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  1. One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently ...

    Authors: Audet-Gilbert Émie, Sylvain François-Étienne, Bouslama Sidki and Derome Nicolas

    Citation: Microbiome 2021 9:109

    Content type: Research

    Published on:

  2. Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic app...

    Authors: Xun Qian, Santosh Gunturu, Jiarong Guo, Benli Chai, James R. Cole, Jie Gu and James M. Tiedje

    Citation: Microbiome 2021 9:108

    Content type: Research

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  3. Donor selection is an important factor influencing the engraftment and efficacy of fecal microbiota transplantation (FMT) for complex conditions associated with microbial dysbiosis. However, the degree, variat...

    Authors: Brooke C. Wilson, Tommi Vatanen, Thilini N. Jayasinghe, Karen S. W. Leong, José G. B. Derraik, Benjamin B. Albert, Valentina Chiavaroli, Darren M. Svirskis, Kathryn L. Beck, Cathryn A. Conlon, Yannan Jiang, William Schierding, David J. Holland, Wayne S. Cutfield and Justin M. O’Sullivan

    Citation: Microbiome 2021 9:107

    Content type: Research

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  4. The gut microbiome and iron status are known to play a role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD), although their complex interaction remains unclear.

    Authors: Jordi Mayneris-Perxachs, Marina Cardellini, Lesley Hoyles, Jèssica Latorre, Francesca Davato, José Maria Moreno-Navarrete, María Arnoriaga-Rodríguez, Matteo Serino, James Abbott, Richard H. Barton, Josep Puig, Xavier Fernández-Real, Wifredo Ricart, Christopher Tomlinson, Mark Woodbridge, Paolo Gentileschi…

    Citation: Microbiome 2021 9:104

    Content type: Research

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  5. Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbio...

    Authors: Selma Cadot, Hang Guan, Moritz Bigalke, Jean-Claude Walser, Georg Jander, Matthias Erb, Marcel G. A. van der Heijden and Klaus Schlaeppi

    Citation: Microbiome 2021 9:103

    Content type: Research

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  6. Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillo...

    Authors: Talisa Doering, Marlene Wall, Lalita Putchim, Tipwimon Rattanawongwan, Roman Schroeder, Ute Hentschel and Anna Roik

    Citation: Microbiome 2021 9:102

    Content type: Research

    Published on:

  7. The characteristics of polycystic ovary syndrome (PCOS), a common reproductive endocrinal disorder, are high incidence, complicated aetiology and poor therapeutic effects. PCOS patients frequently exhibit gut ...

    Authors: Qixin Han, Juan Wang, Weiping Li, Zi-Jiang Chen and Yanzhi Du

    Citation: Microbiome 2021 9:101

    Content type: Research

    Published on:

  8. The objective of this study was to increase understanding of the complex interactions between diet, obesity, and the gut microbiome of adult female non-human primates (NHPs). Subjects consumed either a Western (n

    Authors: Tiffany M. Newman, Carol A. Shively, Thomas C. Register, Susan E. Appt, Hariom Yadav, Rita R. Colwell, Brian Fanelli, Manoj Dadlani, Karlis Graubics, Uyen Thao Nguyen, Sivapriya Ramamoorthy, Beth Uberseder, Kenysha Y. J. Clear, Adam S. Wilson, Kimberly D. Reeves, Mark C. Chappell…

    Citation: Microbiome 2021 9:100

    Content type: Research

    Published on:

  9. Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbi...

    Authors: Jennifer M. Baker, Kevin J. Hinkle, Roderick A. McDonald, Christopher A. Brown, Nicole R. Falkowski, Gary B. Huffnagle and Robert P. Dickson

    Citation: Microbiome 2021 9:99

    Content type: Research

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    The Correction to this article has been published in Microbiome 2021 9:154

  10. RNA interference (RNAi) has emerged as an efficient tool to control insect pests. When insects ingest double-stranded RNAs (dsRNAs) targeted against essential genes, strong gene silencing and mortality can be ...

    Authors: Letian Xu, Shijing Xu, Liuwei Sun, Yiqiu Zhang, Jing Luo, Ralph Bock and Jiang Zhang

    Citation: Microbiome 2021 9:98

    Content type: Research

    Published on:

  11. Although localized aggressive periodontitis (LAP), generalized aggressive periodontitis (GAP), and chronic periodontitis (CP) are microbially driven diseases, our inability to separate disease-specific associa...

    Authors: Khaled Altabtbaei, Pooja Maney, Sukirth M. Ganesan, Shareef M. Dabdoub, Haikady N. Nagaraja and Purnima S. Kumar

    Citation: Microbiome 2021 9:97

    Content type: Research

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  12. Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out ...

    Authors: Dieter M. Tourlousse, Koji Narita, Takamasa Miura, Mitsuo Sakamoto, Akiko Ohashi, Keita Shiina, Masami Matsuda, Daisuke Miura, Mamiko Shimamura, Yoshifumi Ohyama, Atsushi Yamazoe, Yoshihito Uchino, Keishi Kameyama, Shingo Arioka, Jiro Kataoka, Takayoshi Hisada…

    Citation: Microbiome 2021 9:95

    Content type: Methodology

    Published on:

  13. Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stim...

    Authors: Javier A. Ceja-Navarro, Yuan Wang, Daliang Ning, Abelardo Arellano, Leila Ramanculova, Mengting Maggie Yuan, Alyssa Byer, Kelly D. Craven, Malay C. Saha, Eoin L. Brodie, Jennifer Pett-Ridge and Mary K. Firestone

    Citation: Microbiome 2021 9:96

    Content type: Research

    Published on:

  14. The gut microbiota–intestine–liver relationship is emerging as an important factor in multiple hepatic pathologies, but the hepatic sensors and effectors of microbial signals are not well defined.

    Authors: Sharon Ann Barretto, Frederic Lasserre, Marine Huillet, Marion Régnier, Arnaud Polizzi, Yannick Lippi, Anne Fougerat, Elodie Person, Sandrine Bruel, Colette Bétoulières, Claire Naylies, Céline Lukowicz, Sarra Smati, Laurence Guzylack, Maïwenn Olier, Vassilia Théodorou…

    Citation: Microbiome 2021 9:93

    Content type: Research

    Published on:

  15. Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial ...

    Authors: Andre Mu, Daniel McDonald, Alan K. Jarmusch, Cameron Martino, Caitriona Brennan, Mackenzie Bryant, Gregory C. Humphrey, Julia Toronczak, Tara Schwartz, Dominic Nguyen, Gail Ackermann, Anthony D’Onofrio, Steffanie A. Strathdee, Robert T. Schooley, Pieter C. Dorrestein, Rob Knight…

    Citation: Microbiome 2021 9:92

    Content type: Short report

    Published on:

  16. Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral repl...

    Authors: Tao Zuo, Qin Liu, Fen Zhang, Yun Kit Yeoh, Yating Wan, Hui Zhan, Grace C. Y. Lui, Zigui Chen, Amy Y. L. Li, Chun Pan Cheung, Nan Chen, Wenqi Lv, Rita W. Y. Ng, Eugene Y. K. Tso, Kitty S. C. Fung, Veronica Chan…

    Citation: Microbiome 2021 9:91

    Content type: Research

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  17. The objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing...

    Authors: Kayla M. Williamson, Brandie D. Wagner, Charles E. Robertson, Mark J. Stevens, Marci K. Sontag, Peter M. Mourani and J. Kirk Harris

    Citation: Microbiome 2021 9:90

    Content type: Research

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  18. The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the ...

    Authors: Emma Guerin, Andrey N. Shkoporov, Stephen R. Stockdale, Joan Colom Comas, Ekaterina V. Khokhlova, Adam G. Clooney, Karen M. Daly, Lorraine A. Draper, Niamh Stephens, Dimitri Scholz, R. Paul Ross and Colin Hill

    Citation: Microbiome 2021 9:89

    Content type: Research

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  19. Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to...

    Authors: Leda Restrepo, Cristóbal Domínguez-Borbor, Leandro Bajaña, Irma Betancourt, Jenny Rodríguez, Bonny Bayot and Alejandro Reyes

    Citation: Microbiome 2021 9:88

    Content type: Research

    Published on:

  20. Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communiti...

    Authors: Marie-Anne Cambon-Bonavita, Johanne Aubé, Valérie Cueff-Gauchard and Julie Reveillaud

    Citation: Microbiome 2021 9:87

    Content type: Research

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  21. Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities.

    Authors: Chuntao Yin, Juan M. Casa Vargas, Daniel C. Schlatter, Christina H. Hagerty, Scot H. Hulbert and Timothy C. Paulitz

    Citation: Microbiome 2021 9:86

    Content type: Research

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  22. Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria, one of the most widely distributed bacterial phyla in soils, are known for their abi...

    Authors: Yuanyuan Bao, Jan Dolfing, Zhiying Guo, Ruirui Chen, Meng Wu, Zhongpei Li, Xiangui Lin and Youzhi Feng

    Citation: Microbiome 2021 9:84

    Content type: Research

    Published on:

  23. Ulcerative colitis is a type of chronic inflammatory bowel disease closely associated with gut microbiota dysbiosis and intestinal homeostasis dysregulation. Barley leaf (BL) has a long history of use in Tradi...

    Authors: Daotong Li, Yu Feng, Meiling Tian, Junfu Ji, Xiaosong Hu and Fang Chen

    Citation: Microbiome 2021 9:83

    Content type: Research

    Published on:

  24. Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before launching into space. Clean rooms have stringent me...

    Authors: David C. Danko, Maria A. Sierra, James N. Benardini, Lisa Guan, Jason M. Wood, Nitin Singh, Arman Seuylemezian, Daniel J. Butler, Krista Ryon, Katerina Kuchin, Dmitry Meleshko, Chandrima Bhattacharya, Kasthuri J. Venkateswaran and Christopher E. Mason

    Citation: Microbiome 2021 9:82

    Content type: Research

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  25. Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resista...

    Authors: Ishi Keenum, Robert K. Williams, Partha Ray, Emily D. Garner, Katharine F. Knowlton and Amy Pruden

    Citation: Microbiome 2021 9:81

    Content type: Research

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  26. Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including ...

    Authors: Sean Benler, Natalya Yutin, Dmitry Antipov, Mikhail Rayko, Sergey Shmakov, Ayal B. Gussow, Pavel Pevzner and Eugene V. Koonin

    Citation: Microbiome 2021 9:78

    Content type: Research

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  27. Temperate phages influence the density, diversity and function of bacterial populations. Historically, they have been described as carriers of toxins. More recently, they have also been recognised as direct mo...

    Authors: Mirjam Zünd, Hans-Joachim Ruscheweyh, Christopher M. Field, Natalie Meyer, Miguelangel Cuenca, Daniel Hoces, Wolf-Dietrich Hardt and Shinichi Sunagawa

    Citation: Microbiome 2021 9:77

    Content type: Research

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  28. Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented res...

    Authors: Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti and W. Evan Johnson

    Citation: Microbiome 2021 9:76

    Content type: Software article

    Published on:

  29. Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s diseas...

    Authors: Janis R. Bedarf, Naiara Beraza, Hassan Khazneh, Ezgi Özkurt, David Baker, Valeri Borger, Ullrich Wüllner and Falk Hildebrand

    Citation: Microbiome 2021 9:75

    Content type: Research

    Published on:

  30. While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel s...

    Authors: Julien Tap, Stine Störsrud, Boris Le Nevé, Aurélie Cotillard, Nicolas Pons, Joël Doré, Lena Öhman, Hans Törnblom, Muriel Derrien and Magnus Simrén

    Citation: Microbiome 2021 9:74

    Content type: Research

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  31. In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct ...

    Authors: T. Keller-Costa, A. Lago-Lestón, J. P. Saraiva, R. Toscan, S. G. Silva, J. Gonçalves, C. J. Cox, N. Kyrpides, U. Nunes da Rocha and R. Costa

    Citation: Microbiome 2021 9:72

    Content type: Research

    Published on:

  32. Phytoplankton blooms are frequent events in coastal areas and increase the production of organic matter that initially shapes the growth of opportunistic heterotrophic bacteria. However, it is unclear how thes...

    Authors: Yu Han, Nianzhi Jiao, Yao Zhang, Fan Zhang, Chen He, Xuejiao Liang, Ruanhong Cai, Quan Shi and Kai Tang

    Citation: Microbiome 2021 9:71

    Content type: Research

    Published on:

  33. Probiotic milk-fermented microorganism mixtures (e.g., yogurt, kefir) are perceived as contributing to human health, and possibly capable of protecting against bacterial infections. Co-existence of probiotic m...

    Authors: Orit Malka, Dorin Kalson, Karin Yaniv, Reut Shafir, Manikandan Rajendran, Oshrit Ben-David, Ariel Kushmaro, Michael M. Meijler and Raz Jelinek

    Citation: Microbiome 2021 9:70

    Content type: Research

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  34. Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accuratel...

    Authors: Ling Xu, Grady Pierroz, Heidi M.-L. Wipf, Cheng Gao, John W. Taylor, Peggy G. Lemaux and Devin Coleman-Derr

    Citation: Microbiome 2021 9:69

    Content type: Review

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  35. An individual’s microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interac...

    Authors: Mareike C. Janiak, Michael J. Montague, Catalina I. Villamil, Michala K. Stock, Amber E. Trujillo, Allegra N. DePasquale, Joseph D. Orkin, Samuel E. Bauman Surratt, Olga Gonzalez, Michael L. Platt, Melween I. Martínez, Susan C. Antón, Maria Gloria Dominguez-Bello, Amanda D. Melin and James P. Higham

    Citation: Microbiome 2021 9:68

    Content type: Research

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  36. Denitrifying phosphorus removal sludge (DPRS) is widely adopted for nitrogen and phosphorus removal in wastewater treatment but faces threats from heavy metals. However, a lack of understanding of the taxon-sp...

    Authors: Yuan Lin, Liye Wang, Ke Xu, Kan Li and Hongqiang Ren

    Citation: Microbiome 2021 9:67

    Content type: Research

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  37. Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There ...

    Authors: Ryan Cook, Steve Hooton, Urmi Trivedi, Liz King, Christine E. R. Dodd, Jon L. Hobman, Dov J. Stekel, Michael A. Jones and Andrew D. Millard

    Citation: Microbiome 2021 9:65

    Content type: Research

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  38. Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced cha...

    Authors: Sai Guo, Wu Xiong, Xinnan Hang, Zhilei Gao, Zixuan Jiao, Hongjun Liu, Yani Mo, Nan Zhang, George A. Kowalchuk, Rong Li, Qirong Shen and Stefan Geisen

    Citation: Microbiome 2021 9:64

    Content type: Research

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  39. Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These...

    Authors: Davide Albanese, Claudia Coleine, Omar Rota-Stabelli, Silvano Onofri, Susannah G. Tringe, Jason E. Stajich, Laura Selbmann and Claudio Donati

    Citation: Microbiome 2021 9:63

    Content type: Research

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  40. Xylitol, a white or transparent polyol or sugar alcohol, is digestible by colonic microorganisms and promotes the proliferation of beneficial bacteria and the production of short-chain fatty acids (SCFAs), but...

    Authors: Shasha Xiang, Kun Ye, Mian Li, Jian Ying, Huanhuan Wang, Jianzhong Han, Lihua Shi, Jie Xiao, Yubiao Shen, Xiao Feng, Xuan Bao, Yiqing Zheng, Yin Ge, Yalin Zhang, Chang Liu, Jie Chen…

    Citation: Microbiome 2021 9:62

    Content type: Research

    Published on:

  41. The gut microbiome impacts human health through various mechanisms and is involved in the development of a range of non-communicable diseases. Diet is a well-known factor influencing microbe-host interaction i...

    Authors: Taylor A. Breuninger, Nina Wawro, Jakob Breuninger, Sandra Reitmeier, Thomas Clavel, Julia Six-Merker, Giulia Pestoni, Sabine Rohrmann, Wolfgang Rathmann, Annette Peters, Harald Grallert, Christa Meisinger, Dirk Haller and Jakob Linseisen

    Citation: Microbiome 2021 9:61

    Content type: Research

    Published on:

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