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  1. The rumen contains a myriad of microbes whose primary role is to degrade and ferment dietary nutrients, which then provide the host with energy and nutrients. Rumen microbes commonly attach to ingested plant m...

    Authors: Mi-Young Won, Linda B. Oyama, Stephen J. Courtney, Christopher J. Creevey and Sharon A. Huws

    Citation: Microbiome 2020 8:23

    Content type: Research

    Published on:

  2. Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The curre...

    Authors: Xinyu Zhu, Stefano Campanaro, Laura Treu, Rekha Seshadri, Natalia Ivanova, Panagiotis G. Kougias, Nikos Kyrpides and Irini Angelidaki

    Citation: Microbiome 2020 8:22

    Content type: Research

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  3. Metagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in ...

    Authors: Anissa Grieb, Robert M. Bowers, Monike Oggerin, Danielle Goudeau, Janey Lee, Rex R. Malmstrom, Tanja Woyke and Bernhard M. Fuchs

    Citation: Microbiome 2020 8:21

    Content type: Research

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  4. Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved ...

    Authors: Hyun Kim, Kiseok Keith Lee, Jongbum Jeon, William Anthony Harris and Yong-Hwan Lee

    Citation: Microbiome 2020 8:20

    Content type: Research

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  5. The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intes...

    Authors: Said R. Bogatyrev, Justin C. Rolando and Rustem F. Ismagilov

    Citation: Microbiome 2020 8:19

    Content type: Research

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  6. Cell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of in...

    Authors: Philip Burnham, Nardhy Gomez-Lopez, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz, Darshana M. Dadhania, John Richard Lee, Manikkam Suthanthiran, Roberto Romero and Iwijn De Vlaminck

    Citation: Microbiome 2020 8:18

    Content type: Short report

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  7. Bacteriophages (phages) are the most numerous biological entities on Earth and play a crucial role in shaping microbial communities. Investigating the bacteriophage community from soil will shed light not only...

    Authors: Pauline C. Göller, Jose M. Haro-Moreno, Francisco Rodriguez-Valera, Martin J. Loessner and Elena Gómez-Sanz

    Citation: Microbiome 2020 8:17

    Content type: Methodology

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  8. Microorganisms in activated sludge (AS) play key roles in the wastewater treatment processes. However, their ecological behaviors and differences from microorganisms in other environments have mainly been stud...

    Authors: Lin Ye, Ran Mei, Wen-Tso Liu, Hongqiang Ren and Xu-Xiang Zhang

    Citation: Microbiome 2020 8:16

    Content type: Research

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  9. Dietary effects on the gut microbiome play key roles in the pathophysiology of inflammatory disorders, metabolic syndrome, obesity, and behavioral dysregulation. Often overlooked in such studies is the conside...

    Authors: Kathleen E. Morrison, Eldin Jašarević, Christopher D. Howard and Tracy L. Bale

    Citation: Microbiome 2020 8:15

    Content type: Short report

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  10. The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensit...

    Authors: Bachar Cheaib, Hamza Seghouani, Umer Zeeshan Ijaz and Nicolas Derome

    Citation: Microbiome 2020 8:14

    Content type: Research

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  11. Roux-en-Y gastric bypass (RYGB) surgery is a last-resort treatment to induce substantial and sustained weight loss in cases of severe obesity. This anatomical rearrangement affects the intestinal microbiota, b...

    Authors: Sven-Bastiaan Haange, Nico Jehmlich, Ute Krügel, Constantin Hintschich, Dorothee Wehrmann, Mohammed Hankir, Florian Seyfried, Jean Froment, Thomas Hübschmann, Susann Müller, Dirk K. Wissenbach, Kang Kang, Christian Buettner, Gianni Panagiotou, Matthias Noll, Ulrike Rolle-Kampczyk…

    Citation: Microbiome 2020 8:13

    Content type: Research

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  12. The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for micro...

    Authors: Eslam O. Osman, David J. Suggett, Christian R. Voolstra, D. Tye Pettay, Dave R. Clark, Claudia Pogoreutz, Eugenia M. Sampayo, Mark E. Warner and David J. Smith

    Citation: Microbiome 2020 8:8

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2020 8:24

  13. The role of the gut microbiota in Crohn’s disease (CD) is established and fecal microbiota transplantation (FMT) is an attractive therapeutic strategy. No randomized controlled clinical trial results are avail...

    Authors: Harry Sokol, Cecilia Landman, Philippe Seksik, Laurence Berard, Mélissa Montil, Isabelle Nion-Larmurier, Anne Bourrier, Guillaume Le Gall, Valérie Lalande, Alexis De Rougemont, Julien Kirchgesner, Anne Daguenel, Marine Cachanado, Alexandra Rousseau, Élodie Drouet, Michelle Rosenzwajg…

    Citation: Microbiome 2020 8:12

    Content type: Research

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  14. The complex network of interactions occurring between gastrointestinal (GI) and extra-intestinal (EI) parasitic helminths of humans and animals and the resident gut microbial flora is attracting increasing att...

    Authors: Riccardo Scotti, Stuart Southern, Christine Boinett, Timothy P. Jenkins, Alba Cortés and Cinzia Cantacessi

    Citation: Microbiome 2020 8:10

    Content type: Research

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  15. Verticillium wilt of olive (VWO) is caused by the soilborne fungal pathogen Verticillium dahliae. One of the best VWO management measures is the use of tolerant/resistant olive cultivars. Knowledge on the olive-a...

    Authors: Antonio J. Fernández-González, Martina Cardoni, Carmen Gómez-Lama Cabanás, Antonio Valverde-Corredor, Pablo J. Villadas, Manuel Fernández-López and Jesús Mercado-Blanco

    Citation: Microbiome 2020 8:11

    Content type: Research

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  16. Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and...

    Authors: Yaron Krotman, Timur M. Yergaliyev, Rivka Alexander Shani, Yosef Avrahami and Amir Szitenberg

    Citation: Microbiome 2020 8:9

    Content type: Research

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  17. Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors unde...

    Authors: Ray Keren, Jennifer E. Lawrence, Weiqin Zhuang, David Jenkins, Jillian F. Banfield, Lisa Alvarez-Cohen, Lijie Zhou and Ke Yu

    Citation: Microbiome 2020 8:7

    Content type: Research

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  18. High-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts as an adap...

    Authors: Nina Montoya-Ciriaco, Selene Gómez-Acata, Ligia Catalina Muñoz-Arenas, Luc Dendooven, Arturo Estrada-Torres, Aníbal H. Díaz de la Vega-Pérez and Yendi E. Navarro-Noya

    Citation: Microbiome 2020 8:6

    Content type: Research

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  19. The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabol...

    Authors: Rieka Chijiiwa, Masahito Hosokawa, Masato Kogawa, Yohei Nishikawa, Keigo Ide, Chikako Sakanashi, Kai Takahashi and Haruko Takeyama

    Citation: Microbiome 2020 8:5

    Content type: Research

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  20. Stress-induced hormones are essential for plants to modulate their microbiota and dynamically adjust to the environment. Despite the emphasis of the role of the phytohormone ethylene in the plant physiological...

    Authors: Yan Chen, Michael Bonkowski, Yi Shen, Bryan S. Griffiths, Yuji Jiang, Xiaoyue Wang and Bo Sun

    Citation: Microbiome 2020 8:4

    Content type: Research

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  21. It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this regi...

    Authors: Jiajie Feng, Cong Wang, Jiesi Lei, Yunfeng Yang, Qingyun Yan, Xishu Zhou, Xuanyu Tao, Daliang Ning, Mengting M. Yuan, Yujia Qin, Zhou J. Shi, Xue Guo, Zhili He, Joy D. Van Nostrand, Liyou Wu, Rosvel G. Bracho-Garillo…

    Citation: Microbiome 2020 8:3

    Content type: Research

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  22. The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthro...

    Authors: Kihyun Lee, Dae-Wi Kim, Do-Hoon Lee, Yong-Seok Kim, Ji-Hye Bu, Ju-Hee Cha, Cung Nawl Thawng, Eun-Mi Hwang, Hoon Je Seong, Woo Jun Sul, Elizabeth M. H. Wellington, Christopher Quince and Chang-Jun Cha

    Citation: Microbiome 2020 8:2

    Content type: Research

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  23. During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerou...

    Authors: Aaron J. Prussin II, Jessica A. Belser, Werner Bischoff, Scott T. Kelley, Kaisen Lin, William G. Lindsley, Jean Pierre Nshimyimana, Michael Schuit, Zhenyu Wu, Kyle Bibby and Linsey C. Marr

    Citation: Microbiome 2020 8:1

    Content type: Meeting Report

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  24. Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people...

    Authors: Jostein Gohli, Kari Oline Bøifot, Line Victoria Moen, Paulina Pastuszek, Gunnar Skogan, Klas I. Udekwu and Marius Dybwad

    Citation: Microbiome 2019 7:160

    Content type: Research

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  25. Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue a...

    Authors: Francesco Ricci, Vanessa Rossetto Marcelino, Linda L. Blackall, Michael Kühl, Mónica Medina and Heroen Verbruggen

    Citation: Microbiome 2019 7:159

    Content type: Review

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  26. Given the increasing use of gnotobiotic mouse models for deciphering the effects of human microbial communities on host biology, there is a need to develop new methods for characterizing these animals while ma...

    Authors: Ilia G. Halatchev, David O’Donnell, Matthew C. Hibberd and Jeffrey I. Gordon

    Citation: Microbiome 2019 7:158

    Content type: Methodology

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  27. Virophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understandi...

    Authors: David Paez-Espino, Jinglie Zhou, Simon Roux, Stephen Nayfach, Georgios A. Pavlopoulos, Frederik Schulz, Katherine D. McMahon, David Walsh, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Susannah G. Tringe and Nikos C. Kyrpides

    Citation: Microbiome 2019 7:157

    Content type: Research

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  28. The earliest microbial colonizers of the human gut can have life-long consequences for their hosts. Precisely how the neonatal gut bacterial microbiome and virome are initially populated is not well understood...

    Authors: Rabia Maqsood, Rachel Rodgers, Cynthia Rodriguez, Scott A. Handley, I. Malick Ndao, Phillip I. Tarr, Barbara B. Warner, Efrem S. Lim and Lori R. Holtz

    Citation: Microbiome 2019 7:156

    Content type: Research

    Published on:

  29. Ochratoxin A (OTA) is a widespread mycotoxin and induces liver inflammation to human and various species of animals. The intestinal microbiota has critical importance in liver inflammation; however, it remains...

    Authors: Wence Wang, Shuangshuang Zhai, Yaoyao Xia, Hao Wang, Dong Ruan, Ting Zhou, Yongwen Zhu, Hongfu Zhang, Minhong Zhang, Hui Ye, Wenkai Ren and Lin Yang

    Citation: Microbiome 2019 7:151

    Content type: Research

    Published on:

  30. Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly ...

    Authors: Michael Sweet, Alfred Burian, James Fifer, Mark Bulling, David Elliott and Laurie Raymundo

    Citation: Microbiome 2019 7:139

    Content type: Research

    Published on:

  31. Following publication of the original article [1], the authors reported an error in the Additional file 1.

    Authors: Marc D. Auffret, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, R. John Wallace, Tom C. Freeman, Robert Stewart, Mick Watson and Rainer Roehe

    Citation: Microbiome 2019 7:149

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2017 5:159

  32. Following publication of the original article [1], the authors reported an error in Figure 1 and a text on page 13. In Figure 1, some areas are missing and the correct figure is presented here. On page 13, the...

    Authors: Weidong Chen, Kexin Ren, Alain Isabwe, Huihuang Chen, Min Liu and Jun Yang

    Citation: Microbiome 2019 7:148

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2019 7:138

  33. House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically re...

    Authors: Rahel Park, Maria C. Dzialo, Stijn Spaepen, Donat Nsabimana, Kim Gielens, Herman Devriese, Sam Crauwels, Raul Y. Tito, Jeroen Raes, Bart Lievens and Kevin J. Verstrepen

    Citation: Microbiome 2019 7:147

    Content type: Research

    Published on:

  34. Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gen...

    Authors: Emanuela Coller, Alessandro Cestaro, Roberto Zanzotti, Daniela Bertoldi, Massimo Pindo, Simone Larger, Davide Albanese, Enzo Mescalchin and Claudio Donati

    Citation: Microbiome 2019 7:140

    Content type: Research

    Published on:

  35. Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere...

    Authors: Jennifer E. Schmidt, Angela D. Kent, Vanessa L. Brisson and Amélie C. M. Gaudin

    Citation: Microbiome 2019 7:146

    Content type: Research

    Published on:

  36. Regulatory T cell (Treg) deficiency leads to IPEX syndrome, a lethal autoimmune disease, in Human and mice. Dysbiosis of the gut microbiota in Treg-deficient scurfy (SF) mice has been described, but to date, t...

    Authors: Baokun He, Yuying Liu, Thomas K. Hoang, Xiangjun Tian, Christopher M. Taylor, Meng Luo, Dat Q. Tran, Nina Tatevian and J. Marc Rhoads

    Citation: Microbiome 2019 7:145

    Content type: Research

    Published on:

  37. N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answe...

    Authors: Kunkun Fan, Manuel Delgado-Baquerizo, Xisheng Guo, Daozhong Wang, Yanying Wu, Mo Zhu, Wei Yu, Huaiying Yao, Yong-guan Zhu and Haiyan Chu

    Citation: Microbiome 2019 7:143

    Content type: Research

    Published on:

  38. It is now possible to comprehensively characterize the microbiota of the lungs using culture-independent, sequencing-based assays. Several sample types have been used to investigate the lung microbiota, each p...

    Authors: Pierre H. H. Schneeberger, Janice Prescod, Liran Levy, David Hwang, Tereza Martinu and Bryan Coburn

    Citation: Microbiome 2019 7:141

    Content type: Research

    Published on:

  39. The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riveri...

    Authors: Weidong Chen, Kexin Ren, Alain Isabwe, Huihuang Chen, Min Liu and Jun Yang

    Citation: Microbiome 2019 7:138

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2019 7:148

  40. Ear, nose and throat involvement in granulomatosis with polyangiitis (GPA) is frequently the initial disease manifestation. Previous investigations have observed a higher prevalence of Staphylococcus aureus in pa...

    Authors: Josef Wagner, Ewan M. Harrison, Marcos Martinez Del Pero, Beth Blane, Gert Mayer, Johannes Leierer, Seerapani Gopaluni, Mark A. Holmes, Julian Parkhill, Sharon J. Peacock, David R. W. Jayne and Andreas Kronbichler

    Citation: Microbiome 2019 7:137

    Content type: Research

    Published on:

  41. Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that ...

    Authors: Shuaimin Chen, Tatoba R. Waghmode, Ruibo Sun, Eiko E. Kuramae, Chunsheng Hu and Binbin Liu

    Citation: Microbiome 2019 7:136

    Content type: Research

    Published on:

  42. The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse a...

    Authors: Vinicius S. Kavagutti, Adrian-Ştefan Andrei, Maliheh Mehrshad, Michaela M. Salcher and Rohit Ghai

    Citation: Microbiome 2019 7:135

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2020 8:40

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