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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. Content type: Research

    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

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

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

  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. Content type: Research

    Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distr...

    Authors: An Ni Zhang, Li-Guan Li, Liping Ma, Michael R. Gillings, James M. Tiedje and Tong Zhang

    Citation: Microbiome 2018 6:130

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  30. Content type: Research

    The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location i...

    Authors: Jose M. Haro-Moreno, Mario López-Pérez, José R. de la Torre, Antonio Picazo, Antonio Camacho and Francisco Rodriguez-Valera

    Citation: Microbiome 2018 6:128

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  31. Content type: Correction

    Unfortunately, after publication of this article [1], it was noticed that the accession numbers for the study were missing. The correct numbers are PRJNA438554, SRP148953.

    Authors: Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R. Gillings, Hong Chen, Tong Zhang and Yong-Guan Zhu

    Citation: Microbiome 2018 6:127

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    The original article was published in Microbiome 2017 5:84

  32. Content type: Correction

    Following publication of the original article [1], the authors reported an error in the caption of Fig. 4.

    Authors: Xue-Ying Zhang, Gansukh Sukhchuluun, Ting-Bei Bo, Qing-Sheng Chi, Jun-Jie Yang, Bin Chen, Lei Zhang and De-Hua Wang

    Citation: Microbiome 2018 6:126

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    The original article was published in Microbiome 2018 6:103

  33. Content type: Research

    Early life microbiota is an important determinant of immune and metabolic development and may have lasting consequences. The maternal gut microbiota during pregnancy or breastfeeding is important for defining ...

    Authors: Donald D. Nyangahu, Katie S. Lennard, Bryan P. Brown, Matthew G. Darby, Jerome M. Wendoh, Enock Havyarimana, Peter Smith, James Butcher, Alain Stintzi, Nicola Mulder, William Horsnell and Heather B. Jaspan

    Citation: Microbiome 2018 6:124

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  34. Content type: Microbiome Announcement

    Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on...

    Authors: Masood ur Rehman Kayani, Shawn M. Doyle, Naseer Sangwan, Guanqun Wang, Jack A. Gilbert, Brent C. Christner and Ting F. Zhu

    Citation: Microbiome 2018 6:123

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  35. Content type: Research

    The gut microbiome has an important role in infant health and immune development and may be affected by early-life exposures. Maternal diet may influence the infant gut microbiome through vertical transfer of ...

    Authors: Sara N. Lundgren, Juliette C. Madan, Jennifer A. Emond, Hilary G. Morrison, Brock C. Christensen, Margaret R. Karagas and Anne G. Hoen

    Citation: Microbiome 2018 6:109

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  36. Content type: Research

    The transformation of plant photosynthate into soil organic carbon and its recycling to CO2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowl...

    Authors: Evan P. Starr, Shengjing Shi, Steven J. Blazewicz, Alexander J. Probst, Donald J. Herman, Mary K. Firestone and Jillian F. Banfield

    Citation: Microbiome 2018 6:122

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  37. Content type: Research

    One way to improve both the ecological performance and functionality of probiotic bacteria is by combining them with a prebiotic in the form of a synbiotic. However, the degree to which such synbiotic formulat...

    Authors: Janina A. Krumbeck, Heather E. Rasmussen, Robert W. Hutkins, Jennifer Clarke, Krista Shawron, Ali Keshavarzian and Jens Walter

    Citation: Microbiome 2018 6:121

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  38. Content type: Research

    Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and communi...

    Authors: Karoline Faust, Franziska Bauchinger, Béatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D. Washburne, Didier Gonze and Stefanie Widder

    Citation: Microbiome 2018 6:120

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  39. Content type: Methodology

    Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology ...

    Authors: Marcos Parras-Moltó, Ana Rodríguez-Galet, Patricia Suárez-Rodríguez and Alberto López-Bueno

    Citation: Microbiome 2018 6:119

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  40. Content type: Research

    Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are cruc...

    Authors: Muhammad Farhan Ul Haque, Andrew T. Crombie, Scott A. Ensminger, Calin Baciu and J. Colin Murrell

    Citation: Microbiome 2018 6:118

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