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  1. The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for 1 year outside the International Space Sta...

    Authors: Emanuel Ott, Yuko Kawaguchi, Denise Kölbl, Elke Rabbow, Petra Rettberg, Maximilian Mora, Christine Moissl-Eichinger, Wolfram Weckwerth, Akihiko Yamagishi and Tetyana Milojevic

    Citation: Microbiome 2020 8:150

    Content type: Research

    Published on:

  2. Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts’ biology. Yet, little is known about gut microbiota dynamics duri...

    Authors: Andreas Härer, Julián Torres-Dowdall, Sina J. Rometsch, Elizabeth Yohannes, Gonzalo Machado-Schiaffino and Axel Meyer

    Citation: Microbiome 2020 8:149

    Content type: Research

    Published on:

  3. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Oskar Modin, Raquel Liébana, Soroush Saheb-Alam, Britt-Marie Wilén, Carolina Suarez, Malte Hermansson and Frank Persson

    Citation: Microbiome 2020 8:148

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2020 8:132

  4. Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbio...

    Authors: Elin Videvall, Se Jin Song, Hanna M. Bensch, Maria Strandh, Anel Engelbrecht, Naomi Serfontein, Olof Hellgren, Adriaan Olivier, Schalk Cloete, Rob Knight and Charlie K. Cornwallis

    Citation: Microbiome 2020 8:147

    Content type: Research

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  5. Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their ...

    Authors: Joel J. Brown, Sonia M. Rodríguez-Ruano, Anbu Poosakkannu, Giampiero Batani, Justin O. Schmidt, Walter Roachell, Jan Zima Jr, Václav Hypša and Eva Nováková

    Citation: Microbiome 2020 8:146

    Content type: Research

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  6. Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct...

    Authors: Fengzhe Xu, Yuanqing Fu, Ting-yu Sun, Zengliang Jiang, Zelei Miao, Menglei Shuai, Wanglong Gou, Chu-wen Ling, Jian Yang, Jun Wang, Yu-ming Chen and Ju-Sheng Zheng

    Citation: Microbiome 2020 8:145

    Content type: Research

    Published on:

  7. Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide divers...

    Authors: Cecília Pascelli, Patrick W. Laffy, Emmanuelle Botté, Marija Kupresanin, Thomas Rattei, Miguel Lurgi, Timothy Ravasi and Nicole S. Webster

    Citation: Microbiome 2020 8:144

    Content type: Research

    Published on:

  8. “Western” style dietary patterns are characterized by a high proportion of highly processed foods rich in fat and low in fiber. This diet pattern is associated with a myriad of metabolic dysfunctions, includin...

    Authors: Hongli Shi, Yinghua Yu, Danhong Lin, Peng Zheng, Peng Zhang, Minmin Hu, Qiao Wang, Wei Pan, Xiaoying Yang, Tao Hu, Qianqian Li, Renxian Tang, Feng Zhou, Kuiyang Zheng and Xu-Feng Huang

    Citation: Microbiome 2020 8:143

    Content type: Research

    Published on:

  9. The soil mycobiome is composed of a complex and diverse fungal community, which includes functionally diverse species ranging from plant pathogens to mutualists. Among the latter are arbuscular mycorrhizal fun...

    Authors: Yuji Jiang, Lu Luan, Kaijie Hu, Manqiang Liu, Ziyun Chen, Stefan Geisen, Xiaoyun Chen, Huixin Li, Qinsong Xu, Michael Bonkowski and Bo Sun

    Citation: Microbiome 2020 8:142

    Content type: Research

    Published on:

  10. Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced b...

    Authors: Alexandra S. Tauzin, Mariana Rangel Pereira, Liisa D. Van Vliet, Pierre-Yves Colin, Elisabeth Laville, Jeremy Esque, Sandrine Laguerre, Bernard Henrissat, Nicolas Terrapon, Vincent Lombard, Marion Leclerc, Joël Doré, Florian Hollfelder and Gabrielle Potocki-Veronese

    Citation: Microbiome 2020 8:141

    Content type: Research

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  11. The gut-brain axis and the intestinal microbiota are emerging as key players in health and disease. Shifts in intestinal microbiota composition affect a variety of systems; however, evidence of their direct im...

    Authors: Alfonsina D’Amato, Lorenzo Di Cesare Mannelli, Elena Lucarini, Angela L. Man, Gwenaelle Le Gall, Jacopo J. V. Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Mari Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano…

    Citation: Microbiome 2020 8:140

    Content type: Research

    Published on:

  12. Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. L...

    Authors: Shawn P. Brown, Michael A. Grillo, Justin C. Podowski and Katy D. Heath

    Citation: Microbiome 2020 8:139

    Content type: Research

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  13. Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasi...

    Authors: Yanfeng Xue, Limei Lin, Fan Hu, Weiyun Zhu and Shengyong Mao

    Citation: Microbiome 2020 8:138

    Content type: Research

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  14. Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorga...

    Authors: Chengyuan Tao, Rong Li, Wu Xiong, Zongzhuan Shen, Shanshan Liu, Beibei Wang, Yunze Ruan, Stefan Geisen, Qirong Shen and George A. Kowalchuk

    Citation: Microbiome 2020 8:137

    Content type: Research

    Published on:

  15. Gonadal steroid hormones have been suggested as the underlying mechanism responsible for the sexual dimorphism observed in metabolic diseases. Animal studies have also evidenced a causal role of the gut microb...

    Authors: Jordi Mayneris-Perxachs, María Arnoriaga-Rodríguez, Diego Luque-Córdoba, Feliciano Priego-Capote, Vicente Pérez-Brocal, Andrés Moya, Aurelijus Burokas, Rafael Maldonado and José-Manuel Fernández-Real

    Citation: Microbiome 2020 8:136

    Content type: Research

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  16. Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been sho...

    Authors: Hon Lun Wong, Fraser I. MacLeod, Richard Allen White III, Pieter T. Visscher and Brendan P. Burns

    Citation: Microbiome 2020 8:135

    Content type: Research

    Published on:

  17. Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limi...

    Authors: Bastian Seelbinder, Jiarui Chen, Sascha Brunke, Ruben Vazquez-Uribe, Rakesh Santhaman, Anne-Christin Meyer, Felipe Senne de Oliveira Lino, Ka-Fai Chan, Daniel Loos, Lejla Imamovic, Chi-Ching Tsang, Rex Pui-kin Lam, Siddharth Sridhar, Kang Kang, Bernhard Hube, Patrick Chiu-yat Woo…

    Citation: Microbiome 2020 8:133

    Content type: Research

    Published on:

  18. High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences ...

    Authors: Oskar Modin, Raquel Liébana, Soroush Saheb-Alam, Britt-Marie Wilén, Carolina Suarez, Malte Hermansson and Frank Persson

    Citation: Microbiome 2020 8:132

    Content type: Methodology

    Published on:

    The Correction to this article has been published in Microbiome 2020 8:148

  19. Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an e...

    Authors: George Golovko, Khanipov Kamil, Levent Albayrak, Anna M. Nia, Renato Salomon Arroyo Duarte, Sergei Chumakov and Yuriy Fofanov

    Citation: Microbiome 2020 8:131

    Content type: Methodology

    Published on:

  20. Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals in response to ingesting gluten, a protein found in wheat, rye, and barley. Research shows that geneti...

    Authors: Maureen M. Leonard, Hiren Karathia, Meritxell Pujolassos, Jacopo Troisi, Francesco Valitutti, Poorani Subramanian, Stephanie Camhi, Victoria Kenyon, Angelo Colucci, Gloria Serena, Salvatore Cucchiara, Monica Montuori, Basilio Malamisura, Ruggiero Francavilla, Luca Elli, Brian Fanelli…

    Citation: Microbiome 2020 8:130

    Content type: Research

    Published on:

  21. Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contrib...

    Authors: Cheng-Yu Chen, Chih-Kuan Chen, Yi-Ying Chen, Andrew Fang, Grace Tzun-Wen Shaw, Chih-Ming Hung and Daryi Wang

    Citation: Microbiome 2020 8:129

    Content type: Research

    Published on:

  22. The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key role...

    Authors: Aaron McKenna, Umer Zeeshan Ijaz, Carmel Kelly, Mark Linton, William T. Sloan, Brian D. Green, Ursula Lavery, Nick Dorrell, Brendan W. Wren, Anne Richmond, Nicolae Corcionivoschi and Ozan Gundogdu

    Citation: Microbiome 2020 8:128

    Content type: Research

    Published on:

  23. The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rh...

    Authors: Wouter M. A. Sillen, Sofie Thijs, Gennaro Roberto Abbamondi, Roberto De La Torre Roche, Nele Weyens, Jason C. White and Jaco Vangronsveld

    Citation: Microbiome 2020 8:127

    Content type: Research

    Published on:

  24. Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and ev...

    Authors: Da-Shuai Mu, Shuo Wang, Qi-Yun Liang, Zhao-Zhong Du, Renmao Tian, Yang Ouyang, Xin-Peng Wang, Aifen Zhou, Ya Gong, Guan-Jun Chen, Joy Van Nostrand, Yunfeng Yang, Jizhong Zhou and Zong-Jun Du

    Citation: Microbiome 2020 8:126

    Content type: Research

    Published on:

  25. Intestinal microbiota restoration can be achieved by complementing a subject’s perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such...

    Authors: Suryang Kwak, JooHee Choi, Tiffany Hink, Kimberly A. Reske, Kenneth Blount, Courtney Jones, Margaret H. Bost, Xiaoqing Sun, Carey-Ann D. Burnham, Erik R. Dubberke and Gautam Dantas

    Citation: Microbiome 2020 8:125

    Content type: Research

    Published on:

  26. Population outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are a major threat to coral reefs. While biologica...

    Authors: Naohisa Wada, Hideaki Yuasa, Rei Kajitani, Yasuhiro Gotoh, Yoshitoshi Ogura, Dai Yoshimura, Atsushi Toyoda, Sen-Lin Tang, Yukihiro Higashimura, Hugh Sweatman, Zac Forsman, Omri Bronstein, Gal Eyal, Nalinee Thongtham, Takehiko Itoh, Tetsuya Hayashi…

    Citation: Microbiome 2020 8:123

    Content type: Research

    Published on:

  27. Formalin-fixed, paraffin-embedded (FFPE) tissue is the gold standard in pathology tissue storage, representing the largest collections of patient material. Their reliable use for DNA analyses could open a trov...

    Authors: Yensi Flores Bueso, Sidney P. Walker, Glenn Hogan, Marcus J. Claesson and Mark Tangney

    Citation: Microbiome 2020 8:122

    Content type: Methodology

    Published on:

  28. The human microbiota contributes to health and well-being. Antimicrobials (AM) have an immediate effect on microbial diversity and composition in the gut, but next to nothing is known about their long-term con...

    Authors: Sajan C. Raju, Heli Viljakainen, Rejane A. O. Figueiredo, Pertti J. Neuvonen, Johan G. Eriksson, Elisabete Weiderpass and Trine B. Rounge

    Citation: Microbiome 2020 8:121

    Content type: Research

    Published on:

  29. Autism spectrum disorder (ASD) is a developmental disorder, and the effective pharmacological treatments for the core autistic symptoms are currently limited. Increasing evidence, particularly that from clinic...

    Authors: Ying Li, Zheng-Yi Luo, Yu-Ying Hu, Yue-Wei Bi, Jian-Ming Yang, Wen-Jun Zou, Yun-Long Song, Shi Li, Tong Shen, Shu-Ji Li, Lang Huang, Ai-Jun Zhou, Tian-Ming Gao and Jian-Ming Li

    Citation: Microbiome 2020 8:120

    Content type: Research

    Published on:

  30. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Gabriele Berg, Daria Rybakova, Doreen Fischer, Tomislav Cernava, Marie-Christine Champomier Vergès, Trevor Charles, Xiaoyulong Chen, Luca Cocolin, Kellye Eversole, Gema Herrero Corral, Maria Kazou, Linda Kinkel, Lene Lange, Nelson Lima, Alexander Loy, James A. Macklin…

    Citation: Microbiome 2020 8:119

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2020 8:103

  31. Variability in the health effects of dietary fiber might arise from inter-individual differences in the gut microbiota’s ability to ferment these substrates into beneficial metabolites. Our understanding of wh...

    Authors: Nguyen K. Nguyen, Edward C. Deehan, Zhengxiao Zhang, Mingliang Jin, Nami Baskota, Maria Elisa Perez-Muñoz, Janis Cole, Yunus E. Tuncil, Benjamin Seethaler, Ting Wang, Martine Laville, Nathalie M. Delzenne, Stephan C. Bischoff, Bruce R. Hamaker, Inés Martínez, Dan Knights…

    Citation: Microbiome 2020 8:118

    Content type: Research

    Published on:

  32. How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on “Microbiota, symbiosis and individuality: conceptual and philosophical iss...

    Authors: Isobel Ronai, Gregor P. Greslehner, Federico Boem, Judith Carlisle, Adrian Stencel, Javier Suárez, Saliha Bayir, Wiebke Bretting, Joana Formosinho, Anna C. Guerrero, William H. Morgan, Cybèle Prigot-Maurice, Salome Rodeck, Marie Vasse, Jacqueline M. Wallis and Oryan Zacks

    Citation: Microbiome 2020 8:117

    Content type: Meeting Report

    Published on:

  33. Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold envi...

    Authors: Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Alyce M. Hancock, Sarah Brazendale, James Bevington, Simon Roux, David Páez-Espino, Stephen Nayfach, Maureen Berg, Frederik Schulz, I-Min A. Chen, Marcel Huntemann, Nicole Shapiro, Nikos C. Kyrpides, Tanja Woyke…

    Citation: Microbiome 2020 8:116

    Content type: Research

    Published on:

  34. From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as ...

    Authors: Shashank Gupta, Mathis H. Hjelmsø, Jenni Lehtimäki, Xuanji Li, Martin S. Mortensen, Jakob Russel, Urvish Trivedi, Morten A. Rasmussen, Jakob Stokholm, Hans Bisgaard and Søren J. Sørensen

    Citation: Microbiome 2020 8:115

    Content type: Research

    Published on:

  35. Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, althou...

    Authors: Joon Yong Kim, Tae Woong Whon, Mi Young Lim, Yeon Bee Kim, Namhee Kim, Min-Sung Kwon, Juseok Kim, Se Hee Lee, Hak-Jong Choi, In-Hyun Nam, Won-Hyong Chung, Jung-Ha Kim, Jin-Woo Bae, Seong Woon Roh and Young-Do Nam

    Citation: Microbiome 2020 8:114

    Content type: Research

    Published on:

  36. Child undernutrition is a global health issue that is associated with poor sanitation and an altered intestinal microbiota. Immunoglobulin (Ig) A mediates host-microbial homeostasis in the intestine, and acute...

    Authors: Kelsey E. Huus, André Rodriguez-Pozo, Nathalie Kapel, Alison Nestoret, Azimdine Habib, Michel Dede, Amee Manges, Jean-Marc Collard, Philippe J. Sansonetti, Pascale Vonaesch and B. Brett Finlay

    Citation: Microbiome 2020 8:113

    Content type: Research

    Published on:

  37. The increasing incidence of cancer and intestinal mucositis induced by chemotherapeutics are causing worldwide concern. Many approaches such as fecal microbiota transplantation (FMT) have been used to minimize...

    Authors: Pengfei Zhang, Jing Liu, Bohui Xiong, Cong Zhang, Beining Kang, Yishan Gao, Zengkuan Li, Wei Ge, Shunfeng Cheng, Yanan Hao, Wei Shen, Shuai Yu, Liang Chen, Xiangfang Tang, Yong Zhao and Hongfu Zhang

    Citation: Microbiome 2020 8:112

    Content type: Research

    Published on:

  38. Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are th...

    Authors: Masaru K. Nobu, Takashi Narihiro, Ran Mei, Yoichi Kamagata, Patrick K. H. Lee, Po-Heng Lee, Michael J. McInerney and Wen-Tso Liu

    Citation: Microbiome 2020 8:111

    Content type: Research

    Published on:

  39. Feed efficiency is a crucial parameter in swine production, given both its economic and environmental impact. The gut microbiota plays an essential role in nutrient digestibility and is, therefore, likely to a...

    Authors: Matteo Bergamaschi, Francesco Tiezzi, Jeremy Howard, Yi Jian Huang, Kent A. Gray, Constantino Schillebeeckx, Nathan P. McNulty and Christian Maltecca

    Citation: Microbiome 2020 8:110

    Content type: Research

    Published on:

  40. Altered microbiome composition and aberrant promoter hypermethylation of tumor suppressor genes (TSGs) are two important hallmarks of colorectal cancer (CRC). Here we performed concurrent 16S rRNA gene sequenc...

    Authors: Xiaoxuan Xia, William Ka Kei Wu, Sunny Hei Wong, Dabin Liu, Thomas Ngai Yeung Kwong, Geicho Nakatsu, Pearlly S. Yan, Yu-Ming Chuang, Michael Wing-Yan Chan, Olabisi Oluwabukola Coker, Zigui Chen, Yun Kit Yeoh, Liuyang Zhao, Xiansong Wang, Wing Yin Cheng, Matthew Tak Vai Chan…

    Citation: Microbiome 2020 8:108

    Content type: Research

    Published on:

  41. In a pilot study, we found that feces transplantation from elderly individuals to mice significantly caused cognitive impairment. Paenalcaligenes hominis and Escherichia coli are increasingly detected in the fece...

    Authors: Kyung-Eon Lee, Jeon-Kyung Kim, Sang-Kap Han, Dong Yun Lee, Hae-Ji Lee, Sung-Vin Yim and Dong-Hyun Kim

    Citation: Microbiome 2020 8:107

    Content type: Research

    Published on:

  42. Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species ...

    Authors: Yanting Wang, Kai Wang, Lei Huang, Pengsheng Dong, Sipeng Wang, Heping Chen, Zheng Lu, Dandi Hou and Demin Zhang

    Citation: Microbiome 2020 8:106

    Content type: Research

    Published on:

  43. Host-associated microbial communities play an important role in the fitness of insect hosts. However, the factors shaping microbial communities in wild populations, including genetic background, ecological fac...

    Authors: Xing-Zhi Duan, Jing-Tao Sun, Lin-Ting Wang, Xiao-Han Shu, Yan Guo, Matsukura Keiichiro, Yu-Xi Zhu, Xiao-Li Bing, Ary A. Hoffmann and Xiao-Yue Hong

    Citation: Microbiome 2020 8:104

    Content type: Research

    Published on:

  44. The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fi...

    Authors: Gabriele Berg, Daria Rybakova, Doreen Fischer, Tomislav Cernava, Marie-Christine Champomier Vergès, Trevor Charles, Xiaoyulong Chen, Luca Cocolin, Kellye Eversole, Gema Herrero Corral, Maria Kazou, Linda Kinkel, Lene Lange, Nelson Lima, Alexander Loy, James A. Macklin…

    Citation: Microbiome 2020 8:103

    Content type: Commentary

    Published on:

    The Correction to this article has been published in Microbiome 2020 8:119

  45. Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-tem...

    Authors: Jialin Hou, Stefan M. Sievert, Yinzhao Wang, Jeffrey S. Seewald, Vengadesh Perumal Natarajan, Fengping Wang and Xiang Xiao

    Citation: Microbiome 2020 8:102

    Content type: Research

    Published on:

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