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  1. Content type: Research

    Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricular...

    Authors: Dagmara Sirová, Jiří Bárta, Karel Šimek, Thomas Posch, Jiří Pech, James Stone, Jakub Borovec, Lubomír Adamec and Jaroslav Vrba

    Citation: Microbiome 2018 6:225

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  2. Content type: Methodology

    The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA sequences not truly present in the sample. Contaminants come from...

    Authors: Nicole M. Davis, Diana M. Proctor, Susan P. Holmes, David A. Relman and Benjamin J. Callahan

    Citation: Microbiome 2018 6:226

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  3. Content type: Research

    The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the ...

    Authors: Nandan P. Deshpande, Stephen M. Riordan, Natalia Castaño-Rodríguez, Marc R. Wilkins and Nadeem O. Kaakoush

    Citation: Microbiome 2018 6:227

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  4. Content type: Research

    It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches ...

    Authors: Samuel Jacquiod, Inês Nunes, Asker Brejnrod, Martin A. Hansen, Peter E. Holm, Anders Johansen, Kristian K. Brandt, Anders Priemé and Søren J. Sørensen

    Citation: Microbiome 2018 6:223

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  5. Content type: Research

    Currently, the effect of the bacterial community on cast iron corrosion process does not reach consensus. Moreover, some studies have produced contrasting results, suggesting that bacteria can either accelerat...

    Authors: Guijuan Zhang, Bing Li, Jie Liu, Mingqiang Luan, Long Yue, Xiao-Tao Jiang, Ke Yu and Yuntao Guan

    Citation: Microbiome 2018 6:222

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  6. Content type: Research

    Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. Wh...

    Authors: Jessica D. Forbes, Chih-yu Chen, Natalie C. Knox, Ruth-Ann Marrie, Hani El-Gabalawy, Teresa de Kievit, Michelle Alfa, Charles N. Bernstein and Gary Van Domselaar

    Citation: Microbiome 2018 6:221

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  7. Content type: Research

    Antibiotics are commonly used worldwide, and pesticide is a kind of xenobiotic to which humans are frequently exposed. The interactive impact of antibiotics on pesticides has rarely been studied. We aim to inv...

    Authors: Jing Zhan, Yiran Liang, Donghui Liu, Xiaoran Ma, Peize Li, Chang Liu, Xueke Liu, Peng Wang and Zhiqiang Zhou

    Citation: Microbiome 2018 6:224

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  8. Content type: Short report

    Faecal microbiota transplantation (FMT) is used in the treatment of recurrent Clostridium difficile infection. Its success is typically attributed to the restoration of a diverse microbiota. Viruses (including ba...

    Authors: L. A. Draper, F. J. Ryan, M. K. Smith, J. Jalanka, E. Mattila, P. A. Arkkila, R. P. Ross, R. Satokari and C. Hill

    Citation: Microbiome 2018 6:220

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  9. Content type: Research

    Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degr...

    Authors: Ornella Carrión, Nasmille L. Larke-Mejía, Lisa Gibson, Muhammad Farhan Ul Haque, Javier Ramiro-García, Terry J. McGenity and J. Colin Murrell

    Citation: Microbiome 2018 6:219

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  10. Content type: Research

    The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adol...

    Authors: Jesse R. Willis, Pedro González-Torres, Alexandros A. Pittis, Luis A. Bejarano, Luca Cozzuto, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Antonia Valentín, Ewa Ksiezopolska, Carlos Company, Harris Onywera, Magda Montfort, Antonio Hermoso, Susana Iraola-Guzmán, Ester Saus, Annick Labeeuw…

    Citation: Microbiome 2018 6:218

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  11. Content type: Research

    Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional ca...

    Authors: Anna Edlund, Youngik Yang, Shibu Yooseph, Xuesong He, Wenyuan Shi and Jeffrey S. McLean

    Citation: Microbiome 2018 6:217

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  12. Content type: Research

    The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have ...

    Authors: Lise Alonso, Charline Creuzé-des-Châtelliers, Théo Trabac, Audrey Dubost, Yvan Moënne-Loccoz and Thomas Pommier

    Citation: Microbiome 2018 6:216

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  13. Content type: Research

    The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts’ polyextreme conditions, plants interact with ed...

    Authors: Ramona Marasco, María J. Mosqueira, Marco Fusi, Jean-Baptiste Ramond, Giuseppe Merlino, Jenny M. Booth, Gillian Maggs-Kölling, Don A. Cowan and Daniele Daffonchio

    Citation: Microbiome 2018 6:215

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  14. Content type: Correction

    Following publication of the original article [1], the authors reported a typographic error in scientific notation in the number of reads, the text should read as:

    Authors: Nitin Kumar Singh, Jason M. Wood, Fathi Karouia and Kasthuri Venkateswaran

    Citation: Microbiome 2018 6:214

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    The original article was published in Microbiome 2018 6:204

  15. Content type: Research

    Even though human sweat is odorless, bacterial growth and decomposition of specific odor precursors in it is believed to give rise to body odor in humans. While mechanisms of odor generation have been widely s...

    Authors: Tze Hau Lam, Davide Verzotto, Purbita Brahma, Amanda Hui Qi Ng, Ping Hu, Dan Schnell, Jay Tiesman, Rong Kong, Thi My Uyen Ton, Jianjun Li, May Ong, Yang Lu, David Swaile, Ping Liu, Jiquan Liu and Niranjan Nagarajan

    Citation: Microbiome 2018 6:213

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  16. Content type: Research

    Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata ext...

    Authors: Peng Huang, Yan Zhang, Kangpeng Xiao, Fan Jiang, Hengchao Wang, Dazhi Tang, Dan Liu, Bo Liu, Yisong Liu, Xi He, Hua Liu, Xiubin Liu, Zhixing Qing, Conghui Liu, Jialu Huang, Yuwei Ren…

    Citation: Microbiome 2018 6:211

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  17. Content type: Meeting Report

    The National Cancer Institute (NCI) sponsored a 2-day workshop, “Next Steps in Studying the Human Microbiome and Health in Prospective Studies,” in Bethesda, Maryland, May 16–17, 2017. The workshop brought tog...

    Authors: Rashmi Sinha, Habibul Ahsan, Martin Blaser, J. Gregory Caporaso, Joseph Russell Carmical, Andrew T. Chan, Anthony Fodor, Mitchell H. Gail, Curtis C. Harris, Kathy Helzlsouer, Curtis Huttenhower, Rob Knight, Heidi H. Kong, Gabriel Y. Lai, Diane Leigh Smith Hutchinson, Loic Le Marchand…

    Citation: Microbiome 2018 6:210

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  18. Content type: Research

    Microbiome composition is linked to host functional traits including metabolism and immune function. Drivers of microbiome composition are increasingly well-characterised; however, evidence of group-level micr...

    Authors: Rachael E. Antwis, Jessica M. D. Lea, Bryony Unwin and Susanne Shultz

    Citation: Microbiome 2018 6:207

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  19. Content type: Research

    The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many org...

    Authors: Celso Martins, Adélia Varela, Céline C. Leclercq, Oscar Núñez, Tomáš Větrovský, Jenny Renaut, Petr Baldrian and Cristina Silva Pereira

    Citation: Microbiome 2018 6:208

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  20. Content type: Correction

    Following publication of the original article, the authors recognized that the left and right panels in Fig. 6b had been inadvertently switched during reformatting.

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

    Citation: Microbiome 2018 6:206

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    The original article was published in Microbiome 2018 6:153

  21. Content type: Research

    The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-ba...

    Authors: Nitin Kumar Singh, Jason M. Wood, Fathi Karouia and Kasthuri Venkateswaran

    Citation: Microbiome 2018 6:204

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    The Correction to this article has been published in Microbiome 2018 6:214

  22. Content type: Research

    Understanding the mechanism of the sexual dimorphism in susceptibility to obesity and metabolic syndrome (MS) is important for the development of effective interventions for MS.

    Authors: Kanakaraju Kaliannan, Ruairi C. Robertson, Kiera Murphy, Catherine Stanton, Chao Kang, Bin Wang, Lei Hao, Atul K. Bhan and Jing X. Kang

    Citation: Microbiome 2018 6:205

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  23. Content type: Research

    The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility compl...

    Authors: Hooman Derakhshani, Jan C. Plaizier, Jeroen De Buck, Herman W. Barkema and Ehsan Khafipour

    Citation: Microbiome 2018 6:203

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  24. Content type: Research

    Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models’ fundamental biology include the timescales on which microbiota vary and the fact...

    Authors: Justin D. Silverman, Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee and Lawrence A. David

    Citation: Microbiome 2018 6:202

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    The Correction to this article has been published in Microbiome 2018 6:212

  25. Content type: Research

    Travelers’ diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods...

    Authors: Qiyun Zhu, Christopher L. Dupont, Marcus B. Jones, Kevin M. Pham, Zhi-Dong Jiang, Herbert L. DuPont and Sarah K. Highlander

    Citation: Microbiome 2018 6:201

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  26. Content type: Research

    Mastitis, which affects nearly all lactating mammals including human, is generally thought to be caused by local infection of the mammary glands. For treatment, antibiotics are commonly prescribed, which howev...

    Authors: Chen Ma, Zheng Sun, Benhua Zeng, Shi Huang, Jie Zhao, Yong Zhang, Xiaoquan Su, Jian Xu, Hong Wei and Heping Zhang

    Citation: Microbiome 2018 6:200

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  27. Content type: Research

    Gut microbiome characteristics associated with HIV infection are of intense research interest but a deep understanding has been challenged by confounding factors across studied populations. Notably, a Prevotella-...

    Authors: Abigail J. S. Armstrong, Michael Shaffer, Nichole M. Nusbacher, Christine Griesmer, Suzanne Fiorillo, Jennifer M. Schneider, C. Preston Neff, Sam X. Li, Andrew P. Fontenot, Thomas Campbell, Brent E. Palmer and Catherine A. Lozupone

    Citation: Microbiome 2018 6:198

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  28. Content type: Meeting Report

    The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its f...

    Authors: Jacquelyn S. Meisel, Daniel J. Nasko, Brian Brubach, Victoria Cepeda-Espinoza, Jessica Chopyk, Héctor Corrada-Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D. Olson, Nidhi Shah, Sarah M. Allard, Adam L. Bazinet, Nicholas H. Bergman, Alexis Brown, J. Gregory Caporaso…

    Citation: Microbiome 2018 6:197

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  29. Content type: Review

    Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indig...

    Authors: Andrea Coleman, Amanda Wood, Seweryn Bialasiewicz, Robert S. Ware, Robyn L. Marsh and Anders Cervin

    Citation: Microbiome 2018 6:199

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  30. Content type: Research

    Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is c...

    Authors: Jacob S. Leiby, Kevin McCormick, Scott Sherrill-Mix, Erik L. Clarke, Lyanna R. Kessler, Louis J. Taylor, Casey E. Hofstaedter, Aoife M. Roche, Lisa M. Mattei, Kyle Bittinger, Michal A. Elovitz, Rita Leite, Samuel Parry and Frederic D. Bushman

    Citation: Microbiome 2018 6:196

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  31. Content type: Methodology

    Several of the most devastating human diseases are caused by eukaryotic parasites transmitted by arthropod vectors or through food and water contamination. These pathogens only represent a fraction of all unic...

    Authors: Matthew V. Cannon, Haikel Bogale, Lindsay Rutt, Michael Humphrys, Poonum Korpe, Priya Duggal, Jacques Ravel and David Serre

    Citation: Microbiome 2018 6:195

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  32. Content type: Research

    The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen production. Th...

    Authors: Alessandra Fontana, Panagiotis G. Kougias, Laura Treu, Adam Kovalovszki, Giorgio Valle, Fabrizio Cappa, Lorenzo Morelli, Irini Angelidaki and Stefano Campanaro

    Citation: Microbiome 2018 6:194

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  33. Content type: Research

    Postnatal development of early life microbiota influences immunity, metabolism, neurodevelopment, and infant health. Microbiome development occurs at multiple body sites, with distinct community compositions a...

    Authors: Alex Grier, Andrew McDavid, Bokai Wang, Xing Qiu, James Java, Sanjukta Bandyopadhyay, Hongmei Yang, Jeanne Holden-Wiltse, Haeja A Kessler, Ann L Gill, Heidie Huyck, Ann R Falsey, David J Topham, Kristin M Scheible, Mary T Caserta, Gloria S Pryhuber…

    Citation: Microbiome 2018 6:193

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  34. Content type: Research

    The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characteriz...

    Authors: Janko Tackmann, Natasha Arora, Thomas Sebastian Benedikt Schmidt, João Frederico Matias Rodrigues and Christian von Mering

    Citation: Microbiome 2018 6:192

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  35. Content type: Research

    Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provi...

    Authors: Joshua P. Earl, Nithin D. Adappa, Jaroslaw Krol, Archana S. Bhat, Sergey Balashov, Rachel L. Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich and Joshua Chang Mell

    Citation: Microbiome 2018 6:190

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  36. Content type: Research

    Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hyp...

    Authors: Sean Benler, Ana Georgina Cobián-Güemes, Katelyn McNair, Shr-Hau Hung, Kyle Levi, Rob Edwards and Forest Rohwer

    Citation: Microbiome 2018 6:191

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  37. Content type: Research

    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

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  38. Content type: Research

    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

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  39. Content type: Research

    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

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  40. Content type: Research

    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

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  41. Content type: Research

    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

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  42. 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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  43. 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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  44. 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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  45. 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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