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  1. Content type: Research

    Understanding the host impact on its symbiotic microbiota is important in redirecting the rumen microbiota and thus improving animal performance. The current study aimed to understand how rumen microbiota were...

    Authors: Mi Zhou, Yong-Jia Peng, Yanhong Chen, Christen M. Klinger, Masahito Oba, Jian-Xin Liu and Le Luo Guan

    Citation: Microbiome 2018 6:62

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  2. Content type: Research

    Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade compl...

    Authors: Angélique Gobet, Laëtitia Mest, Morgan Perennou, Simon M Dittami, Claire Caralp, Céline Coulombet, Sylvain Huchette, Sabine Roussel, Gurvan Michel and Catherine Leblanc

    Citation: Microbiome 2018 6:60

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  3. Content type: Review

    Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often refe...

    Authors: M. Amine Hassani, Paloma Durán and Stéphane Hacquard

    Citation: Microbiome 2018 6:58

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  4. Content type: Research

    Changes in hygiene and dietary habits, including increased consumption of foods high in fat, simple sugars, and salt that are known to impact the composition and function of the intestinal microbiota, may expl...

    Authors: Pedro M. Miranda, Giada De Palma, Viktoria Serkis, Jun Lu, Marc P. Louis-Auguste, Justin L. McCarville, Elena F. Verdu, Stephen M. Collins and Premysl Bercik

    Citation: Microbiome 2018 6:57

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  5. Content type: Research

    Gut microbiota composition and function are symbiotically linked with host health and altered in metabolic, inflammatory and neurodegenerative disorders. Three recognised mechanisms exist by which the microbio...

    Authors: Lesley Hoyles, Tom Snelling, Umm-Kulthum Umlai, Jeremy K. Nicholson, Simon R. Carding, Robert C. Glen and Simon McArthur

    Citation: Microbiome 2018 6:55

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  6. Content type: Research

    Calorie restriction (CR), which has a potent anti-inflammaging effect, has been demonstrated to induce dramatic changes in the gut microbiota. Whether the modulated gut microbiota contributes to the attenuatio...

    Authors: Fengwei Pan, Liying Zhang, Min Li, Yingxin Hu, Benhua Zeng, Huijuan Yuan, Liping Zhao and Chenhong Zhang

    Citation: Microbiome 2018 6:54

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  7. Content type: Research

    One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops...

    Authors: E. Gonzalez, F. E. Pitre, A. P. Pagé, J. Marleau, W. Guidi Nissim, M. St-Arnaud, M. Labrecque, S. Joly, E. Yergeau and N. J. B. Brereton

    Citation: Microbiome 2018 6:53

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  8. Content type: Review

    The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants ...

    Authors: Mohammadhossein Ravanbakhsh, Rashmi Sasidharan, Laurentius A. C. J. Voesenek, George A. Kowalchuk and Alexandre Jousset

    Citation: Microbiome 2018 6:52

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  9. Content type: Correction

    Following publication of the original article [1] it came to the attention of the Production Editor that Figs. 1 and 2 had not been replaced with the newly revised figures supplied by the authors (the original...

    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 6:51

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    The original article was published in Microbiome 2018 6:35

  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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    The Correction to this article has been published in Microbiome 2018 6:51

  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. Content type: Research

    Numerous studies have thus far characterized the temporal dynamics of the skin microbiota of healthy individuals. However, there is no information regarding the dynamics of different microbial association netw...

    Authors: Marcus H. Y. Leung, Xinzhao Tong, David Wilkins, Hedwig H. L. Cheung and Patrick K. H. Lee

    Citation: Microbiome 2018 6:26

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  30. 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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  31. Content type: Software

    Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Advancing methods for monitoring of environmental media (e.g., wastewater, agricultural w...

    Authors: Gustavo Arango-Argoty, Emily Garner, Amy Pruden, Lenwood S. Heath, Peter Vikesland and Liqing Zhang

    Citation: Microbiome 2018 6:23

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  32. Content type: Research

    Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust ...

    Authors: Juan P. Maestre, Wiley Jennings, Dennis Wylie, Sharon D. Horner, Jeffrey Siegel and Kerry A. Kinney

    Citation: Microbiome 2018 6:22

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  33. Content type: Research

    The skin harbors complex communities of resident microorganisms, yet little is known of their physiological roles and the molecular mechanisms that mediate cutaneous host-microbe interactions. Here, we profile...

    Authors: Jacquelyn S. Meisel, Georgia Sfyroera, Casey Bartow-McKenney, Ciara Gimblet, Julia Bugayev, Joseph Horwinski, Brian Kim, Jonathan R. Brestoff, Amanda S. Tyldsley, Qi Zheng, Brendan P. Hodkinson, David Artis and Elizabeth A. Grice

    Citation: Microbiome 2018 6:20

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  34. Content type: Research

    The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR)...

    Authors: Julie Reveillaud, Rika Anderson, Sintra Reves-Sohn, Colleen Cavanaugh and Julie A. Huber

    Citation: Microbiome 2018 6:19

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  35. Content type: Research

    High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties...

    Authors: Jia Liu, Ahmed Abdelfattah, John Norelli, Erik Burchard, Leonardo Schena, Samir Droby and Michael Wisniewski

    Citation: Microbiome 2018 6:18

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  36. Content type: Methodology

    Most of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, ...

    Authors: Garold Fuks, Michael Elgart, Amnon Amir, Amit Zeisel, Peter J. Turnbaugh, Yoav Soen and Noam Shental

    Citation: Microbiome 2018 6:17

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  37. Content type: Research

    Bacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, little is presently known about the integrated biogeography of planktonic and sedimentary bacterial communities ...

    Authors: Tang Liu, An Ni Zhang, Jiawen Wang, Shufeng Liu, Xiaotao Jiang, Chenyuan Dang, Tao Ma, Sitong Liu, Qian Chen, Shuguang Xie, Tong Zhang and Jinren Ni

    Citation: Microbiome 2018 6:16

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  38. Content type: Research

    Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be man...

    Authors: Kyle Hartman, Marcel G. A. van der Heijden, Raphaël A. Wittwer, Samiran Banerjee, Jean-Claude Walser and Klaus Schlaeppi

    Citation: Microbiome 2018 6:14

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    The Correction to this article has been published in Microbiome 2018 6:74

  39. Content type: Research

    Crohn’s disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been c...

    Authors: Gavin M. Douglas, Richard Hansen, Casey M. A. Jones, Katherine A. Dunn, André M. Comeau, Joseph P. Bielawski, Rachel Tayler, Emad M. El-Omar, Richard K. Russell, Georgina L. Hold, Morgan G. I. Langille and Johan Van Limbergen

    Citation: Microbiome 2018 6:13

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  40. Content type: Research

    No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes tha...

    Authors: Laura Tipton, Christian L. Müller, Zachary D. Kurtz, Laurence Huang, Eric Kleerup, Alison Morris, Richard Bonneau and Elodie Ghedin

    Citation: Microbiome 2018 6:12

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  41. Content type: Methodology

    Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of “resistomes” (the ensemble of genes encoding antimicrobial resistance in a given microbio...

    Authors: Val F. Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J. Willems, Fernando de la Cruz and Teresa M. Coque

    Citation: Microbiome 2018 6:11

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