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  1. 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 Published on:

  2. 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

  3. 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 Published on:

  4. 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 Published on:

  5. 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 Published on:

  6. 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 Published on:

  7. 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 Published on:

  8. 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 Published on:

  9. 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:

  10. 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:

  11. 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 Published on:

  12. 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 Published on:

  13. 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

  15. 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 Published on:

  16. 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 Published on:

  17. 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 Published on:

  18. 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 Published on:

  19. 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:

  20. 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 Published on:

  21. 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 Published on:

  22. 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 Published on:

  23. 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

  24. 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:

  25. 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 Published on:

  26. 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:

  27. 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:

  29. 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

  31. 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:

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

  32. 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:

  33. 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 Published on:

  36. 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:

  38. 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:

  40. 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 Published on:

  41. 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:

  42. 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 Published on:

  43. 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 Published on:

  44. 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:

  45. 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

  46. 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 Published on:

  47. 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:

  48. 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:

  49. 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:

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

  50. 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 Published on:
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