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  1. Content type: Research

    Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be man...

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

    Citation: Microbiome 2018 6:14

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  2. Content type: Research

    No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes tha...

    Authors: Laura Tipton, Christian L. Müller, Zachary D. Kurtz, Laurence Huang, Eric Kleerup, Alison Morris, Richard Bonneau and Elodie Ghedin

    Citation: Microbiome 2018 6:12

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  3. Content type: Methodology

    Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of “resistomes” (the ensemble of genes encoding antimicrobial resistance in a given microbio...

    Authors: Val F. Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J. Willems, Fernando de la Cruz and Teresa M. Coque

    Citation: Microbiome 2018 6:11

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  4. Content type: Research

    Crohn’s disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been c...

    Authors: Gavin M. Douglas, Richard Hansen, Casey M. A. Jones, Katherine A. Dunn, André M. Comeau, Joseph P. Bielawski, Rachel Tayler, Emad M. El-Omar, Richard K. Russell, Georgina L. Hold, Morgan G. I. Langille and Johan Van Limbergen

    Citation: Microbiome 2018 6:13

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  5. Content type: Research

    While almost all infants are infected with respiratory syncytial virus (RSV) before the age of 2 years, only a small percentage develops severe disease. Previous studies suggest that the nasopharyngeal microbi...

    Authors: Thomas H. A. Ederveen, Gerben Ferwerda, Inge M. Ahout, Marloes Vissers, Ronald de Groot, Jos Boekhorst, Harro M. Timmerman, Martijn A. Huynen, Sacha A. F. T. van Hijum and Marien I. de Jonge

    Citation: Microbiome 2018 6:10

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  6. Content type: Research

    Microbiota integrity is essential for a growing number of physiological processes. Consequently, disruption of microbiota homeostasis correlates with a variety of pathological states. Importantly, commensal mi...

    Authors: Soner Yildiz, Béryl Mazel-Sanchez, Matheswaran Kandasamy, Balaji Manicassamy and Mirco Schmolke

    Citation: Microbiome 2018 6:9

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  7. Content type: Research

    Oral taxa are often found in the chronic obstructive pulmonary disease (COPD) lung microbiota, but it is not clear if this is due to a physiologic process such as aspiration or experimental contamination at th...

    Authors: Alexa A. Pragman, Tianmeng Lyu, Joshua A. Baller, Trevor J. Gould, Rosemary F. Kelly, Cavan S. Reilly, Richard E. Isaacson and Chris H. Wendt

    Citation: Microbiome 2018 6:7

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  8. Content type: Short report

    Many insects developing on nutritionally unbalanced diets have evolved symbiotic associations with vertically transmitted intracellular bacteria (endosymbionts) that provide them with metabolic components, the...

    Authors: Justin Maire, Carole Vincent-Monégat, Florent Masson, Anna Zaidman-Rémy and Abdelaziz Heddi

    Citation: Microbiome 2018 6:6

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  9. Content type: Research

    Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the ...

    Authors: Yi-Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S. Zaramela, Ji-Dong Gu, Bo-Zhong Mu and Karsten Zengler

    Citation: Microbiome 2018 6:5

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  10. Content type: Research

    In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are n...

    Authors: Duc Lu, Francesco Tiezzi, Constantino Schillebeeckx, Nathan P. McNulty, Clint Schwab, Caleb Shull and Christian Maltecca

    Citation: Microbiome 2018 6:4

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  11. Content type: Research

    The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The maj...

    Authors: Ramona Marasco, Eleonora Rolli, Marco Fusi, Grégoire Michoud and Daniele Daffonchio

    Citation: Microbiome 2018 6:3

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  12. Content type: Research

    The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation be...

    Authors: Pamela N. Luna, Kohei Hasegawa, Nadim J. Ajami, Janice A. Espinola, David M. Henke, Joseph F. Petrosino, Pedro A. Piedra, Ashley F. Sullivan, Carlos A. Camargo Jr., Chad A. Shaw and Jonathan M. Mansbach

    Citation: Microbiome 2018 6:2

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  13. Content type: Research

    Movile Cave (Mangalia, Romania) is a unique ecosystem where the food web is sustained by microbial primary production, analogous to deep-sea hydrothermal vents. Specifically, chemoautotrophic microbes deriving...

    Authors: Deepak Kumaresan, Jason Stephenson, Andrew C. Doxey, Hina Bandukwala, Elliot Brooks, Alexandra Hillebrand-Voiculescu, Andrew S. Whiteley and J Colin Murrell

    Citation: Microbiome 2018 6:1

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  14. Content type: Research

    The constant increase of aquaculture production and wealthy seafood consumption has forced the industry to explore alternative and more sustainable raw aquafeed materials, and plant ingredients have been used ...

    Authors: María Carla Piazzon, Josep Alvar Calduch-Giner, Belén Fouz, Itziar Estensoro, Paula Simó-Mirabet, Mónica Puyalto, Vasileios Karalazos, Oswaldo Palenzuela, Ariadna Sitjà-Bobadilla and Jaume Pérez-Sánchez

    Citation: Microbiome 2017 5:164

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  15. Content type: Research

    Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in nat...

    Authors: Miguel Carda-Diéguez, Rohit Ghai, Francisco Rodríguez-Valera and Carmen Amaro

    Citation: Microbiome 2017 5:162

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  16. Content type: Research

    Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducte...

    Authors: Tiantian Ren, Stan Boutin, Murray M. Humphries, Ben Dantzer, Jamieson C. Gorrell, David W. Coltman, Andrew G. McAdam and Martin Wu

    Citation: Microbiome 2017 5:163

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  17. Content type: Research article

    The human gut microbiome has been linked to numerous components of health and disease. However, approximately 25% of the bacterial species in the gut remain uncultured, which limits our ability to properly und...

    Authors: Kathrin Fenn, Philip Strandwitz, Eric J. Stewart, Eric Dimise, Sarah Rubin, Shreya Gurubacharya, Jon Clardy and Kim Lewis

    Citation: Microbiome 2017 5:161

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  18. Content type: Research

    Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We th...

    Authors: Mohammad Razavi, Nachiket P. Marathe, Michael R. Gillings, Carl-Fredrik Flach, Erik Kristiansson and D. G. Joakim Larsson

    Citation: Microbiome 2017 5:160

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  19. Content type: Research

    Identification of factors that influence the neonatal gut microbiome is urgently needed to guide clinical practices that support growth of healthy preterm infants. Here, we examined the influence of nutrition ...

    Authors: Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja A. Kessler, Ann L. Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas J. Mariani, Rita M. Ryan, Lori Scholer, Kristin M. Scheible, Yi-Horng Lee, Mary T. Caserta, Gloria S. Pryhuber…

    Citation: Microbiome 2017 5:158

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  20. Content type: Research

    The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associa...

    Authors: Marc D. Auffret, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, R. John Wallace, Tom C. Freeman, Robert Stewart, Mick Watson and Rainer Roehe

    Citation: Microbiome 2017 5:159

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  21. Content type: Software

    Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of micro...

    Authors: Kai Cheng, Zhibin Ning, Xu Zhang, Leyuan Li, Bo Liao, Janice Mayne, Alain Stintzi and Daniel Figeys

    Citation: Microbiome 2017 5:157

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  22. Content type: Research

    Working toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and eco...

    Authors: H. Pieter J. van Veelen, Joana Falcao Salles and B. Irene Tieleman

    Citation: Microbiome 2017 5:156

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  23. Content type: Research

    Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential ris...

    Authors: Liping Ma, Bing Li, Xiao-Tao Jiang, Yu-Lin Wang, Yu Xia, An-Dong Li and Tong Zhang

    Citation: Microbiome 2017 5:154

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