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  1. Content type: Research

    Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a cr...

    Authors: Katri Korpela, Anne Salonen, Outi Vepsäläinen, Marjo Suomalainen, Carolin Kolmeder, Markku Varjosalo, Sini Miettinen, Kaarina Kukkonen, Erkki Savilahti, Mikael Kuitunen and Willem M de Vos

    Citation: Microbiome 2018 6:182

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  2. Content type: Research

    Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunitie...

    Authors: Cervin Guyomar, Fabrice Legeai, Emmanuelle Jousselin, Christophe Mougel, Claire Lemaitre and Jean-Christophe Simon

    Citation: Microbiome 2018 6:181

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  3. Content type: Research

    The specific interactions of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and the lung microbiota in infection are entirely unexplored. Studies in cancer and other infectious diseas...

    Authors: Anthony M Cadena, Yixuan Ma, Tao Ding, MacKenzie Bryant, Pauline Maiello, Adam Geber, Philana Ling Lin, JoAnne L Flynn and Elodie Ghedin

    Citation: Microbiome 2018 6:180

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  4. Content type: Research

    Pediatric asthma is the most common chronic childhood disease in the USA, currently affecting ~ 7 million children. This heterogeneous syndrome is thought to encompass various disease phenotypes of clinically ...

    Authors: Marcos Pérez-Losada, Kayla J Authelet, Claire E Hoptay, Christine Kwak, Keith A Crandall and Robert J Freishtat

    Citation: Microbiome 2018 6:179

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  5. Content type: Research

    Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encep...

    Authors: Zhiqiang Wu, Liang Lu, Jiang Du, Li Yang, Xianwen Ren, Bo Liu, Jinyong Jiang, Jian Yang, Jie Dong, Lilian Sun, Yafang Zhu, Yuhui Li, Dandan Zheng, Chi Zhang, Haoxiang Su, Yuting Zheng…

    Citation: Microbiome 2018 6:178

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  6. Content type: Research

    Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total...

    Authors: Maliheh Mehrshad, Michaela M Salcher, Yusuke Okazaki, Shin-ichi Nakano, Karel Šimek, Adrian-Stefan Andrei and Rohit Ghai

    Citation: Microbiome 2018 6:176

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  7. Content type: Research

    It is becoming evident that certain features of human microbiota, encoded by distinct autochthonous taxa, promote disease. As a result, borders between the so-called opportunistic pathogens, pathobionts, and c...

    Authors: Silke Rath, Tatjana Rud, André Karch, Dietmar Helmut Pieper and Marius Vital

    Citation: Microbiome 2018 6:174

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  8. Content type: Research

    Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cu...

    Authors: Johannes Alneberg, Christofer M. G. Karlsson, Anna-Maria Divne, Claudia Bergin, Felix Homa, Markus V. Lindh, Luisa W. Hugerth, Thijs J. G. Ettema, Stefan Bertilsson, Anders F. Andersson and Jarone Pinhassi

    Citation: Microbiome 2018 6:173

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  9. Content type: Research

    The metabolic syndrome (MetS) epidemic is associated with economic development, lifestyle transition and dysbiosis of gut microbiota, but these associations are rarely studied at the population scale. Here, we...

    Authors: Yan He, Wei Wu, Shan Wu, Hui-Min Zheng, Pan Li, Hua-Fang Sheng, Mu-Xuan Chen, Zi-Hui Chen, Gui-Yuan Ji, Zhong-Dai-Xi Zheng, Prabhakar Mujagond, Xiao-Jiao Chen, Zu-Hua Rong, Peng Chen, Li-Yi Lyu, Xian Wang…

    Citation: Microbiome 2018 6:172

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  10. Content type: Research

    Weaning is a period of marked physiological change. The introduction of solid foods and the changes in milk consumption are accompanied by significant gastrointestinal, immune, developmental, and microbial ada...

    Authors: Samanta Michelini, Biju Balakrishnan, Silvia Parolo, Alice Matone, Jane A. Mullaney, Wayne Young, Olivier Gasser, Clare Wall, Corrado Priami, Rosario Lombardo and Martin Kussmann

    Citation: Microbiome 2018 6:171

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  11. Content type: Research

    Grazing is a major modulator of biodiversity and productivity in grasslands. However, our understanding of grazing-induced changes in below-ground communities, processes, and soil productivity is limited. Here...

    Authors: Weibing Xun, Ruirui Yan, Yi Ren, Dongyan Jin, Wu Xiong, Guishan Zhang, Zhongli Cui, Xiaoping Xin and Ruifu Zhang

    Citation: Microbiome 2018 6:170

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  12. Content type: Research

    Darwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a cla...

    Authors: Alice J. Michel, Lewis M. Ward, Shana K. Goffredi, Katherine S. Dawson, Daniel T. Baldassarre, Alec Brenner, Kiyoko M. Gotanda, John E. McCormack, Sean W. Mullin, Ariel O’Neill, Gabrielle S. Tender, J. Albert C. Uy, Kristie Yu, Victoria J. Orphan and Jaime A. Chaves

    Citation: Microbiome 2018 6:167

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  13. Content type: Research

    Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but...

    Authors: Charlotte D. Vavourakis, Adrian-Stefan Andrei, Maliheh Mehrshad, Rohit Ghai, Dimitry Y. Sorokin and Gerard Muyzer

    Citation: Microbiome 2018 6:168

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  14. Content type: Research

    The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the meta...

    Authors: Jingjing Peng, Carl-Eric Wegner, Qicheng Bei, Pengfei Liu and Werner Liesack

    Citation: Microbiome 2018 6:169

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  15. Content type: Research

    Microbial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass de...

    Authors: Keith Arora-Williams, Scott W. Olesen, Benjamin P. Scandella, Kyle Delwiche, Sarah J. Spencer, Elise M. Myers, Sonali Abraham, Alyssa Sooklal and Sarah P. Preheim

    Citation: Microbiome 2018 6:165

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  16. Content type: Research

    Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (rCDI). The use of freeze-dried, encapsulated donor material for FMT (cap-FMT) allows for an easy rou...

    Authors: Christopher Staley, Thomas Kaiser, Byron P. Vaughn, Carolyn T. Graiziger, Matthew J. Hamilton, Tauseef ur Rehman, Kevin Song, Alexander Khoruts and Michael J. Sadowsky

    Citation: Microbiome 2018 6:166

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  17. Content type: Research

    Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habi...

    Authors: Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William Inskeep, Natalia N. Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramunas Stepanauskas and Tanja Woyke

    Citation: Microbiome 2018 6:161

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  18. Content type: Research

    Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the e...

    Authors: Marius Bredon, Jessica Dittmer, Cyril Noël, Bouziane Moumen and Didier Bouchon

    Citation: Microbiome 2018 6:162

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  19. Content type: Research

    Targeted amplicon deep sequencing (TADS) of the 16S rRNA gene is commonly used to explore and characterize bacterial microbiomes. Meanwhile, attempts to apply TADS to the detection and characterization of enti...

    Authors: Briana R. Flaherty, Eldin Talundzic, Joel Barratt, Kristine J. Kines, Christian Olsen, Meredith Lane, Mili Sheth and Richard S. Bradbury

    Citation: Microbiome 2018 6:164

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  20. Content type: Meeting Report

    Here, we summarize a symposium entitled “Microbiology of the Built Environment: Implications for Health and Design” that was presented at the National Council for Science and the Environment (NCSE) 17th Nation...

    Authors: Ashleigh Bope, Mark H. Weir, Amy Pruden, Michael Morowitz, Jade Mitchell and Karen C. Dannemiller

    Citation: Microbiome 2018 6:160

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  21. Content type: Research

    Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure...

    Authors: Jun Yuan, Jun Zhao, Tao Wen, Mengli Zhao, Rong Li, Pim Goossens, Qiwei Huang, Yang Bai, Jorge M. Vivanco, George A. Kowalchuk, Roeland L. Berendsen and Qirong Shen

    Citation: Microbiome 2018 6:156

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  22. Content type: Research

    Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associa...

    Authors: Thao T. B. Ho, Maureen W. Groer, Bradley Kane, Alyson L. Yee, Benjamin A. Torres, Jack A. Gilbert and Akhil Maheshwari

    Citation: Microbiome 2018 6:157

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  23. Content type: Methodology

    Recent advances in sequencing technologies and bioinformatics tools have allowed for large-scale microbiome studies that are rapidly advancing medical research. However, small changes in technique or analysis ...

    Authors: Jeffrey M. Bender, Fan Li, Helty Adisetiyo, David Lee, Sara Zabih, Long Hung, Thomas A. Wilkinson, Pia S. Pannaraj, Rosemary C. She, Jennifer Dien Bard, Nicole H. Tobin and Grace M. Aldrovandi

    Citation: Microbiome 2018 6:155

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  24. Content type: Research

    Psoriasis impacts 1–3% of the world’s population and is characterized by hyper-proliferation of keratinocytes and increased inflammation. At the molecular level, psoriasis is commonly driven by a Th17 response...

    Authors: Hsin-Wen Chang, Di Yan, Rasnik Singh, Jared Liu, Xueyan Lu, Derya Ucmak, Kristina Lee, Ladan Afifi, Douglas Fadrosh, John Leech, Kimberly S. Vasquez, Margaret M. Lowe, Michael D. Rosenblum, Tiffany C. Scharschmidt, Susan V. Lynch and Wilson Liao

    Citation: Microbiome 2018 6:154

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  25. Content type: Research

    Host-microbe balance maintains intestinal homeostasis and strongly influences inflammatory conditions such as inflammatory bowel diseases (IBD). Here we focused on bacteria-fungi interactions and their implica...

    Authors: Bruno Sovran, Julien Planchais, Sarah Jegou, Marjolene Straube, Bruno Lamas, Jane Mea Natividad, Allison Agus, Louise Dupraz, Jérémy Glodt, Grégory Da Costa, Marie-Laure Michel, Philippe Langella, Mathias L. Richard and Harry Sokol

    Citation: Microbiome 2018 6:152

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  26. Content type: Methodology

    Fetal growth restriction, pre-eclampsia, and pre-term birth are major adverse pregnancy outcomes. These complications are considerable contributors to fetal/maternal morbidity and mortality worldwide. A signif...

    Authors: Susanne Lager, Marcus C. de Goffau, Ulla Sovio, Sharon J. Peacock, Julian Parkhill, D. Stephen Charnock-Jones and Gordon C. S. Smith

    Citation: Microbiome 2018 6:151

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  27. Content type: Research

    Cigarette smoking is a known risk factor in a number of gastrointestinal (GI) diseases in which the microbiota is implicated, including duodenal ulcer and Crohn’s disease. Smoking has the potential to alter th...

    Authors: Erin R. Shanahan, Ayesha Shah, Natasha Koloski, Marjorie M. Walker, Nicholas J. Talley, Mark Morrison and Gerald J. Holtmann

    Citation: Microbiome 2018 6:150

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  28. Content type: Research

    Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome...

    Authors: Ari Ugarte, Riccardo Vicedomini, Juliana Bernardes and Alessandra Carbone

    Citation: Microbiome 2018 6:149

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  29. Content type: Research

    The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacter...

    Authors: Priscila Bascuñán, Juan Pablo Niño-Garcia, Yadira Galeano-Castañeda, David Serre and Margarita M. Correa

    Citation: Microbiome 2018 6:148

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  30. Content type: Research

    The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine inverteb...

    Authors: Marlène Chiarello, Jean-Christophe Auguet, Yvan Bettarel, Corinne Bouvier, Thomas Claverie, Nicholas A. J. Graham, Fabien Rieuvilleneuve, Elliot Sucré, Thierry Bouvier and Sébastien Villéger

    Citation: Microbiome 2018 6:147

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  31. Content type: Research

    Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nu...

    Authors: Shuo Jiao, Weimin Chen, Jieli Wang, Nini Du, Qiaoping Li and Gehong Wei

    Citation: Microbiome 2018 6:146

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  32. Content type: Research

    Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a “gold standard” protocol for viral DNA extraction with associated in...

    Authors: Christian Milani, Eoghan Casey, Gabriele Andrea Lugli, Rebecca Moore, Joanna Kaczorowska, Conor Feehily, Marta Mangifesta, Leonardo Mancabelli, Sabrina Duranti, Francesca Turroni, Francesca Bottacini, Jennifer Mahony, Paul D. Cotter, Fionnuala M. McAuliffe, Douwe van Sinderen and Marco Ventura

    Citation: Microbiome 2018 6:145

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  33. Content type: Short report

    The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of host organellar sequences (mitochondrial and/or plastid), which share a common ancestor...

    Authors: Connor R. Fitzpatrick, Patricia Lu-Irving, Julia Copeland, David S. Guttman, Pauline W. Wang, David A. Baltrus, Katrina M. Dlugosch and Marc T. J. Johnson

    Citation: Microbiome 2018 6:144

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  34. Content type: Research

    Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of v...

    Authors: Késia Silva Lourenço, Afnan K. A. Suleiman, A. Pijl, J. A. van Veen, H. Cantarella and E. E. Kuramae

    Citation: Microbiome 2018 6:142

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  35. Content type: Research

    Pathogen colonization inside tick tissues is a significant aspect of the overall competence of a vector. Amblyomma maculatum is a competent vector of the spotted fever group rickettsiae, Rickettsia parkeri. When

    Authors: Khemraj Budachetri, Deepak Kumar, Gary Crispell, Christine Beck, Gregory Dasch and Shahid Karim

    Citation: Microbiome 2018 6:141

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  36. Content type: Research

    Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome (WNS), has led to the deaths of millions of hibernating bats in the United States of America (USA) and Canada. Efficient strate...

    Authors: Amanpreet Singh, Erica Lasek-Nesselquist, Vishnu Chaturvedi and Sudha Chaturvedi

    Citation: Microbiome 2018 6:139

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  37. Content type: Research

    Microorganisms drive high rates of methanogenesis and carbon mineralization in wetland ecosystems. These signals are especially pronounced in the Prairie Pothole Region of North America, the tenth largest wetl...

    Authors: Paula Dalcin Martins, Robert E. Danczak, Simon Roux, Jeroen Frank, Mikayla A. Borton, Richard A. Wolfe, Marie N. Burris and Michael J. Wilkins

    Citation: Microbiome 2018 6:138

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  38. Content type: Methodology

    Dysbiosis of the human gut microbiome is defined as a maladaptive or clinically relevant deviation of the community profile from the healthy or normal state. Dysbiosis has been implicated in an extensive set o...

    Authors: Emmanuel Montassier, Gabriel A. Al-Ghalith, Benjamin Hillmann, Kimberly Viskocil, Amanda J. Kabage, Christopher E. McKinlay, Michael J. Sadowsky, Alexander Khoruts and Dan Knights

    Citation: Microbiome 2018 6:137

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  39. Content type: Research

    Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied ...

    Authors: Jia Zhu, Ming Liao, Ziting Yao, Wenying Liang, Qibin Li, Jianlun Liu, Huawei Yang, Yinan Ji, Wei Wei, Aihua Tan, Siyuan Liang, Yang Chen, Haisong Lin, Xiujuan Zhu, Shengzhu Huang, Jiarong Tian…

    Citation: Microbiome 2018 6:136

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  40. Content type: Research

    Behcet’s disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but...

    Authors: Zi Ye, Ni Zhang, Chunyan Wu, Xinyuan Zhang, Qingfeng Wang, Xinyue Huang, Liping Du, Qingfeng Cao, Jihong Tang, Chunjiang Zhou, Shengping Hou, Yue He, Qian Xu, Xiao Xiong, Aize Kijlstra, Nan Qin…

    Citation: Microbiome 2018 6:135

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  41. Content type: Research

    Different dietary approaches, such as gluten and casein free diets, or the use of probiotics and prebiotics have been suggested in autistic spectrum disorders in order to reduce gastrointestinal (GI) disturban...

    Authors: Roberta Grimaldi, Glenn R. Gibson, Jelena Vulevic, Natasa Giallourou, Josué L. Castro-Mejía, Lars H. Hansen, E. Leigh Gibson, Dennis S. Nielsen and Adele Costabile

    Citation: Microbiome 2018 6:133

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  42. Content type: Research

    As the gut microbiota contributes to metabolic health, it is important to determine specific diet-microbiota interactions that influence host metabolism. Bile acids and dietary fat source can alter phenotypes ...

    Authors: Sarah Just, Stanislas Mondot, Josef Ecker, Katrin Wegner, Eva Rath, Laura Gau, Theresa Streidl, Genevieve Hery-Arnaud, Sinah Schmidt, Till Robin Lesker, Valentin Bieth, Andreas Dunkel, Till Strowig, Thomas Hofmann, Dirk Haller, Gerhard Liebisch…

    Citation: Microbiome 2018 6:134

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