dalmasso, Angela McCann, R. Paul Ross and Colin Hill

    Citation: Microbiome 2018 6:68

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  36. Content type: Research

     The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and ...

    Authors: Matthew R. Mason, Stephanie Chambers, Shareef M. Dabdoub, Sarat Thikkurissy and Purnima S. Kumar

    Citation: Microbiome 2018 6:67

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  37. Content type: Research

    Post-infarction cardiovascular remodeling and heart failure are the leading cause of myocardial infarction (MI)-driven death during the past decades. Experimental observations have involved intestinal microbio...

    Authors: Xin Zhou, Jing Li, Junli Guo, Bin Geng, Wenjie Ji, Qian Zhao, Jinlong Li, Xinlin Liu, Junxiang Liu, Zhaozeng Guo, Wei Cai, Yongqiang Ma, Dong Ren, Jun Miao, Shaobo Chen, Zhuoli Zhang…

    Citation: Microbiome 2018 6:66

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  38. Content type: Research

    Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of...

    Authors: Jeffrey K. Cornuault, Marie-Agnès Petit, Mahendra Mariadassou, Leandro Benevides, Elisabeth Moncaut, Philippe Langella, Harry Sokol and Marianne De Paepe

    Citation: Microbiome 2018 6:65

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  39. Content type: Research

    Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize am...

    Authors: Jo De Vrieze, Ameet J. Pinto, William T. Sloan and Umer Zeeshan Ijaz

    Citation: Microbiome 2018 6:63

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