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  2. Content type: Research

    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

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  3. Content type: Research

    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

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  4. Content type: Research

    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

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  5. Content type: Research

    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

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  6. Content type: Review

    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

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  7. Content type: Research

    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

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  8. Content type: Short report

    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

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  9. Content type: Research

    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

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  10. Content type: Research

    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

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  11. Content type: Research

    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

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  12. Content type: Research

    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

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  13. Content type: Research

    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

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  14. Content type: Research

    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

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  15. Content type: Research

    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

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  16. Content type: Research

    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

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  17. Content type: Methodology

    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

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  19. Content type: Research

    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

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  20. Content type: Research

    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

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  21. Content type: Research

    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

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  22. Content type: Research

    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

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  23. Content type: Research

    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

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  24. Content type: Research

    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

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  25. Content type: Research

    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

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  26. Content type: Research

    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

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  27. Content type: Research

    The plant microbiota is crucial for plant health and growth. Recently, vertical transmission of a beneficial core microbiota was identified for crop seeds, but for native plants, complementary mechanisms are a...

    Authors: Birgit Wassermann, Tomislav Cernava, Henry Müller, Christian Berg and Gabriele Berg

    Citation: Microbiome 2019 7:108

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  28. Content type: Research

    Early treatment is key for optimizing the therapeutic success of drugs, and the current initiating treatment that blocks the progression of bone destruction during the pre-arthritic stages remains unsatisfacto...

    Authors: Hudan Pan, Ruijin Guo, Yanmei Ju, Qi Wang, Jie Zhu, Ying Xie, Yanfang Zheng, Ting Li, Zhongqiu Liu, Linlin Lu, Fei Li, Bin Tong, Liang Xiao, Xun Xu, Elaine Lai-Han Leung, Runze Li…

    Citation: Microbiome 2019 7:107

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  29. Content type: Research

    Streptococcus pneumoniae is a significant global pathogen that colonises the nasopharynx of healthy children. Pneumococcal conjugate vaccines, which reduce nasopharyngeal colonisation of vaccine-type S. pneumonia...

    Authors: Laura K. Boelsen, Eileen M. Dunne, Moana Mika, Stefanie Eggers, Cattram D. Nguyen, F. Tupou Ratu, Fiona M. Russell, E. Kim Mulholland, Markus Hilty and Catherine Satzke

    Citation: Microbiome 2019 7:106

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  30. Content type: Research

    Dysbiosis of gut microbiota exists in the pathogenesis of many autoimmune diseases, including systemic lupus erythematosus (lupus). Lupus patients who experienced pregnancy usually had more severe disease flar...

    Authors: Qinghui Mu, Xavier Cabana-Puig, Jiangdi Mao, Brianna Swartwout, Leila Abdelhamid, Thomas E. Cecere, Haifeng Wang, Christopher M. Reilly and Xin M. Luo

    Citation: Microbiome 2019 7:105

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  31. Content type: Research

    Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in mi...

    Authors: Jiarui Chen, Shelby E. McIlroy, Anand Archana, David M. Baker and Gianni Panagiotou

    Citation: Microbiome 2019 7:104

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  32. Content type: Research

    Accumulating evidence is supporting the protective effect of whole grains against several chronic diseases. Simultaneously, our knowledge is increasing on the impact of gut microbiota on our health and on how ...

    Authors: Ville M. Koistinen, Olli Kärkkäinen, Klaudyna Borewicz, Iman Zarei, Jenna Jokkala, Valérie Micard, Natalia Rosa-Sibakov, Seppo Auriola, Anna-Marja Aura, Hauke Smidt and Kati Hanhineva

    Citation: Microbiome 2019 7:103

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  33. Content type: Research

    Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumul...

    Authors: Irina M. Velsko, James A. Fellows Yates, Franziska Aron, Richard W. Hagan, Laurent A. F. Frantz, Louise Loe, Juan Bautista Rodriguez Martinez, Eros Chaves, Chris Gosden, Greger Larson and Christina Warinner

    Citation: Microbiome 2019 7:102

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  34. Content type: Research

    The past decade of microbiome research has concentrated on cataloging the diversity of taxa in different environments. The next decade is poised to focus on microbial traits and function. Most existing methods...

    Authors: Sharon Bewick, Eliezer Gurarie, Jake L. Weissman, Jess Beattie, Cyrus Davati, Rachel Flint, Peter Thielen, Florian Breitwieser, David Karig and William F. Fagan

    Citation: Microbiome 2019 7:101

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  35. Content type: Research

    The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbi...

    Authors: Natalia Molinero, Lorena Ruiz, Christian Milani, Isabel Gutiérrez-Díaz, Borja Sánchez, Marta Mangifesta, José Segura, Isabel Cambero, Ana Belén Campelo, Carmen María García-Bernardo, Ana Cabrera, José Ignacio Rodríguez, Sonia González, Juan Miguel Rodríguez, Marco Ventura, Susana Delgado…

    Citation: Microbiome 2019 7:100

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  36. Content type: Research

    Eukaryotes are ubiquitous in natural environments such as soil and freshwater. Little is known of their presence in drinking water distribution systems (DWDSs) or of the environmental conditions that affect th...

    Authors: Jenni Inkinen, Balamuralikrishna Jayaprakash, Sallamaari Siponen, Anna-Maria Hokajärvi, Anna Pursiainen, Jenni Ikonen, Ivan Ryzhikov, Martin Täubel, Ari Kauppinen, Jussi Paananen, Ilkka T. Miettinen, Eila Torvinen, Mikko Kolehmainen and Tarja Pitkänen

    Citation: Microbiome 2019 7:99

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  37. Content type: Research

    Western-style diets arouse neuroinflammation and impair emotional and cognitive behavior in humans and animals. Our previous study showed that a high-fructose diet caused the hippocampal neuroinflammatory resp...

    Authors: Jian-Mei Li, Rong Yu, Li-Ping Zhang, Shi-Yu Wen, Shui-Juan Wang, Xiao-Yang Zhang, Qiang Xu and Ling-Dong Kong

    Citation: Microbiome 2019 7:98

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  38. Content type: Short report

    Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to ...

    Authors: Nachiket P. Marathe, Fanny Berglund, Mohammad Razavi, Chandan Pal, Johannes Dröge, Sharvari Samant, Erik Kristiansson and D. G. Joakim Larsson

    Citation: Microbiome 2019 7:97

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  40. Content type: Short report

    The skin is colonized by a large number of microorganisms, most of which are beneficial or harmless. However, disease states of skin have specific microbiome compositions that are different from those of healt...

    Authors: Bernhard Paetzold, Jesse R. Willis, João Pereira de Lima, Nastassia Knödlseder, Holger Brüggemann, Sven R. Quist, Toni Gabaldón and Marc Güell

    Citation: Microbiome 2019 7:95

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  41. Content type: Research

    Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Altho...

    Authors: Bettina Glasl, David G. Bourne, Pedro R. Frade, Torsten Thomas, Britta Schaffelke and Nicole S. Webster

    Citation: Microbiome 2019 7:94

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  42. Content type: Research

    Marine bacteria form complex relationships with eukaryotic hosts, from obligate symbioses to pathogenic interactions. These interactions can be tightly regulated by bioactive molecules, creating a complex syst...

    Authors: Kristen E. Whalen, Jamie W. Becker, Anna M. Schrecengost, Yongjie Gao, Nicole Giannetti and Elizabeth L. Harvey

    Citation: Microbiome 2019 7:93

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  43. Content type: Research

    The symbiotic rumen microbiota is essential for the digestion of plant fibers and contributes to the variation of production and health traits in ruminants. However, to date, the heritability of rumen microbia...

    Authors: Fuyong Li, Changxi Li, Yanhong Chen, Junhong Liu, Chunyan Zhang, Barry Irving, Carolyn Fitzsimmons, Graham Plastow and Le Luo Guan

    Citation: Microbiome 2019 7:92

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  46. Content type: Software

    Microbiomes are complex aggregates of organisms, each of which has its own extensive metabolic network. A variety of metabolites are exchanged between the microbes. The challenge we address is understanding th...

    Authors: Markus Krummenacker, Mario Latendresse and Peter D Karp

    Citation: Microbiome 2019 7:89

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  47. Content type: Software

    Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effe...

    Authors: G. A. Arango-Argoty, D. Dai, A. Pruden, P. Vikesland, L. S. Heath and L. Zhang

    Citation: Microbiome 2019 7:88

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  48. Content type: Research

    Residual disinfection is often used to suppress biological growth in drinking water distribution systems (DWDSs), but not without undesirable side effects. In this study, water-main biofilms, drinking water, a...

    Authors: Michael B. Waak, Raymond M. Hozalski, Cynthia Hallé and Timothy M. LaPara

    Citation: Microbiome 2019 7:87

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  49. Content type: Research

    Beef cattle in North America frequently receive an antibiotic injection after feedlot placement to control and manage bovine respiratory disease. The potential collateral effect of these antibiotics on the bov...

    Authors: Devin B. Holman, Wenzhu Yang and Trevor W. Alexander

    Citation: Microbiome 2019 7:86

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  50. Content type: Research

    The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ...

    Authors: Limei Lin, Fei Xie, Daming Sun, Junhua Liu, Weiyun Zhu and Shengyong Mao

    Citation: Microbiome 2019 7:83

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