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  1. Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using a disinfectant. The impact of these contrasti...

    Authors: Zihan Dai, Maria C. Sevillano-Rivera, Szymon T. Calus, Q. Melina Bautista-de los Santos, A. Murat Eren, Paul W. J. J. van der Wielen, Umer Z. Ijaz and Ameet J. Pinto

    Citation: Microbiome 2020 8:42

    Content type: Research

    Published on:

  2. New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after the...

    Authors: Maria-Elisabeth Böhm, Mohammad Razavi, Nachiket P. Marathe, Carl-Fredrik Flach and D. G. Joakim Larsson

    Citation: Microbiome 2020 8:41

    Content type: Research

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  3. Following publication of the original article [1], the authors reported that an affiliation of the first author was missing.

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

    Citation: Microbiome 2020 8:40

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2019 7:135

  4. The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, t...

    Authors: Lingdi Zhang, Christian V. Forst, Aubree Gordon, Gabrielle Gussin, Adam B. Geber, Porfirio J. Fernandez, Tao Ding, Lauren Lashua, Minghui Wang, Angel Balmaseda, Richard Bonneau, Bin Zhang and Elodie Ghedin

    Citation: Microbiome 2020 8:39

    Content type: Research

    Published on:

  6. Resident soil microbiota play key roles in sustaining the core ecosystem processes of terrestrial Antarctica, often involving unique taxa with novel functional traits. However, the full scope of biodiversity a...

    Authors: Eden Zhang, Loïc M. Thibaut, Aleks Terauds, Mark Raven, Mark M. Tanaka, Josie van Dorst, Sin Yin Wong, Sally Crane and Belinda C. Ferrari

    Citation: Microbiome 2020 8:37

    Content type: Research

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  8. There are a variety of bioinformatic pipelines and downstream analysis methods for analyzing 16S rRNA marker-gene surveys. However, appropriate assessment datasets and metrics are needed as there is limited gu...

    Authors: Nathan D. Olson, M. Senthil Kumar, Shan Li, Domenick J. Braccia, Stephanie Hao, Winston Timp, Marc L. Salit, O. Colin Stine and Hector Corrada Bravo

    Citation: Microbiome 2020 8:35

    Content type: Methodology

    Published on:

  9. Apicomplexans are the causative agents of major human diseases such as malaria and toxoplasmosis. A novel group of apicomplexans, recently named corallicolids, have been detected in corals inhabiting tropical ...

    Authors: Samuel A. Vohsen, Kaitlin E. Anderson, Andrea M. Gade, Harald R. Gruber-Vodicka, Richard P. Dannenberg, Eslam O. Osman, Nicole Dubilier, Charles R. Fisher and Iliana B. Baums

    Citation: Microbiome 2020 8:34

    Content type: Research

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  10. Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of such effects is limited due to a lack of rapid and scalable assay to compreh...

    Authors: Leyuan Li, Zhibin Ning, Xu Zhang, Janice Mayne, Kai Cheng, Alain Stintzi and Daniel Figeys

    Citation: Microbiome 2020 8:33

    Content type: Research

    Published on:

  11. Recently, increasing evidence supports that some complex diseases are not attributed to a given pathogen, but dysbiosis in the host intestinal microbiota (IM). The full intestinal ecosystem alterations, rather...

    Authors: Zhijian Huang, Shenzheng Zeng, Jinbo Xiong, Dongwei Hou, Renjun Zhou, Chengguang Xing, Dongdong Wei, Xisha Deng, Lingfei Yu, Hao Wang, Zhixuan Deng, Shaoping Weng, Satapornvanit Kriengkrai, Daliang Ning, Jizhong Zhou and Jianguo He

    Citation: Microbiome 2020 8:32

    Content type: Research

    Published on:

  13. There is an important need for the development of fast and robust methods to quantify the diversity and temporal dynamics of microbial communities in complex environmental samples. Because tandem mass spectrom...

    Authors: Olivier Pible, François Allain, Virginie Jouffret, Karen Culotta, Guylaine Miotello and Jean Armengaud

    Citation: Microbiome 2020 8:30

    Content type: Methodology

    Published on:

  14. The gut microbiota has the potential to influence the efficacy of cancer therapy. Here, we investigated the contribution of the intestinal microbiome on treatment outcomes in a heterogeneous cohort that includ...

    Authors: Yoshitaro Heshiki, Ruben Vazquez-Uribe, Jin Li, Yueqiong Ni, Scott Quainoo, Lejla Imamovic, Jun Li, Maria Sørensen, Billy K. C. Chow, Glen J. Weiss, Aimin Xu, Morten O. A. Sommer and Gianni Panagiotou

    Citation: Microbiome 2020 8:28

    Content type: Research

    Published on:

  15. Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on frac...

    Authors: Wu Xiong, Yuqi Song, Keming Yang, Yian Gu, Zhong Wei, George A. Kowalchuk, Yangchun Xu, Alexandre Jousset, Qirong Shen and Stefan Geisen

    Citation: Microbiome 2020 8:27

    Content type: Research

    Published on:

  16. Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has b...

    Authors: Jian Cao, Yongfei Hu, Fei Liu, Yanan Wang, Yuhai Bi, Na Lv, Jing Li, Baoli Zhu and George F. Gao

    Citation: Microbiome 2020 8:26

    Content type: Research

    Published on:

  18. Following publication of the original article [1], the authors reported an error on the legend of of P.damicornis in Fig. 1.

    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 8:24

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2020 8:8

  19. 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:

  20. 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

    Published on:

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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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  24. 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

    Published on:

  25. 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

    Published on:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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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  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

  37. 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

    Published on:

  38. 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

    Published on:

  39. 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

    Published on:

  40. 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

    Published on:

  41. 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

    Published on:

  42. 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

    Published on:

  43. 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

    Published on:

  44. 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

    Published on:

  45. 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

    Published on:

  46. 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:

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