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  1. 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

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  2. 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

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  3. 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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  4. 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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  5. 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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  6. 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

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  7. 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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  8. 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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  10. 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

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  11. 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

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  12. 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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  13. 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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  16. 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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  17. 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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  18. 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

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  19. 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

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  20. 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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  22. 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

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  23. 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

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  24. 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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  25. 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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  26. 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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  27. 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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  29. 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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  30. 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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  31. 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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  32. 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

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  33. 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

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  35. Spinal cord injury (SCI) patients display disruption of gut microbiome, and gut dysbiosis exacerbate neurological impairment in SCI models. Cumulative data support an important role of gut microbiome in SCI. H...

    Authors: Yingli Jing, Yan Yu, Fan Bai, Limiao Wang, Degang Yang, Chao Zhang, Chuan Qin, Mingliang Yang, Dong Zhang, Yanbing Zhu, Jianjun Li and Zhiguo Chen

    Citation: Microbiome 2021 9:59

    Content type: Research

    Published on:

  37. Plants are naturally associated with root microbiota, which are microbial communities influential to host fitness. Thus, it is important to understand how plants control root microbiota. Epigenetic factors reg...

    Authors: Richa Kaushal, Li Peng, Sunil K. Singh, Mengrui Zhang, Xinlian Zhang, Juan I. Vílchez, Zhen Wang, Danxia He, Yu Yang, Suhui Lv, Zhongtian Xu, Rafael J. L. Morcillo, Wei Wang, Weichang Huang, Paul W. Paré, Chun-Peng Song…

    Citation: Microbiome 2021 9:57

    Content type: Research

    Published on:

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

    Authors: Jason W. Arnold, Jeffery Roach, Salvador Fabela, Emily Moorfield, Shengli Ding, Eric Blue, Suzanne Dagher, Scott Magness, Rita Tamayo, Jose M. Bruno-Barcena and M. Andrea Azcarate-Peril

    Citation: Microbiome 2021 9:56

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2021 9:31

  39. The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SI...

    Authors: Hannes Petruschke, Christian Schori, Sebastian Canzler, Sarah Riesbeck, Anja Poehlein, Rolf Daniel, Daniel Frei, Tina Segessemann, Johannes Zimmerman, Georgios Marinos, Christoph Kaleta, Nico Jehmlich, Christian H. Ahrens and Martin von Bergen

    Citation: Microbiome 2021 9:55

    Content type: Research

    Published on:

  40. The oral microbiota is acquired very early, but the factors shaping its acquisition are not well understood. Previous studies comparing monozygotic (MZ) and dizygotic (DZ) twins have suggested that host geneti...

    Authors: Chiranjit Mukherjee, Christina O. Moyer, Heidi M. Steinkamp, Shahr B. Hashmi, Clifford J. Beall, Xiaohan Guo, Ai Ni, Eugene J. Leys and Ann L. Griffen

    Citation: Microbiome 2021 9:54

    Content type: Research

    Published on:

  41. Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and enviro...

    Authors: Hannah Holland-Moritz, Julia E. M. Stuart, Lily R. Lewis, Samantha N. Miller, Michelle C. Mack, Jose Miguel Ponciano, Stuart F. McDaniel and Noah Fierer

    Citation: Microbiome 2021 9:53

    Content type: Research

    Published on:

  42. Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut ...

    Authors: Antonio Reverter, Maria Ballester, Pamela A. Alexandre, Emilio Mármol-Sánchez, Antoni Dalmau, Raquel Quintanilla and Yuliaxis Ramayo-Caldas

    Citation: Microbiome 2021 9:52

    Content type: Research

    Published on:

  43. The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with s...

    Authors: Claudia Wylezich, Sten Calvelage, Kore Schlottau, Ute Ziegler, Anne Pohlmann, Dirk Höper and Martin Beer

    Citation: Microbiome 2021 9:51

    Content type: Methodology

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  44. Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth’s ecosystems, potential extraterrestri...

    Authors: Alexandra Kristin Bashir, Lisa Wink, Stefanie Duller, Petra Schwendner, Charles Cockell, Petra Rettberg, Alexander Mahnert, Kristina Beblo-Vranesevic, Maria Bohmeier, Elke Rabbow, Frederic Gaboyer, Frances Westall, Nicolas Walter, Patricia Cabezas, Laura Garcia-Descalzo, Felipe Gomez…

    Citation: Microbiome 2021 9:50

    Content type: Research

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  45. Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes ...

    Authors: Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May and Paul Wilmes

    Citation: Microbiome 2021 9:49

    Content type: Software article

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  46. Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignoc...

    Authors: Daniel R. Leadbeater, Nicola C. Oates, Joseph P. Bennett, Yi Li, Adam A. Dowle, Joe D. Taylor, Juliana Sanchez Alponti, Alexander T. Setchfield, Anna M. Alessi, Thorunn Helgason, Simon J. McQueen-Mason and Neil C. Bruce

    Citation: Microbiome 2021 9:48

    Content type: Research

    Published on:

  47. The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived f...

    Authors: Zhiming Li, Jingjing Xia, Liuyiqi Jiang, Yimei Tan, Yitai An, Xingyu Zhu, Jie Ruan, Zhihua Chen, Hefu Zhen, Yanyun Ma, Zhuye Jie, Liang Xiao, Huanming Yang, Jian Wang, Karsten Kristiansen, Xun Xu…

    Citation: Microbiome 2021 9:47

    Content type: Research

    Published on:

  48. The sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing molecules and plays a fundamental role in cellular and ecosystem-level processes, influencing biological c...

    Authors: Adrien Vigneron, Perrine Cruaud, Alexander I. Culley, Raoul-Marie Couture, Connie Lovejoy and Warwick F. Vincent

    Citation: Microbiome 2021 9:46

    Content type: Research

    Published on:

  49. Graves’ disease (GD) is an autoimmune condition in which autoantibodies to the thyrotropin receptor (TSHR) cause hyperthyroidism. About 50% of GD patients also have Graves’ orbitopathy (GO), an intractable dis...

    Authors: Sajad Moshkelgosha, Hedda Luise Verhasselt, Giulia Masetti, Danila Covelli, Filippo Biscarini, Mareike Horstmann, Anke Daser, Astrid M. Westendorf, Christoph Jesenek, Svenja Philipp, Salvador Diaz-Cano, J. Paul Banga, Daryn Michael, Sue Plummer, Julian R. Marchesi, Anja Eckstein…

    Citation: Microbiome 2021 9:45

    Content type: Research

    Published on:

  50. Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and parti...

    Authors: Meggie Hudspith, Laura Rix, Michelle Achlatis, Jeremy Bougoure, Paul Guagliardo, Peta L. Clode, Nicole S. Webster, Gerard Muyzer, Mathieu Pernice and Jasper M. de Goeij

    Citation: Microbiome 2021 9:44

    Content type: Research

    Published on:

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