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  1. Content type: Research

    Plants can adapt to edaphic stress, such as nutrient deficiency, toxicity and biotic challenges, by controlled transcriptomic responses, including microbiome interactions. Traditionally studied in model plant ...

    Authors: Ellen Young, Manus Carey, Andrew A. Meharg and Caroline Meharg

    Citation: Microbiome 2018 6:48

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  2. Content type: Review

    The holobiont concept was first developed for coral ecosystems but has been extended to multiple organisms, including plants and other animals. Studies on insect-associated microbial communities have produced ...

    Authors: Morgane Guégan, Karima Zouache, Colin Démichel, Guillaume Minard, Van Tran Van, Patrick Potier, Patrick Mavingui and Claire Valiente Moro

    Citation: Microbiome 2018 6:49

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  3. Content type: Research

    The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with res...

    Authors: Aaron M. Walsh, Fiona Crispie, Orla O’Sullivan, Laura Finnegan, Marcus J. Claesson and Paul D. Cotter

    Citation: Microbiome 2018 6:50

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  4. Content type: Research

    The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community’s taxonomic profile natural...

    Authors: Alexander Eng and Elhanan Borenstein

    Citation: Microbiome 2018 6:45

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  5. Content type: Research

    In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose ...

    Authors: A. E. Naas, L. M. Solden, A. D. Norbeck, H. Brewer, L. H. Hagen, I. M. Heggenes, A. C. McHardy, R. I. Mackie, L. Paša-Tolić, M. Ø. Arntzen, V. G. H. Eijsink, N. M. Koropatkin, M. Hess, K. C. Wrighton and P. B. Pope

    Citation: Microbiome 2018 6:44

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  6. Content type: Research

    The human intestine and its microbiota is the most common infection site for soil-transmitted helminths (STHs), which affect the well-being of ~ 1.5 billion people worldwide. The complex cross-kingdom interact...

    Authors: Bruce A. Rosa, Taniawati Supali, Lincoln Gankpala, Yenny Djuardi, Erliyani Sartono, Yanjiao Zhou, Kerstin Fischer, John Martin, Rahul Tyagi, Fatorma K. Bolay, Peter U. Fischer, Maria Yazdanbakhsh and Makedonka Mitreva

    Citation: Microbiome 2018 6:33

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  7. Content type: Methodology

    Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencin...

    Authors: Clarisse A. Marotz, Jon G. Sanders, Cristal Zuniga, Livia S. Zaramela, Rob Knight and Karsten Zengler

    Citation: Microbiome 2018 6:42

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  8. Content type: Methodology

    The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for...

    Authors: Mo Han, Lilan Hao, Yuxiang Lin, Fang Li, Jian Wang, Huanming Yang, Liang Xiao, Karsten Kristiansen, Huijue Jia and Junhua Li

    Citation: Microbiome 2018 6:43

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  9. Content type: Research

    Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacter...

    Authors: Marc W. Van Goethem, Rian Pierneef, Oliver K. I. Bezuidt, Yves Van De Peer, Don A. Cowan and Thulani P. Makhalanyane

    Citation: Microbiome 2018 6:40

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  10. Content type: Research

    To investigate whether alterations in the developing intestinal microbiota and immune markers precede celiac disease (CD) onset in infants at familial risk of developing the disease.

    Authors: Marta Olivares, Alan W. Walker, Amalia Capilla, Alfonso Benítez-Páez, Francesc Palau, Julian Parkhill, Gemma Castillejo and Yolanda Sanz

    Citation: Microbiome 2018 6:36

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  11. Content type: Research

    Multidrug-resistant bacteria represent a substantial global burden for human health, potentially fuelled by migration waves: in 2015, 476,649 refugees applied for asylum in Germany mostly as a result of the Sy...

    Authors: Robert Häsler, Christian Kautz, Ateequr Rehman, Rainer Podschun, Volker Gassling, Pius Brzoska, Jon Sherlock, Jan-Thorsten Gräsner, Gesine Hoppenstedt, Sabine Schubert, Astrid Ferlinz, Wolfgang Lieb, Matthias Laudes, Femke-Anouska Heinsen, Jens Scholz, Dag Harmsen…

    Citation: Microbiome 2018 6:37

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  12. Content type: Research

    Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host...

    Authors: Kelly Brener-Raffalli, Camille Clerissi, Jeremie Vidal-Dupiol, Mehdi Adjeroud, François Bonhomme, Marine Pratlong, Didier Aurelle, Guillaume Mitta and Eve Toulza

    Citation: Microbiome 2018 6:39

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  13. Content type: Research

    Dysbiosis of the gut microbiota has been implicated in the pathogenesis of many autoimmune conditions including type 1 diabetes (T1D). It is unknown whether changes in the gut microbiota observed in T1D are du...

    Authors: Jane A. Mullaney, Juliette E. Stephens, Mary-Ellen Costello, Cai Fong, Brooke E. Geeling, Patrick G. Gavin, Casey M. Wright, Timothy D. Spector, Matthew A. Brown and Emma E. Hamilton-Williams

    Citation: Microbiome 2018 6:35

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  14. Content type: Software

    Microbial longitudinal studies are powerful experimental designs utilized to classify diseases, determine prognosis, and analyze microbial systems dynamics. In longitudinal studies, only identifying differenti...

    Authors: Ahmed A. Metwally, Jie Yang, Christian Ascoli, Yang Dai, Patricia W. Finn and David L. Perkins

    Citation: Microbiome 2018 6:32

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  15. Content type: Research

    Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in anima...

    Authors: Wenguang Xiong, Yulin Wang, Yongxue Sun, Liping Ma, Qinglin Zeng, Xiaotao Jiang, Andong Li, Zhenling Zeng and Tong Zhang

    Citation: Microbiome 2018 6:34

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  16. Content type: Research

    Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperativ...

    Authors: M. A. Cregger, A. M. Veach, Z. K. Yang, M. J. Crouch, R. Vilgalys, G. A. Tuskan and C. W. Schadt

    Citation: Microbiome 2018 6:31

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  17. Content type: Research

    Gut microbiota provide functions of importance to influence hosts’ food digestion, metabolism, and protection against pathogens. Factors that affect the composition and functions of gut microbial communities a...

    Authors: Yinghua Zha, Alexander Eiler, Frank Johansson and Richard Svanbäck

    Citation: Microbiome 2018 6:28

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  18. Content type: Commentary

    In the cervicovaginal environment, the production of hydrogen peroxide (H2O2) by vaginal Lactobacillus spp. is often mentioned as a critical factor to the in vivo vaginal microbiota antimicrobial properties. We p...

    Authors: Gilda Tachedjian, Deirdre E. O’Hanlon and Jacques Ravel

    Citation: Microbiome 2018 6:29

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  19. Content type: Research

    The relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of...

    Authors: Yu Shi, Yuntao Li, Xingjia Xiang, Ruibo Sun, Teng Yang, Dan He, Kaoping Zhang, Yingying Ni, Yong-Guan Zhu, Jonathan M. Adams and Haiyan Chu

    Citation: Microbiome 2018 6:27

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  20. Content type: Research

    Floor dust is commonly used for microbial determinations in epidemiological studies to estimate early-life indoor microbial exposures. Resuspension of floor dust and its impact on infant microbial exposure is,...

    Authors: Heidi K. Hyytiäinen, Balamuralikrishna Jayaprakash, Pirkka V. Kirjavainen, Sampo E. Saari, Rauno Holopainen, Jorma Keskinen, Kaarle Hämeri, Anne Hyvärinen, Brandon E. Boor and Martin Täubel

    Citation: Microbiome 2018 6:25

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