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  1. 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
  2. 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
  3. 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

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

  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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

    The original article was published in Microbiome 2019 7:76

  13. 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
  14. 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
  15. 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
  16. 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
  17. 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

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

  18. 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

    The Correction to this article has been published in Microbiome 2021 9:30

  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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

    The original article was published in Microbiome 2018 6:187

  29. 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
  30. 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
  31. 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
  32. 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

    The Correction to this article has been published in Microbiome 2022 10:42

  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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