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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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

  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  16. 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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  17. Content type: Review

    Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often refe...

    Authors: M. Amine Hassani, Paloma Durán and Stéphane Hacquard

    Citation: Microbiome 2018 6:58

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  18. Content type: Research

    Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade compl...

    Authors: Angélique Gobet, Laëtitia Mest, Morgan Perennou, Simon M Dittami, Claire Caralp, Céline Coulombet, Sylvain Huchette, Sabine Roussel, Gurvan Michel and Catherine Leblanc

    Citation: Microbiome 2018 6:60

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  19. Content type: Research

    Understanding the host impact on its symbiotic microbiota is important in redirecting the rumen microbiota and thus improving animal performance. The current study aimed to understand how rumen microbiota were...

    Authors: Mi Zhou, Yong-Jia Peng, Yanhong Chen, Christen M. Klinger, Masahito Oba, Jian-Xin Liu and Le Luo Guan

    Citation: Microbiome 2018 6:62

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  21. Content type: Research

    Changes in hygiene and dietary habits, including increased consumption of foods high in fat, simple sugars, and salt that are known to impact the composition and function of the intestinal microbiota, may expl...

    Authors: Pedro M. Miranda, Giada De Palma, Viktoria Serkis, Jun Lu, Marc P. Louis-Auguste, Justin L. McCarville, Elena F. Verdu, Stephen M. Collins and Premysl Bercik

    Citation: Microbiome 2018 6:57

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  23. Content type: Research

    Gut microbiota composition and function are symbiotically linked with host health and altered in metabolic, inflammatory and neurodegenerative disorders. Three recognised mechanisms exist by which the microbio...

    Authors: Lesley Hoyles, Tom Snelling, Umm-Kulthum Umlai, Jeremy K. Nicholson, Simon R. Carding, Robert C. Glen and Simon McArthur

    Citation: Microbiome 2018 6:55

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  24. Content type: Review

    The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants ...

    Authors: Mohammadhossein Ravanbakhsh, Rashmi Sasidharan, Laurentius A. C. J. Voesenek, George A. Kowalchuk and Alexandre Jousset

    Citation: Microbiome 2018 6:52

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  25. Content type: Research

    Calorie restriction (CR), which has a potent anti-inflammaging effect, has been demonstrated to induce dramatic changes in the gut microbiota. Whether the modulated gut microbiota contributes to the attenuatio...

    Authors: Fengwei Pan, Liying Zhang, Min Li, Yingxin Hu, Benhua Zeng, Huijuan Yuan, Liping Zhao and Chenhong Zhang

    Citation: Microbiome 2018 6:54

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  26. Content type: Research

    One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops...

    Authors: E. Gonzalez, F. E. Pitre, A. P. Pagé, J. Marleau, W. Guidi Nissim, M. St-Arnaud, M. Labrecque, S. Joly, E. Yergeau and N. J. B. Brereton

    Citation: Microbiome 2018 6:53

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  27. Content type: Research

    Plants can adapt to edaphic stress, such as nutrient deficiency, toxicity and biotic challenges, by controlled transcriptomic responses, including microbiome interactions. Traditionally studied in model plant ...

    Authors: Ellen Young, Manus Carey, Andrew A. Meharg and Caroline Meharg

    Citation: Microbiome 2018 6:48

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  28. Content type: Review

    The holobiont concept was first developed for coral ecosystems but has been extended to multiple organisms, including plants and other animals. Studies on insect-associated microbial communities have produced ...

    Authors: Morgane Guégan, Karima Zouache, Colin Démichel, Guillaume Minard, Van Tran Van, Patrick Potier, Patrick Mavingui and Claire Valiente Moro

    Citation: Microbiome 2018 6:49

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  29. Content type: Research

    The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with res...

    Authors: Aaron M. Walsh, Fiona Crispie, Orla O’Sullivan, Laura Finnegan, Marcus J. Claesson and Paul D. Cotter

    Citation: Microbiome 2018 6:50

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  30. Content type: Correction

    Following publication of the original article [1] it came to the attention of the Production Editor that Figs. 1 and 2 had not been replaced with the newly revised figures supplied by the authors (the original...

    Authors: Jane A. Mullaney, Juliette E. Stephens, Mary-Ellen Costello, Cai Fong, Brooke E. Geeling, Patrick G. Gavin, Casey M. Wright, Timothy D. Spector, Matthew A. Brown and Emma E. Hamilton-Williams

    Citation: Microbiome 2018 6:51

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    The original article was published in Microbiome 2018 6:35

  33. Content type: Research

    The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community’s taxonomic profile natural...

    Authors: Alexander Eng and Elhanan Borenstein

    Citation: Microbiome 2018 6:45

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  34. Content type: Research

    In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose ...

    Authors: A. E. Naas, L. M. Solden, A. D. Norbeck, H. Brewer, L. H. Hagen, I. M. Heggenes, A. C. McHardy, R. I. Mackie, L. Paša-Tolić, M. Ø. Arntzen, V. G. H. Eijsink, N. M. Koropatkin, M. Hess, K. C. Wrighton and P. B. Pope

    Citation: Microbiome 2018 6:44

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  35. Content type: Research

    The human intestine and its microbiota is the most common infection site for soil-transmitted helminths (STHs), which affect the well-being of ~ 1.5 billion people worldwide. The complex cross-kingdom interact...

    Authors: Bruce A. Rosa, Taniawati Supali, Lincoln Gankpala, Yenny Djuardi, Erliyani Sartono, Yanjiao Zhou, Kerstin Fischer, John Martin, Rahul Tyagi, Fatorma K. Bolay, Peter U. Fischer, Maria Yazdanbakhsh and Makedonka Mitreva

    Citation: Microbiome 2018 6:33

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  36. Content type: Methodology

    Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencin...

    Authors: Clarisse A. Marotz, Jon G. Sanders, Cristal Zuniga, Livia S. Zaramela, Rob Knight and Karsten Zengler

    Citation: Microbiome 2018 6:42

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  37. Content type: Methodology

    The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for...

    Authors: Mo Han, Lilan Hao, Yuxiang Lin, Fang Li, Jian Wang, Huanming Yang, Liang Xiao, Karsten Kristiansen, Huijue Jia and Junhua Li

    Citation: Microbiome 2018 6:43

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  39. Content type: Research

    Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacter...

    Authors: Marc W. Van Goethem, Rian Pierneef, Oliver K. I. Bezuidt, Yves Van De Peer, Don A. Cowan and Thulani P. Makhalanyane

    Citation: Microbiome 2018 6:40

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  41. Content type: Research

    To investigate whether alterations in the developing intestinal microbiota and immune markers precede celiac disease (CD) onset in infants at familial risk of developing the disease.

    Authors: Marta Olivares, Alan W. Walker, Amalia Capilla, Alfonso Benítez-Páez, Francesc Palau, Julian Parkhill, Gemma Castillejo and Yolanda Sanz

    Citation: Microbiome 2018 6:36

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  42. Content type: Research

    Multidrug-resistant bacteria represent a substantial global burden for human health, potentially fuelled by migration waves: in 2015, 476,649 refugees applied for asylum in Germany mostly as a result of the Sy...

    Authors: Robert Häsler, Christian Kautz, Ateequr Rehman, Rainer Podschun, Volker Gassling, Pius Brzoska, Jon Sherlock, Jan-Thorsten Gräsner, Gesine Hoppenstedt, Sabine Schubert, Astrid Ferlinz, Wolfgang Lieb, Matthias Laudes, Femke-Anouska Heinsen, Jens Scholz, Dag Harmsen…

    Citation: Microbiome 2018 6:37

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  43. Content type: Research

    Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host...

    Authors: Kelly Brener-Raffalli, Camille Clerissi, Jeremie Vidal-Dupiol, Mehdi Adjeroud, François Bonhomme, Marine Pratlong, Didier Aurelle, Guillaume Mitta and Eve Toulza

    Citation: Microbiome 2018 6:39

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  44. Content type: Research

    Dysbiosis of the gut microbiota has been implicated in the pathogenesis of many autoimmune conditions including type 1 diabetes (T1D). It is unknown whether changes in the gut microbiota observed in T1D are du...

    Authors: Jane A. Mullaney, Juliette E. Stephens, Mary-Ellen Costello, Cai Fong, Brooke E. Geeling, Patrick G. Gavin, Casey M. Wright, Timothy D. Spector, Matthew A. Brown and Emma E. Hamilton-Williams

    Citation: Microbiome 2018 6:35

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    The Correction to this article has been published in Microbiome 2018 6:51

  45. Content type: Software

    Microbial longitudinal studies are powerful experimental designs utilized to classify diseases, determine prognosis, and analyze microbial systems dynamics. In longitudinal studies, only identifying differenti...

    Authors: Ahmed A. Metwally, Jie Yang, Christian Ascoli, Yang Dai, Patricia W. Finn and David L. Perkins

    Citation: Microbiome 2018 6:32

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  46. Content type: Research

    Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in anima...

    Authors: Wenguang Xiong, Yulin Wang, Yongxue Sun, Liping Ma, Qinglin Zeng, Xiaotao Jiang, Andong Li, Zhenling Zeng and Tong Zhang

    Citation: Microbiome 2018 6:34

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  47. Content type: Research

    Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperativ...

    Authors: M. A. Cregger, A. M. Veach, Z. K. Yang, M. J. Crouch, R. Vilgalys, G. A. Tuskan and C. W. Schadt

    Citation: Microbiome 2018 6:31

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  49. Content type: Research

    Gut microbiota provide functions of importance to influence hosts’ food digestion, metabolism, and protection against pathogens. Factors that affect the composition and functions of gut microbial communities a...

    Authors: Yinghua Zha, Alexander Eiler, Frank Johansson and Richard Svanbäck

    Citation: Microbiome 2018 6:28

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  50. Content type: Commentary

    In the cervicovaginal environment, the production of hydrogen peroxide (H2O2) by vaginal Lactobacillus spp. is often mentioned as a critical factor to the in vivo vaginal microbiota antimicrobial properties. We p...

    Authors: Gilda Tachedjian, Deirdre E. O’Hanlon and Jacques Ravel

    Citation: Microbiome 2018 6:29

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