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  1. Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged u...

    Authors: Hong-Yi Li, Hang Wang, Hai-Tiao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A Gilbert and Zhi-Jian Zhang

    Citation: Microbiome 2018 6:187

    Content type: Research

    Published on:

  2. Clostridiales and Bacteroidales are uniquely adapted to the gut environment and have co-evolved with their hosts resulting in convergent microbiome patterns within mammalian species. As a result, members of Clost...

    Authors: Adélaïde Roguet, A. Murat Eren, Ryan J Newton and Sandra L McLellan

    Citation: Microbiome 2018 6:185

    Content type: Research

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  3. Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically c...

    Authors: Peng Li, Yong Xue, Jialiang Shi, Aihu Pan, Xueming Tang and Feng Ming

    Citation: Microbiome 2018 6:184

    Content type: Research

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  4. The ecological consequences of mercury (Hg) pollution—one of the major pollutants worldwide—on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from tw...

    Authors: Yu-Rong Liu, Manuel Delgado-Baquerizo, Li Bi, Jun Zhu and Ji-Zheng He

    Citation: Microbiome 2018 6:183

    Content type: Research

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  5. Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust...

    Authors: Ashkaan K. Fahimipour, Erica M. Hartmann, Andrew Siemens, Jeff Kline, David A. Levin, Hannah Wilson, Clarisse M. Betancourt-Román, GZ Brown, Mark Fretz, Dale Northcutt, Kyla N. Siemens, Curtis Huttenhower, Jessica L. Green and Kevin Van Den Wymelenberg

    Citation: Microbiome 2018 6:175

    Content type: Research

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  6. 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

    Content type: Research

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  7. 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

    Content type: Research

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  8. 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

    Content type: Research

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  9. 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

    Content type: Research

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  10. 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

    Content type: Research

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  11. 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

    Content type: Research

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  12. 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

    Content type: Research

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  13. 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

    Content type: Research

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  14. 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

    Content type: Research

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  15. 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

    Content type: Research

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  16. 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

    Content type: Research

    Published on:

  17. 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

    Content type: Research

    Published on:

  18. 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

    Content type: Research

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  19. 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

    Content type: Research

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  20. 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

    Content type: Research

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  21. 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

    Content type: Research

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  22. 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

    Content type: Research

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  23. 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

    Content type: Research

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  24. 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

    Content type: Research

    Published on:

  25. 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

    Content type: Meeting Report

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  26. 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

    Content type: Research

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  27. 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

    Content type: Research

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  28. 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

    Content type: Methodology

    Published on:

  29. 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

    Content type: Research

    Published on:

  30. Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, this method does not usually pro...

    Authors: Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen and Eugene J. Leys

    Citation: Microbiome 2018 6:153

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2018 6:206

  31. 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

    Content type: Research

    Published on:

  32. 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

    Content type: Methodology

    Published on:

    The Correction to this article has been published in Microbiome 2018 6:188

  33. 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

    Content type: Research

    Published on:

  34. 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

    Content type: Research

    Published on:

  35. 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

    Content type: Research

    Published on:

  36. 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

    Content type: Research

    Published on:

  37. 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

    Content type: Research

    Published on:

  38. 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

    Content type: Research

    Published on:

  39. 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

    Content type: Short report

    Published on:

  40. 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

    Content type: Research

    Published on:

  41. 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

    Content type: Research

    Published on:

  42. 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

    Content type: Research

    Published on:

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