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  1. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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

  6. 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

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  7. 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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  8. 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

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  9. 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

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  10. 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

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  11. Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they h...

    Authors: Christopher M. Bellas and Ruben Sommaruga

    Citation: Microbiome 2021 9:13

    Content type: Research

    Published on:

  12. Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut mic...

    Authors: Zhixiang Yan, Feixiang He, Fei Xiao, Huanhuan He, Dan Li, Li Cong, Lu Lin, Huijin Zhu, Yanyan Wu, Ru Yan, Xiaofeng Li and Hong Shan

    Citation: Microbiome 2021 9:12

    Content type: Research

    Published on:

  13. Non-caloric artificial sweeteners (NCAS) are widely used as a substitute for dietary sugars to control body weight or glycemia. Paradoxically, some interventional studies in humans and rodents have shown unfav...

    Authors: Joan Serrano, Kathleen R. Smith, Audra L. Crouch, Vandana Sharma, Fanchao Yi, Veronika Vargova, Traci E. LaMoia, Lydia M. Dupont, Vanida Serna, Fenfen Tang, Laisa Gomes-Dias, Joshua J. Blakeslee, Emmanuel Hatzakis, Scott N. Peterson, Matthew Anderson, Richard E. Pratley…

    Citation: Microbiome 2021 9:11

    Content type: Research

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  14. 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

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  15. 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:

  16. Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classifi...

    Authors: Laura-Jayne Gardiner, Niina Haiminen, Filippo Utro, Laxmi Parida, Ed Seabolt, Ritesh Krishna and James H. Kaufman

    Citation: Microbiome 2021 9:4

    Content type: Short report

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  17. An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.

    Authors: Paul H. Roy, Sally R. Partridge and Ruth M. Hall

    Citation: Microbiome 2021 9:3

    Content type: Letter to the Editor

    Published on:

  18. The inaugural “Microbiome for Mars” virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duratio...

    Authors: Michael LaPelusa, Dorit Donoviel, Sergio E. Branzini, Paul E. Carlson Jr, Stephanie Culler, Amrita K. Cheema, Rima Kaddurah-Daouk, Denise Kelly, Isabelle de Cremoux, Rob Knight, Rosa Krajmalnik-Brown, Stephen L. Mayo, Sarkis K. Mazmanian, Emeran A. Mayer, Joseph F. Petrosino and Keith Garrison

    Citation: Microbiome 2021 9:2

    Content type: Meeting report

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  19. Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest...

    Authors: Briana R. Flaherty, Joel Barratt, Meredith Lane, Eldin Talundzic and Richard S. Bradbury

    Citation: Microbiome 2021 9:1

    Content type: Research

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  20. Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening dis...

    Authors: Antonio Suppa, Jouni Kvist, Xiaojing Li, Vignesh Dhandapani, Hanan Almulla, Antoine Y. Tian, Stephen Kissane, Jiarui Zhou, Alessio Perotti, Hayley Mangelson, Kyle Langford, Valeria Rossi, James B. Brown and Luisa Orsini

    Citation: Microbiome 2020 8:170

    Content type: Research

    Published on:

  21. 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

  22. 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

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  23. 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

    Published on:

  24. 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:

  25. 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:

  26. 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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  27. 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

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  28. 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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  29. 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

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  30. 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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  31. 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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  32. 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:

  33. 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

    Published on:

  34. 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:

  35. 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:

  36. 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

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  37. 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

    Published on:

  38. 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

    Published on:

  39. 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

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  40. 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:

  41. 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

  42. 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:

  43. 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:

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