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  1. 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:

  2. 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:

  3. 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

  4. 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

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  5. 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

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  6. 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:

  7. 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

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  8. 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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  9. 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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  10. 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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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-...

    Authors: I. Raimundo, R. Silva, L. Meunier, S. M. Valente, A. Lago-Lestón, T. Keller-Costa and R. Costa

    Citation: Microbiome 2021 9:43

    Content type: Research

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

    Authors: Ju-Hyeong Park, Angela R. Lemons, Jerry Roseman, Brett J. Green and Jean M. Cox-Ganser

    Citation: Microbiome 2021 9:42

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2021 9:15

  18. Quality control including assessment of batch variabilities and confirmation of repeatability and reproducibility are integral component of high throughput omics studies including microbiome research. Batch ef...

    Authors: Shirin Moossavi, Kelsey Fehr, Ehsan Khafipour and Meghan B. Azad

    Citation: Microbiome 2021 9:41

    Content type: Short report

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  19. The spread of antibiotic resistance has become one of the most urgent threats to global health, which is estimated to cause 700,000 deaths each year globally. Its surrogates, antibiotic resistance genes (ARGs)...

    Authors: Yu Li, Zeling Xu, Wenkai Han, Huiluo Cao, Ramzan Umarov, Aixin Yan, Ming Fan, Huan Chen, Carlos M. Duarte, Lihua Li, Pak-Leung Ho and Xin Gao

    Citation: Microbiome 2021 9:40

    Content type: Methodology

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  20. The gut microbiota plays a central role in host physiology and in several pathological mechanisms in humans. Antibiotics compromise the composition and functions of the gut microbiota inducing long-lasting det...

    Authors: Francesco Strati, Meritxell Pujolassos, Claudia Burrello, Maria Rita Giuffrè, Georgia Lattanzi, Flavio Caprioli, Jacopo Troisi and Federica Facciotti

    Citation: Microbiome 2021 9:39

    Content type: Research

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  21. Microbial endocrinology, which is the study of neuroendocrine-based interkingdom signaling, provides a causal mechanistic framework for understanding the bi-directional crosstalk between the host and microbiom...

    Authors: Joshua M. Lyte, James Keane, Julia Eckenberger, Nicholas Anthony, Sandip Shrestha, Daya Marasini, Karrie M. Daniels, Valentina Caputi, Annie M. Donoghue and Mark Lyte

    Citation: Microbiome 2021 9:38

    Content type: Research

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  22. Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database...

    Authors: Jiarong Guo, Ben Bolduc, Ahmed A. Zayed, Arvind Varsani, Guillermo Dominguez-Huerta, Tom O. Delmont, Akbar Adjie Pratama, M. Consuelo Gazitúa, Dean Vik, Matthew B. Sullivan and Simon Roux

    Citation: Microbiome 2021 9:37

    Content type: Software article

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  23. In the past decade, there has been increasing interest in mosquito microbiome research, leading to large amounts of data on different mosquito species, with various underlying physiological characteristics, an...

    Authors: Nsa Dada, Natapong Jupatanakul, Guillaume Minard, Sarah M. Short, Jewelna Akorli and Luis Martinez Villegas

    Citation: Microbiome 2021 9:36

    Content type: Review

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  24. The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability o...

    Authors: Weibing Xun, Yunpeng Liu, Wei Li, Yi Ren, Wu Xiong, Zhihui Xu, Nan Zhang, Youzhi Miao, Qirong Shen and Ruifu Zhang

    Citation: Microbiome 2021 9:35

    Content type: Research

    Published on:

  25. Parkinson’s disease (PD) is a neurodegenerative disorder with no absolute cure. The evidence of the involvement of gut microbiota in PD pathogenesis suggests the need to identify certain molecule(s) derived fr...

    Authors: Yan-fang Hou, Chang Shan, Si-yue Zhuang, Qian-qian Zhuang, Arijit Ghosh, Ke-cheng Zhu, Xiao-ke Kong, Shu-min Wang, Yan-ling Gong, Yu-ying Yang, Bei Tao, Li-hao Sun, Hong-Yan Zhao, Xing-zhi Guo, Wei-qing Wang, Guang Ning…

    Citation: Microbiome 2021 9:34

    Content type: Research

    Published on:

  26. While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from ...

    Authors: Ryan A. Blaustein, Lisa-Marie Michelitsch, Adam J. Glawe, Hansung Lee, Stefanie Huttelmaier, Nancy Hellgeth, Sarah Ben Maamar and Erica M. Hartmann

    Citation: Microbiome 2021 9:32

    Content type: Research

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  27. Identifying which taxa are targeted by immunoglobulins can uncover important host-microbe interactions. Immunoglobulin binding of commensal taxa can be assayed by sorting bound bacteria from samples and using ...

    Authors: Matthew A. Jackson, Claire Pearson, Nicholas E. Ilott, Kelsey E. Huus, Ahmed N. Hegazy, Jonathan Webber, B. Brett Finlay, Andrew J. Macpherson, Fiona Powrie and Lilian H. Lam

    Citation: Microbiome 2021 9:33

    Content type: Methodology

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  28. Prebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysb...

    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 9:31

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2021 9:56

  29. Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconcl...

    Authors: Wisnu Adi Wicaksono, Peter Kusstatscher, Sabine Erschen, Tamara Reisenhofer-Graber, Martin Grube, Tomislav Cernava and Gabriele Berg

    Citation: Microbiome 2021 9:29

    Content type: Research

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  30. Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients with steroid-refractory/dependent graft-versus-host disease (GvHD) are h...

    Authors: M. C. Zanella, S. Cordey, F. Laubscher, M. Docquier, G. Vieille, C. Van Delden, V. Braunersreuther, Mc Kee TA, J. A. Lobrinus, S. Masouridi-Levrat, Y. Chalandon, L. Kaiser and D. L. Vu

    Citation: Microbiome 2021 9:28

    Content type: Research

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  31. Human health is closely interconnected with its microbiome. Resilient microbiomes in, on, and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of...

    Authors: Alexander Mahnert, Cyprien Verseux, Petra Schwendner, Kaisa Koskinen, Christina Kumpitsch, Marcus Blohs, Lisa Wink, Daniela Brunner, Theodora Goessler, Daniela Billi and Christine Moissl-Eichinger

    Citation: Microbiome 2021 9:27

    Content type: Research

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  32. Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes in food availability and diet. However, outside of dietary shifts, other potential environmental drivers o...

    Authors: Alice Baniel, Katherine R. Amato, Jacinta C. Beehner, Thore J. Bergman, Arianne Mercer, Rachel F. Perlman, Lauren Petrullo, Laurie Reitsema, Sierra Sams, Amy Lu and Noah Snyder-Mackler

    Citation: Microbiome 2021 9:26

    Content type: Research

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  33. Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to e...

    Authors: Jeremiah J. Minich, Farhana Ali, Clarisse Marotz, Pedro Belda-Ferre, Leslie Chiang, Justin P. Shaffer, Carolina S. Carpenter, Daniel McDonald, Jack Gilbert, Sarah M. Allard, Eric E. Allen, Rob Knight, Daniel A. Sweeney and Austin D. Swafford

    Citation: Microbiome 2021 9:25

    Content type: Research

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  34. Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence sim...

    Authors: Yusuke Okazaki, Shohei Fujinaga, Michaela M. Salcher, Cristiana Callieri, Atsushi Tanaka, Ayato Kohzu, Hideo Oyagi, Hideyuki Tamaki and Shin-ichi Nakano

    Citation: Microbiome 2021 9:24

    Content type: Research

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  35. Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways...

    Authors: Leeann Klassen, Greta Reintjes, Jeffrey P. Tingley, Darryl R. Jones, Jan-Hendrik Hehemann, Adam D. Smith, Timothy D. Schwinghamer, Carol Arnosti, Long Jin, Trevor W. Alexander, Carolyn Amundsen, Dallas Thomas, Rudolf Amann, Tim A. McAllister and D. Wade Abbott

    Citation: Microbiome 2021 9:23

    Content type: Research

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  36. Skin, the largest organ of the human body by weight, hosts a diversity of microorganisms that can influence health. The microbial residents of the skin are now appreciated for their roles in host immune intera...

    Authors: Kristin H. Loomis, Susan K. Wu, Amanda Ernlund, Kristina Zudock, Allison Reno, Kianna Blount and David K. Karig

    Citation: Microbiome 2021 9:22

    Content type: Research

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

    Authors: Allison M. Veach, Reese Morris, Daniel Z. Yip, Zamin K. Yang, Nancy L. Engle, Melissa A. Cregger, Timothy J. Tschaplinski and Christopher W. Schadt

    Citation: Microbiome 2021 9:21

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2019 7:76

  38. Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the ...

    Authors: Dong Li, Haowei Ni, Shuo Jiao, Yahai Lu, Jizhong Zhou, Bo Sun and Yuting Liang

    Citation: Microbiome 2021 9:20

    Content type: Research

    Published on:

  39. The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and cruciall...

    Authors: Sally Hilton, Emma Picot, Susanne Schreiter, David Bass, Keith Norman, Anna E. Oliver, Jonathan D. Moore, Tim H. Mauchline, Peter R. Mills, Graham R. Teakle, Ian M. Clark, Penny R. Hirsch, Christopher J. van der Gast and Gary D. Bending

    Citation: Microbiome 2021 9:19

    Content type: Research

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  40. As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core ...

    Authors: Zhiqiang Wu, Yelin Han, Bo Liu, Hongying Li, Guangjian Zhu, Alice Latinne, Jie Dong, Lilin Sun, Haoxiang Su, Liguo Liu, Jiang Du, Siyu Zhou, Mingxing Chen, Anamika Kritiyakan, Sathaporn Jittapalapong, Kittipong Chaisiri…

    Citation: Microbiome 2021 9:18

    Content type: Research

    Published on:

  41. High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at...

    Authors: Ya Wang, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann and Curtis Huttenhower

    Citation: Microbiome 2021 9:17

    Content type: Research

    Published on:

  42. Characterizing indoor microbial communities using molecular methods provides insight into bacterial assemblages present in environments that can influence occupants’ health. We conducted an environmental asses...

    Authors: Ju-Hyeong Park, Angela R. Lemons, Jerry Roseman, Brett J. Green and Jean M. Cox-Ganser

    Citation: Microbiome 2021 9:15

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2021 9:42

  43. For more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid,...

    Authors: Martin J. Blaser, Suzanne Devkota, Kathy D. McCoy, David A. Relman, Moran Yassour and Vincent B. Young

    Citation: Microbiome 2021 9:8

    Content type: Commentary

    Published on:

  44. A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their s...

    Authors: Marcus C. de Goffau, D. Stephen Charnock-Jones, Gordon C. S. Smith and Julian Parkhill

    Citation: Microbiome 2021 9:6

    Content type: Letter to the Editor

    Published on:

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