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

    Authors: Hong-Yi Li, Hang Wang, Hai-Tao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A. Gilbert and Zhi-Jian Zhang

    Citation: Microbiome 2020 8:169

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2018 6:187

  2. The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in...

    Authors: M. Carla Piazzon, Fernando Naya-Català, Erick Perera, Oswaldo Palenzuela, Ariadna Sitjà-Bobadilla and Jaume Pérez-Sánchez

    Citation: Microbiome 2020 8:168

    Content type: Research

    Published on:

  3. Early microbial colonization triggers processes that result in intestinal maturation and immune priming. Perinatal factors, especially those associated with birth, including both mode and place of delivery are...

    Authors: M. Selma-Royo, M. Calatayud Arroyo, I. García-Mantrana, A. Parra-Llorca, R. Escuriet, C. Martínez-Costa and M. C. Collado

    Citation: Microbiome 2020 8:167

    Content type: Research

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  4. Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional ...

    Authors: Michael T. France, Bing Ma, Pawel Gajer, Sarah Brown, Michael S. Humphrys, Johanna B. Holm, L. Elaine Waetjen, Rebecca M. Brotman and Jacques Ravel

    Citation: Microbiome 2020 8:166

    Content type: Research

    Published on:

  5. Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activi...

    Authors: Arghavan Alisoltani, Monalisa T. Manhanzva, Matthys Potgieter, Christina Balle, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Michelle du Plessis, Nina Radzey, Zac McDonald, Bridget Calder, Imane Allali, Nicola Mulder, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien…

    Citation: Microbiome 2020 8:165

    Content type: Research

    Published on:

  6. The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more susta...

    Authors: Oscar Mencía-Ares, Raúl Cabrera-Rubio, José Francisco Cobo-Díaz, Avelino Álvarez-Ordóñez, Manuel Gómez-García, Héctor Puente, Paul D. Cotter, Fiona Crispie, Ana Carvajal, Pedro Rubio and Héctor Argüello

    Citation: Microbiome 2020 8:164

    Content type: Research

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  7. Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characteriz...

    Authors: F. H. Coutinho, P. J. Cabello-Yeves, R. Gonzalez-Serrano, R. Rosselli, M. López-Pérez, T. I. Zemskaya, A. S. Zakharenko, V. G. Ivanov and F. Rodriguez-Valera

    Citation: Microbiome 2020 8:163

    Content type: Research

    Published on:

  8. The capability of gut microbiota in degrading foods and drugs administered orally can result in diversified efficacies and toxicity interpersonally and cause significant impact on human health. Production of a...

    Authors: Wei-Kai Wu, Suraphan Panyod, Po-Yu Liu, Chieh-Chang Chen, Hsien-Li Kao, Hsiao-Li Chuang, Ying-Hsien Chen, Hsin-Bai Zou, Han-Chun Kuo, Ching-Hua Kuo, Ben-Yang Liao, Tina H. T. Chiu, Ching-Hu Chung, Angela Yu-Chen Lin, Yi-Chia Lee, Sen-Lin Tang…

    Citation: Microbiome 2020 8:162

    Content type: Research

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  9. The microbiota presents a compartmentalized distribution across different gut segments. Hence, the exogenous microbiota from a particular gut segment might only invade its homologous gut location during microb...

    Authors: Na Li, Bin Zuo, Shimeng Huang, Benhua Zeng, Dandan Han, Tiantian Li, Ting Liu, Zhenhua Wu, Hong Wei, Jiangchao Zhao and Junjun Wang

    Citation: Microbiome 2020 8:161

    Content type: Research

    Published on:

  11. Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted...

    Authors: Alicia Moreno-Sabater, Gaelle Autaa, Delphine Sterlin, Amenie Jerbi, Remy Villette, Johanna B. Holm, Christophe Parizot, Sameh Selim, Yaye Senghor, Pascale Ghillani-Dalbin, Claude Bachmeyer, Christophe Hennequin, Guy Gorochov and Martin Larsen

    Citation: Microbiome 2020 8:159

    Content type: Methodology

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  12. Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently ...

    Authors: Manuel Kleiner, Brian Bushnell, Kenneth E. Sanderson, Lora V. Hooper and Breck A. Duerkop

    Citation: Microbiome 2020 8:158

    Content type: Research

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  13. Cooling towers are a major source of large community-associated outbreaks of Legionnaires’ disease, a severe pneumonia. This disease is contracted when inhaling aerosols that are contaminated with bacteria fro...

    Authors: Kiran Paranjape, Émilie Bédard, Deeksha Shetty, Mengqi Hu, Fiona Chan Pak Choon, Michèle Prévost and Sébastien P. Faucher

    Citation: Microbiome 2020 8:157

    Content type: Research

    Published on:

  14. The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities...

    Authors: Lu Zhang, Xiaodong Fang, Herui Liao, Zhenmiao Zhang, Xin Zhou, Lijuan Han, Yang Chen, Qinwei Qiu and Shuai Cheng Li

    Citation: Microbiome 2020 8:156

    Content type: Research

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  15. Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retriev...

    Authors: Lei Liu, Yulin Wang, You Che, Yiqiang Chen, Yu Xia, Ruibang Luo, Suk Hang Cheng, Chunmiao Zheng and Tong Zhang

    Citation: Microbiome 2020 8:155

    Content type: Research

    Published on:

  16. The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and micr...

    Authors: Anna J. Jasinska, Tien S. Dong, Venu Lagishetty, William Katzka, Jonathan P. Jacobs, Christopher A. Schmitt, Jennifer Danzy Cramer, Dongzhu Ma, Willem G. Coetzer, J. Paul Grobler, Trudy R. Turner, Nelson Freimer, Ivona Pandrea and Cristian Apetrei

    Citation: Microbiome 2020 8:154

    Content type: Research

    Published on:

  17. Chronic immune-mediated diseases are rapidly expanding and notoriously difficult to cure. Altered relatively stable intestinal microbiota configurations are associated with several of these diseases, and with ...

    Authors: Maarten Van de Guchte, Sebastian D. Burz, Julie Cadiou, Jiangbo Wu, Stanislas Mondot, Hervé M. Blottière and Joël Doré

    Citation: Microbiome 2020 8:153

    Content type: Research

    Published on:

  18. The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticle...

    Authors: Wei Lin, Wensi Zhang, Greig A. Paterson, Qiyun Zhu, Xiang Zhao, Rob Knight, Dennis A. Bazylinski, Andrew P. Roberts and Yongxin Pan

    Citation: Microbiome 2020 8:152

    Content type: Research

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  19. The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant t...

    Authors: Célio Dias Santos-Júnior, Hugo Sarmento, Fernando Pellon de Miranda, Flávio Henrique-Silva and Ramiro Logares

    Citation: Microbiome 2020 8:151

    Content type: Research

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  20. 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:

  21. 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:

  22. 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

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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:

  26. 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:

  27. “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:

  28. 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:

  29. 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

    Published on:

  30. 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:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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:

  34. 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

    Published on:

  35. 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:

  37. 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:

  38. 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

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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

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