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  2. 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:

  3. 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

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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

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  9. 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

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  10. 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:

  12. 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:

  13. 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

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  14. 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

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  15. 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:

  16. 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

  17. 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:

  18. 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

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  19. 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:

  20. 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

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  21. 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

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  22. 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

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  23. 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:

  24. 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:

  25. 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:

  27. 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:

  28. 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:

  29. 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:

  31. 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:

  32. 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

  33. 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:

  35. Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little informati...

    Authors: Marcus H. Y. Leung, Xinzhao Tong, Philippe Bastien, Florent Guinot, Arthur Tenenhaus, Brice M. R. Appenzeller, Richard J. Betts, Sakina Mezzache, Jing Li, Nasrine Bourokba, Lionel Breton, Cécile Clavaud and Patrick K. H. Lee

    Citation: Microbiome 2020 8:100

    Content type: Research

    Published on:

  36. It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw ...

    Authors: Jinxin Liu, Yuanting Zhu, Michele Jay-Russell, Danielle G. Lemay and David A. Mills

    Citation: Microbiome 2020 8:99

    Content type: Research

    Published on:

  37. Effective standardisation of methodologies to analyse the microbiome is essential to the entire microbiome community. Despite the microbiome field being established for over a decade, there are no accredited o...

    Authors: Gregory C. A. Amos, Alastair Logan, Saba Anwar, Martin Fritzsche, Ryan Mate, Thomas Bleazard and Sjoerd Rijpkema

    Citation: Microbiome 2020 8:98

    Content type: Research

    Published on:

  38. Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponge...

    Authors: Sheila Podell, Jessica M. Blanton, Aaron Oliver, Michelle A. Schorn, Vinayak Agarwal, Jason S. Biggs, Bradley S. Moore and Eric E. Allen

    Citation: Microbiome 2020 8:97

    Content type: Research

    Published on:

  39. Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humif...

    Authors: Martyna Marynowska, Xavier Goux, David Sillam-Dussès, Corinne Rouland-Lefèvre, Rashi Halder, Paul Wilmes, Piotr Gawron, Yves Roisin, Philippe Delfosse and Magdalena Calusinska

    Citation: Microbiome 2020 8:96

    Content type: Research

    Published on:

  40. The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied ...

    Authors: Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori and Michiaki Hamada

    Citation: Microbiome 2020 8:95

    Content type: Research

    Published on:

  41. Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methan...

    Authors: Cui-Jing Zhang, Jie Pan, Yang Liu, Chang-Hai Duan and Meng Li

    Citation: Microbiome 2020 8:94

    Content type: Research

    Published on:

  42. The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differ...

    Authors: Michael P. Doane, Megan M. Morris, Bhavya Papudeshi, Lauren Allen, Dnyanada Pande, John M. Haggerty, Shaili Johri, Abigail C. Turnlund, Meredith Peterson, Dovi Kacev, Andy Nosal, Deni Ramirez, Kevin Hovel, Julia Ledbetter, Amanda Alker, Jackeline Avalos…

    Citation: Microbiome 2020 8:93

    Content type: Research

    Published on:

  43. Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce ...

    Authors: Félix Picazo, Annika Vilmi, Juha Aalto, Janne Soininen, Emilio O. Casamayor, Yongqin Liu, Qinglong Wu, Lijuan Ren, Jizhong Zhou, Ji Shen and Jianjun Wang

    Citation: Microbiome 2020 8:92

    Content type: Research

    Published on:

  44. Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has rece...

    Authors: Christopher McMullen, Trevor W. Alexander, Renaud Léguillette, Matthew Workentine and Edouard Timsit

    Citation: Microbiome 2020 8:91

    Content type: Research

    Published on:

  45. Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart com...

    Authors: Kristopher Kieft, Zhichao Zhou and Karthik Anantharaman

    Citation: Microbiome 2020 8:90

    Content type: Methodology

    Published on:

  46. Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial fir...

    Authors: Shao-Ming Gao, Axel Schippers, Nan Chen, Yang Yuan, Miao-Miao Zhang, Qi Li, Bin Liao, Wen-Sheng Shu and Li-Nan Huang

    Citation: Microbiome 2020 8:89

    Content type: Research

    Published on:

  47. Bacteroides thetaiotaomicron (Bt) is a prominent member of the human intestinal microbiota that, like all gram-negative bacteria, naturally generates nanosized outer membrane vesicles (OMVs) which bud off from th...

    Authors: Lydia Durant, Régis Stentz, Alistair Noble, Johanne Brooks, Nadezhda Gicheva, Durga Reddi, Matthew J. O’Connor, Lesley Hoyles, Anne L. McCartney, Ripple Man, E. Tobias Pring, Stella Dilke, Philip Hendy, Jonathan P. Segal, Dennis N. F. Lim, Ravi Misra…

    Citation: Microbiome 2020 8:88

    Content type: Research

    Published on:

  49. Inanimate surfaces within a hospital serve as a reservoir of microbial life that may colonize patients and ultimately result in healthcare associated infections (HAIs). Critically ill patients in intensive car...

    Authors: Jessica Chopyk, Kevan Akrami, Tovia Bavly, Ji H. Shin, Leila K. Schwanemann, Melissa Ly, Richa Kalia, Ying Xu, Scott T. Kelley, Atul Malhotra, Francesca J. Torriani, Daniel A. Sweeney and David T. Pride

    Citation: Microbiome 2020 8:86

    Content type: Research

    Published on:

  50. The alarming spread of antimicrobial resistance requires the development of novel anti-infective drugs. Despite the recent research focus on the human microbiome and its likely value to understand and exploit ...

    Authors: Yao Liu, Yuanzhen Liu, Zixiu Du, Lidan Zhang, Juan Chen, Zhen Shen, Qian Liu, Juanxiu Qin, Huiying Lv, Hua Wang, Lei He, Junlan Liu, Qian Huang, Yuhui Sun, Michael Otto and Min Li

    Citation: Microbiome 2020 8:85

    Content type: Research

    Published on:

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