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  1. Given the increasing use of gnotobiotic mouse models for deciphering the effects of human microbial communities on host biology, there is a need to develop new methods for characterizing these animals while ma...

    Authors: Ilia G. Halatchev, David O’Donnell, Matthew C. Hibberd and Jeffrey I. Gordon

    Citation: Microbiome 2019 7:158

    Content type: Methodology

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  2. Virophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understandi...

    Authors: David Paez-Espino, Jinglie Zhou, Simon Roux, Stephen Nayfach, Georgios A. Pavlopoulos, Frederik Schulz, Katherine D. McMahon, David Walsh, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Susannah G. Tringe and Nikos C. Kyrpides

    Citation: Microbiome 2019 7:157

    Content type: Research

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  3. The earliest microbial colonizers of the human gut can have life-long consequences for their hosts. Precisely how the neonatal gut bacterial microbiome and virome are initially populated is not well understood...

    Authors: Rabia Maqsood, Rachel Rodgers, Cynthia Rodriguez, Scott A. Handley, I. Malick Ndao, Phillip I. Tarr, Barbara B. Warner, Efrem S. Lim and Lori R. Holtz

    Citation: Microbiome 2019 7:156

    Content type: Research

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  8. Ochratoxin A (OTA) is a widespread mycotoxin and induces liver inflammation to human and various species of animals. The intestinal microbiota has critical importance in liver inflammation; however, it remains...

    Authors: Wence Wang, Shuangshuang Zhai, Yaoyao Xia, Hao Wang, Dong Ruan, Ting Zhou, Yongwen Zhu, Hongfu Zhang, Minhong Zhang, Hui Ye, Wenkai Ren and Lin Yang

    Citation: Microbiome 2019 7:151

    Content type: Research

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  10. Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly ...

    Authors: Michael Sweet, Alfred Burian, James Fifer, Mark Bulling, David Elliott and Laurie Raymundo

    Citation: Microbiome 2019 7:139

    Content type: Research

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  11. Following publication of the original article [1], the authors reported an error in the Additional file 1.

    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 2019 7:149

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2017 5:159

  12. Following publication of the original article [1], the authors reported an error in Figure 1 and a text on page 13. In Figure 1, some areas are missing and the correct figure is presented here. On page 13, the...

    Authors: Weidong Chen, Kexin Ren, Alain Isabwe, Huihuang Chen, Min Liu and Jun Yang

    Citation: Microbiome 2019 7:148

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2019 7:138

  13. House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically re...

    Authors: Rahel Park, Maria C. Dzialo, Stijn Spaepen, Donat Nsabimana, Kim Gielens, Herman Devriese, Sam Crauwels, Raul Y. Tito, Jeroen Raes, Bart Lievens and Kevin J. Verstrepen

    Citation: Microbiome 2019 7:147

    Content type: Research

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  14. Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gen...

    Authors: Emanuela Coller, Alessandro Cestaro, Roberto Zanzotti, Daniela Bertoldi, Massimo Pindo, Simone Larger, Davide Albanese, Enzo Mescalchin and Claudio Donati

    Citation: Microbiome 2019 7:140

    Content type: Research

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  15. Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere...

    Authors: Jennifer E. Schmidt, Angela D. Kent, Vanessa L. Brisson and Amélie C. M. Gaudin

    Citation: Microbiome 2019 7:146

    Content type: Research

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  16. Regulatory T cell (Treg) deficiency leads to IPEX syndrome, a lethal autoimmune disease, in Human and mice. Dysbiosis of the gut microbiota in Treg-deficient scurfy (SF) mice has been described, but to date, t...

    Authors: Baokun He, Yuying Liu, Thomas K. Hoang, Xiangjun Tian, Christopher M. Taylor, Meng Luo, Dat Q. Tran, Nina Tatevian and J. Marc Rhoads

    Citation: Microbiome 2019 7:145

    Content type: Research

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  18. N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answe...

    Authors: Kunkun Fan, Manuel Delgado-Baquerizo, Xisheng Guo, Daozhong Wang, Yanying Wu, Mo Zhu, Wei Yu, Huaiying Yao, Yong-guan Zhu and Haiyan Chu

    Citation: Microbiome 2019 7:143

    Content type: Research

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  20. It is now possible to comprehensively characterize the microbiota of the lungs using culture-independent, sequencing-based assays. Several sample types have been used to investigate the lung microbiota, each p...

    Authors: Pierre H. H. Schneeberger, Janice Prescod, Liran Levy, David Hwang, Tereza Martinu and Bryan Coburn

    Citation: Microbiome 2019 7:141

    Content type: Research

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  21. The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riveri...

    Authors: Weidong Chen, Kexin Ren, Alain Isabwe, Huihuang Chen, Min Liu and Jun Yang

    Citation: Microbiome 2019 7:138

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2019 7:148

  22. Ear, nose and throat involvement in granulomatosis with polyangiitis (GPA) is frequently the initial disease manifestation. Previous investigations have observed a higher prevalence of Staphylococcus aureus in pa...

    Authors: Josef Wagner, Ewan M. Harrison, Marcos Martinez Del Pero, Beth Blane, Gert Mayer, Johannes Leierer, Seerapani Gopaluni, Mark A. Holmes, Julian Parkhill, Sharon J. Peacock, David R. W. Jayne and Andreas Kronbichler

    Citation: Microbiome 2019 7:137

    Content type: Research

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  23. Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that ...

    Authors: Shuaimin Chen, Tatoba R. Waghmode, Ruibo Sun, Eiko E. Kuramae, Chunsheng Hu and Binbin Liu

    Citation: Microbiome 2019 7:136

    Content type: Research

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  24. The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse a...

    Authors: Vinicius S. Kavagutti, Adrian-Ştefan Andrei, Maliheh Mehrshad, Michaela M. Salcher and Rohit Ghai

    Citation: Microbiome 2019 7:135

    Content type: Research

    Published on:

  26. The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of m...

    Authors: Philipp Rausch, Malte Rühlemann, Britt M. Hermes, Shauni Doms, Tal Dagan, Katja Dierking, Hanna Domin, Sebastian Fraune, Jakob von Frieling, Ute Hentschel, Femke-Anouska Heinsen, Marc Höppner, Martin T. Jahn, Cornelia Jaspers, Kohar Annie B. Kissoyan, Daniela Langfeldt…

    Citation: Microbiome 2019 7:133

    Content type: Research

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  27. Recent evidence suggests that the commensal microbes act as a barrier against invading pathogens and enteric infections are the consequences of multi-layered interactions among commensals, pathogens, and the h...

    Authors: Jin Sun You, Ji Hyun Yong, Gwang Hee Kim, Sungmin Moon, Ki Taek Nam, Ji Hwan Ryu, Mi Young Yoon and Sang Sun Yoon

    Citation: Microbiome 2019 7:132

    Content type: Research

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  28. Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic he...

    Authors: Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank M. Aarestrup, Klaus Gottlob Müller and Sünje Johanna Pamp

    Citation: Microbiome 2019 7:131

    Content type: Research

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  29. The gut microbiome is an important determinant of human health. Its composition has been shown to be influenced by multiple environmental factors and likely by host genetic variation. In the framework of the Mili...

    Authors: Petar Scepanovic, Flavia Hodel, Stanislas Mondot, Valentin Partula, Allyson Byrd, Christian Hammer, Cécile Alanio, Jacob Bergstedt, Etienne Patin, Mathilde Touvier, Olivier Lantz, Matthew L. Albert, Darragh Duffy, Lluis Quintana-Murci and Jacques Fellay

    Citation: Microbiome 2019 7:130

    Content type: Research

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  30. The last few years have seen tremendous growth in human microbiome research, with a particular focus on the links to both mental and physical health and disease. Medical and experimental settings provide initi...

    Authors: Varsha Dave Badal, Dustin Wright, Yannis Katsis, Ho-Cheol Kim, Austin D. Swafford, Rob Knight and Chun-Nan Hsu

    Citation: Microbiome 2019 7:129

    Content type: Review

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  31. Sharp increases in food production worldwide are attributable to agricultural intensification aided by heavy use of agrochemicals. This massive use of pesticides and fertilizers in combination with global clim...

    Authors: Tao Lu, Qi Zhang, Michel Lavoie, Youchao Zhu, Yizhi Ye, Jun Yang, Hans W. Paerl, Haifeng Qian and Yong-Guan Zhu

    Citation: Microbiome 2019 7:128

    Content type: Research

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  32. Rodent models are invaluable for studying biological processes in the context of whole organisms. The reproducibility of such research is based on an assumption of metabolic similarity between experimental ani...

    Authors: David William Randall, Julius Kieswich, Jonathan Swann, Kieran McCafferty, Christoph Thiemermann, Michael Curtis, Lesley Hoyles and Muhammed Magdi Yaqoob

    Citation: Microbiome 2019 7:127

    Content type: Short report

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  33. The microbiome has been implicated in the initiation and persistence of inflammatory bowel disease. Despite the fact that diet is one of the most potent modulators of microbiome composition and function and th...

    Authors: Shuai Wang, Rene Martins, Megan C. Sullivan, Elliot S. Friedman, Ana M. Misic, Ayah El-Fahmawi, Elaine Cristina Pereira De Martinis, Kevin O’Brien, Ying Chen, Charles Bradley, Grace Zhang, Alexander S. F. Berry, Christopher A. Hunter, Robert N. Baldassano, Mark P. Rondeau and Daniel P. Beiting

    Citation: Microbiome 2019 7:126

    Content type: Research

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  34. Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of in...

    Authors: Lydie Kerdraon, Matthieu Barret, Valérie Laval and Frédéric Suffert

    Citation: Microbiome 2019 7:125

    Content type: Research

    Published on:

  35. Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests ...

    Authors: Shelby E. Gantt, Steven E. McMurray, Amber D. Stubler, Christopher M. Finelli, Joseph R. Pawlik and Patrick M. Erwin

    Citation: Microbiome 2019 7:124

    Content type: Research

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  36. The interconnectivities of built and natural environments can serve as conduits for the proliferation and dissemination of antibiotic resistance genes (ARGs). Several studies have compared the broad spectrum o...

    Authors: Suraj Gupta, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden and Peter Vikesland

    Citation: Microbiome 2019 7:123

    Content type: Research

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  37. The metabolic capacities of anammox bacteria and associated microbial community interactions in partial-nitritation anammox (PNA) reactors have received considerable attention for their crucial roles in energy...

    Authors: Yulin Wang, Qigui Niu, Xu Zhang, Lei Liu, Yubo Wang, Yiqiang Chen, Mishty Negi, Daniel Figeys, Yu-You Li and Tong Zhang

    Citation: Microbiome 2019 7:122

    Content type: Research

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  38. Mosquitoes are the most important invertebrate viral vectors in humans and harbor a high diversity of understudied viruses, which has been shown in many mosquito virome studies in recent years. These studies g...

    Authors: Chenyan Shi, Leen Beller, Ward Deboutte, Kwe Claude Yinda, Leen Delang, Anubis Vega-Rúa, Anna-Bella Failloux and Jelle Matthijnssens

    Citation: Microbiome 2019 7:121

    Content type: Research

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  39. Coastal environments are dynamic and rapidly changing. Living organisms in coastal environments are known to synthesise large quantities of organic osmolytes, which they use to cope with osmotic stresses. The ...

    Authors: Helen J. Jones, Eileen Kröber, Jason Stephenson, Michaela A. Mausz, Eleanor Jameson, Andrew Millard, Kevin J. Purdy and Yin Chen

    Citation: Microbiome 2019 7:120

    Content type: Research

    Published on:

  40. Elucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity an...

    Authors: Yoshihiko Suzuki, Suguru Nishijima, Yoshikazu Furuta, Jun Yoshimura, Wataru Suda, Kenshiro Oshima, Masahira Hattori and Shinichi Morishita

    Citation: Microbiome 2019 7:119

    Content type: Research

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  41. The dynamics of microbial communities is driven by a range of interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood. With the increasing availability of high-t...

    Authors: Chenhao Li, Kern Rei Chng, Junmei Samantha Kwah, Tamar V. Av-Shalom, Lisa Tucker-Kellogg and Niranjan Nagarajan

    Citation: Microbiome 2019 7:118

    Content type: Methodology

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  43. Inflammasomes have been found to interact with the gut microbiota, and this effect is associated with depression, but the mechanisms underlying this interaction have not been elucidated in detail.

    Authors: Yuan Zhang, Rongrong Huang, Mengjing Cheng, Lirui Wang, Jie Chao, Junxu Li, Peng Zheng, Peng Xie, Zhijun Zhang and Honghong Yao

    Citation: Microbiome 2019 7:116

    Content type: Research

    Published on:

  44. Multistate foodborne disease outbreaks and recalls of apples and apple products contaminated with Listeria monocytogenes demonstrate the need for improved pathogen control in the apple supply chain. Apple process...

    Authors: Xiaoqing Tan, Taejung Chung, Yi Chen, Dumitru Macarisin, Luke LaBorde and Jasna Kovac

    Citation: Microbiome 2019 7:115

    Content type: Research

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  45. Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not ...

    Authors: Juan E. Pérez-Jaramillo, Mattias de Hollander, Camilo A. Ramírez, Rodrigo Mendes, Jos M. Raaijmakers and Víctor J. Carrión

    Citation: Microbiome 2019 7:114

    Content type: Research

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  46. Space environment imposes a range of challenges to mammalian physiology and the gut microbiota, and interactions between the two are thought to be important in mammalian health in space. While previous finding...

    Authors: Peng Jiang, Stefan J. Green, George E. Chlipala, Fred W. Turek and Martha Hotz Vitaterna

    Citation: Microbiome 2019 7:113

    Content type: Research

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  47. Sugar loss due to storage rot has a substantial economic impact on the sugar industry. The gradual spread of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps is an ongoing cha...

    Authors: Peter Kusstatscher, Christin Zachow, Karsten Harms, Johann Maier, Herbert Eigner, Gabriele Berg and Tomislav Cernava

    Citation: Microbiome 2019 7:112

    Content type: Research

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  48. Normal mammalian development and homeostasis are dependent upon the gut microbiota. Antibiotics, essential for the treatment and prophylaxis of bacterial infections, can have collateral effects on the gut micr...

    Authors: Aonghus Lavelle, Thomas Walter Hoffmann, Hang-Phuong Pham, Philippe Langella, Eric Guédon and Harry Sokol

    Citation: Microbiome 2019 7:111

    Content type: Research

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  49. Whole-genome “shotgun” (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be ch...

    Authors: Samuel S. Minot and Amy D. Willis

    Citation: Microbiome 2019 7:110

    Content type: Research

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  50. Despite recent advances in the understanding of the swine gut microbiome at different growth stages, a comprehensive longitudinal study of the lifetime (birth to market) dynamics of the swine gut microbiome is...

    Authors: Xiaofan Wang, Tsungcheng Tsai, Feilong Deng, Xiaoyuan Wei, Jianmin Chai, Joshua Knapp, Jason Apple, Charles V. Maxwell, Jung Ae Lee, Ying Li and Jiangchao Zhao

    Citation: Microbiome 2019 7:109

    Content type: Research

    Published on:

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