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  1. Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh p...

    Authors: Sharon A. Huws, Joan E. Edwards, Wanchang Lin, Francesco Rubino, Mark Alston, David Swarbreck, Shabhonam Caim, Pauline Rees Stevens, Justin Pachebat, Mi-Young Won, Linda B. Oyama, Christopher J. Creevey and Alison H. Kingston-Smith
    Citation: Microbiome 2021 9:143
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2021 9:168

  2. Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plasti...

    Authors: Robyn J. Wright, Rafael Bosch, Morgan G. I. Langille, Matthew I. Gibson and Joseph A. Christie-Oleza
    Citation: Microbiome 2021 9:141
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2021 9:155

  3. Bile acids play key roles in gut metabolism, cell signaling, and microbiome composition. While the liver is responsible for the production of primary bile acids, microbes in the gut modify these compounds into...

    Authors: Douglas V. Guzior and Robert A. Quinn
    Citation: Microbiome 2021 9:140
    Content type: Review Published on:

  4. Bariatric surgery, used to achieve effective weight loss in individuals with severe obesity, modifies the gut microbiota and systemic metabolism in both humans and animal models. The aim of the current study w...

    Authors: Jia V. Li, Hutan Ashrafian, Magali Sarafian, Daniel Homola, Laura Rushton, Grace Barker, Paula Momo Cabrera, Matthew R. Lewis, Ara Darzi, Edward Lin, Nana Adwoa Gletsu-Miller, Stephen L. Atkin, Thozhukat Sathyapalan, Nigel J. Gooderham, Jeremy K. Nicholson, Julian R. Marchesi…
    Citation: Microbiome 2021 9:139
    Content type: Research Published on:

  5. Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor mic...

    Authors: Xi Fu, Zheyuan Ou, Mei Zhang, Yi Meng, Yanling Li, Jikai Wen, Qiansheng Hu, Xin Zhang, Dan Norbäck, Yiqun Deng, Zhuohui Zhao and Yu Sun
    Citation: Microbiome 2021 9:138
    Content type: Research Published on:

  6. Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as p...

    Authors: Fei Xie, Wei Jin, Huazhe Si, Yuan Yuan, Ye Tao, Junhua Liu, Xiaoxu Wang, Chengjian Yang, Qiushuang Li, Xiaoting Yan, Limei Lin, Qian Jiang, Lei Zhang, Changzheng Guo, Chris Greening, Rasmus Heller…
    Citation: Microbiome 2021 9:137
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:228

  7. Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth’s expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments in...

    Authors: Liang Shen, Yongqin Liu, Michelle A. Allen, Baiqing Xu, Ninglian Wang, Timothy J. Williams, Feng Wang, Yuguang Zhou, Qing Liu and Ricardo Cavicchioli
    Citation: Microbiome 2021 9:136
    Content type: Research Published on:

  8. Terrestrial hot spring settings span a broad spectrum of physicochemistries. Physicochemical parameters, such as pH and temperature, are key factors influencing differences in microbial composition across dive...

    Authors: Chanenath Sriaporn, Kathleen A. Campbell, Martin J. Van Kranendonk and Kim M. Handley
    Citation: Microbiome 2021 9:135
    Content type: Research Published on:

  9. The phenotypes of allergic airway diseases are influenced by the interplay between host genetics and the gut microbiota, which may be modulated by probiotics. We investigated the probiotic effects on allergic ...

    Authors: Mateus B. Casaro, Andrew M. Thomas, Eduardo Mendes, Claudio Fukumori, Willian R. Ribeiro, Fernando A. Oliveira, Amanda R. Crisma, Gilson M. Murata, Bruna Bizzarro, Anderson Sá-Nunes, Joao C. Setubal, Marcia P. A. Mayer, Flaviano S. Martins, Angélica T. Vieira, Ana T. F. B. Antiorio, Wothan Tavares-de-Lima…
    Citation: Microbiome 2021 9:134
    Content type: Short report Published on:

    The Correction to this article has been published in Microbiome 2021 9:159

  10. Matched-set data arise frequently in microbiome studies. For example, we may collect pre- and post-treatment samples from a set of individuals, or use important confounding variables to match data from case pa...

    Authors: Zhengyi Zhu, Glen A. Satten, Caroline Mitchell and Yi-Juan Hu
    Citation: Microbiome 2021 9:133
    Content type: Methodology Published on:

  11. SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic ...

    Authors: Clarisse Marotz, Pedro Belda-Ferre, Farhana Ali, Promi Das, Shi Huang, Kalen Cantrell, Lingjing Jiang, Cameron Martino, Rachel E. Diner, Gibraan Rahman, Daniel McDonald, George Armstrong, Sho Kodera, Sonya Donato, Gertrude Ecklu-Mensah, Neil Gottel…
    Citation: Microbiome 2021 9:132
    Content type: Research Published on:

  12. Microbiome interactions are important determinants for ecosystem functioning, stability, and health. In previous studies, it was often observed that bacteria suppress potentially pathogenic fungal species that...

    Authors: Jing Wang, Chaoyun Xu, Qiming Sun, Jinrong Xu, Yunrong Chai, Gabriele Berg, Tomislav Cernava, Zhonghua Ma and Yun Chen
    Citation: Microbiome 2021 9:131
    Content type: Research Published on:

  13. Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequen...

    Authors: Benjamin J. Callahan, Dmitry Grinevich, Siddhartha Thakur, Michael A. Balamotis and Tuval Ben Yehezkel
    Citation: Microbiome 2021 9:130
    Content type: Research Published on:

  14. The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this m...

    Authors: David Wilkins, Xinzhao Tong, Marcus H. Y. Leung, Christopher E. Mason and Patrick K. H. Lee
    Citation: Microbiome 2021 9:129
    Content type: Research Published on:

  15. Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance ...

    Authors: Yuanyuan Mo, Feng Peng, Xiaofei Gao, Peng Xiao, Ramiro Logares, Erik Jeppesen, Kexin Ren, Yuanyuan Xue and Jun Yang
    Citation: Microbiome 2021 9:128
    Content type: Research Published on:

  16. Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnersh...

    Authors: Till Röthig, Giulia Puntin, Jane C. Y. Wong, Alfred Burian, Wendy McLeod and David M. Baker
    Citation: Microbiome 2021 9:127
    Content type: Research Published on:

  17. Feed contributes most to livestock production costs. Improving feed efficiency is crucial to increase profitability and sustainability for animal production. Host genetics and the gut microbiota can both influ...

    Authors: Chaoliang Wen, Wei Yan, Chunning Mai, Zhongyi Duan, Jiangxia Zheng, Congjiao Sun and Ning Yang
    Citation: Microbiome 2021 9:126
    Content type: Research Published on:

  18. The skin is the exterior interface of the human body with the environment. Despite its harsh physical landscape, the skin is colonized by diverse commensal microbes. In this review, we discuss recent insights ...

    Authors: Manon Boxberger, Valérie Cenizo, Nadim Cassir and Bernard La Scola
    Citation: Microbiome 2021 9:125
    Content type: Review Published on:

  19. Obesity and vaginal microbiome (VMB) dysbiosis are each risk factors for adverse reproductive and oncological health outcomes in women. Here, we investigated the relationship between obesity, vaginal bacterial...

    Authors: Olivia Raglan, David A. MacIntyre, Anita Mitra, Yun S. Lee, Ann Smith, Nada Assi, Jaya Nautiyal, Sanjay Purkayastha, Marc J. Gunter, Hani Gabra, Julian R. Marchesi, Phillip R. Bennett and Maria Kyrgiou
    Citation: Microbiome 2021 9:124
    Content type: Research Published on:

  20. The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-b...

    Authors: Yacine Amar, Ilias Lagkouvardos, Rafaela L. Silva, Oluwaseun Ayodeji Ishola, Bärbel U. Foesel, Susanne Kublik, Anne Schöler, Sebastian Niedermeier, Rachela Bleuel, Alexander Zink, Klaus Neuhaus, Michael Schloter, Tilo Biedermann and Martin Köberle
    Citation: Microbiome 2021 9:123
    Content type: Research Published on:

  21. Successful chemoprevention or chemotherapy is achieved through targeted delivery of prophylactic agents during initial phases of carcinogenesis or therapeutic agents to malignant tumors. Bacteria can be used a...

    Authors: Yusook Chung, Yongku Ryu, Byung Chull An, Yeo-Sang Yoon, Oksik Choi, Tai Yeub Kim, Jaekyung Yoon, Jun Young Ahn, Ho Jin Park, Soon-Kyeong Kwon, Jihyun F. Kim and Myung Jun Chung
    Citation: Microbiome 2021 9:122
    Content type: Research Published on:

  22. The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of...

    Authors: M. H. Y. Leung, X. Tong, K. O. Bøifot, D. Bezdan, D. J. Butler, D. C. Danko, J. Gohli, D. C. Green, M. T. Hernandez, F. J. Kelly, S. Levy, G. Mason-Buck, M. Nieto-Caballero, D. Syndercombe-Court, K. Udekwu, B. G. Young…
    Citation: Microbiome 2021 9:112
    Content type: Research Published on:

  23. Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and ex...

    Authors: Paula B. Matheus Carnevali, Adi Lavy, Alex D. Thomas, Alexander Crits-Christoph, Spencer Diamond, Raphaël Méheust, Matthew R. Olm, Allison Sharrar, Shufei Lei, Wenming Dong, Nicola Falco, Nicholas Bouskill, Michelle E. Newcomer, Peter Nico, Haruko Wainwright, Dipankar Dwivedi…
    Citation: Microbiome 2021 9:121
    Content type: Research Published on:

  25. In gut microbiome studies, the cultured gut microbial resource plays essential roles, such as helping to unravel gut microbial functions and host-microbe interactions. Although several major studies have been ...

    Authors: Chang Liu, Meng-Xuan Du, Rexiding Abuduaini, Hai-Ying Yu, Dan-Hua Li, Yu-Jing Wang, Nan Zhou, Min-Zhi Jiang, Peng-Xia Niu, Shan-Shan Han, Hong-He Chen, Wen-Yu Shi, Linhuan Wu, Yu-Hua Xin, Juncai Ma, Yuguang Zhou…
    Citation: Microbiome 2021 9:119
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:163

  26. Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm...

    Authors: Denise P. Silva, Helena D. M. Villela, Henrique F. Santos, Gustavo A. S. Duarte, José Roberto Ribeiro, Angela M. Ghizelini, Caren L. S. Vilela, Phillipe M. Rosado, Carolline S. Fazolato, Erika P. Santoro, Flavia L. Carmo, Dalton S. Ximenes, Adriana U. Soriano, Caio T. C. C. Rachid, Rebecca L. Vega Thurber and Raquel S. Peixoto
    Citation: Microbiome 2021 9:118
    Content type: Research Published on:

  27. There is general consensus that consumption of dietary fermentable fiber improves cardiometabolic health, in part by promoting mutualistic microbes and by increasing production of beneficial metabolites in the...

    Authors: Sofia M. Murga-Garrido, Qilin Hong, Tzu-Wen L. Cross, Evan R. Hutchison, Jessica Han, Sydney P. Thomas, Eugenio I. Vivas, John Denu, Danilo G. Ceschin, Zheng-Zheng Tang and Federico E. Rey
    Citation: Microbiome 2021 9:117
    Content type: Research Published on:

  29. The endoglycosidase heparanase which degrades heparan sulfate proteoglycans, exerts a pro-inflammatory mediator in various inflammatory disorders. However, the function and underlying mechanism of heparanase i...

    Authors: Yuanyuan Lei, Li Tang, Shuang Liu, Shiping Hu, Lingyi Wu, Yaojiang Liu, Min Yang, Shengjie Huang, Xuefeng Tang, Tao Tang, Xiaoyan Zhao, Israel Vlodavsky, Shuo Zeng, Bo Tang and Shiming Yang
    Citation: Microbiome 2021 9:115
    Content type: Research Published on:

  30. Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual’s reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we ca...

    Authors: Eran Elhaik, Sofia Ahsanuddin, Jake M. Robinson, Emily M. Foster and Christopher E. Mason
    Citation: Microbiome 2021 9:114
    Content type: Commentary Published on:

  32. Microbiome research has gained considerable interest due to the emerging evidence of its impact on human and animal health. As in other animals, the gut-associated microbiota of mosquitoes affect host fitness ...

    Authors: Cintia Cansado-Utrilla, Serena Y. Zhao, Philip J. McCall, Kerri L. Coon and Grant L. Hughes
    Citation: Microbiome 2021 9:111
    Content type: Review Published on:

  33. Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional...

    Authors: Renxing Liang, Zhou Li, Maggie C. Y. Lau Vetter, Tatiana A. Vishnivetskaya, Oksana G. Zanina, Karen G. Lloyd, Susan M. Pfiffner, Elizaveta M. Rivkina, Wei Wang, Jessica Wiggins, Jennifer Miller, Robert L. Hettich and Tullis C. Onstott
    Citation: Microbiome 2021 9:110
    Content type: Research Published on:

  34. One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently ...

    Authors: Audet-Gilbert Émie, Sylvain François-Étienne, Bouslama Sidki and Derome Nicolas
    Citation: Microbiome 2021 9:109
    Content type: Research Published on:

  35. Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic app...

    Authors: Xun Qian, Santosh Gunturu, Jiarong Guo, Benli Chai, James R. Cole, Jie Gu and James M. Tiedje
    Citation: Microbiome 2021 9:108
    Content type: Research Published on:

  36. Donor selection is an important factor influencing the engraftment and efficacy of fecal microbiota transplantation (FMT) for complex conditions associated with microbial dysbiosis. However, the degree, variat...

    Authors: Brooke C. Wilson, Tommi Vatanen, Thilini N. Jayasinghe, Karen S. W. Leong, José G. B. Derraik, Benjamin B. Albert, Valentina Chiavaroli, Darren M. Svirskis, Kathryn L. Beck, Cathryn A. Conlon, Yannan Jiang, William Schierding, David J. Holland, Wayne S. Cutfield and Justin M. O’Sullivan
    Citation: Microbiome 2021 9:107
    Content type: Research Published on:

  39. The gut microbiome and iron status are known to play a role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD), although their complex interaction remains unclear.

    Authors: Jordi Mayneris-Perxachs, Marina Cardellini, Lesley Hoyles, Jèssica Latorre, Francesca Davato, José Maria Moreno-Navarrete, María Arnoriaga-Rodríguez, Matteo Serino, James Abbott, Richard H. Barton, Josep Puig, Xavier Fernández-Real, Wifredo Ricart, Christopher Tomlinson, Mark Woodbridge, Paolo Gentileschi…
    Citation: Microbiome 2021 9:104
    Content type: Research Published on:

  40. Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbio...

    Authors: Selma Cadot, Hang Guan, Moritz Bigalke, Jean-Claude Walser, Georg Jander, Matthias Erb, Marcel G. A. van der Heijden and Klaus Schlaeppi
    Citation: Microbiome 2021 9:103
    Content type: Research Published on:

  41. Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillo...

    Authors: Talisa Doering, Marlene Wall, Lalita Putchim, Tipwimon Rattanawongwan, Roman Schroeder, Ute Hentschel and Anna Roik
    Citation: Microbiome 2021 9:102
    Content type: Research Published on:

  42. The characteristics of polycystic ovary syndrome (PCOS), a common reproductive endocrinal disorder, are high incidence, complicated aetiology and poor therapeutic effects. PCOS patients frequently exhibit gut ...

    Authors: Qixin Han, Juan Wang, Weiping Li, Zi-Jiang Chen and Yanzhi Du
    Citation: Microbiome 2021 9:101
    Content type: Research Published on:

  43. The objective of this study was to increase understanding of the complex interactions between diet, obesity, and the gut microbiome of adult female non-human primates (NHPs). Subjects consumed either a Western (n

    Authors: Tiffany M. Newman, Carol A. Shively, Thomas C. Register, Susan E. Appt, Hariom Yadav, Rita R. Colwell, Brian Fanelli, Manoj Dadlani, Karlis Graubics, Uyen Thao Nguyen, Sivapriya Ramamoorthy, Beth Uberseder, Kenysha Y. J. Clear, Adam S. Wilson, Kimberly D. Reeves, Mark C. Chappell…
    Citation: Microbiome 2021 9:100
    Content type: Research Published on:

  44. Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbi...

    Authors: Jennifer M. Baker, Kevin J. Hinkle, Roderick A. McDonald, Christopher A. Brown, Nicole R. Falkowski, Gary B. Huffnagle and Robert P. Dickson
    Citation: Microbiome 2021 9:99
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2021 9:154

  45. RNA interference (RNAi) has emerged as an efficient tool to control insect pests. When insects ingest double-stranded RNAs (dsRNAs) targeted against essential genes, strong gene silencing and mortality can be ...

    Authors: Letian Xu, Shijing Xu, Liuwei Sun, Yiqiu Zhang, Jing Luo, Ralph Bock and Jiang Zhang
    Citation: Microbiome 2021 9:98
    Content type: Research Published on:

  46. Although localized aggressive periodontitis (LAP), generalized aggressive periodontitis (GAP), and chronic periodontitis (CP) are microbially driven diseases, our inability to separate disease-specific associa...

    Authors: Khaled Altabtbaei, Pooja Maney, Sukirth M. Ganesan, Shareef M. Dabdoub, Haikady N. Nagaraja and Purnima S. Kumar
    Citation: Microbiome 2021 9:97
    Content type: Research Published on:

  47. Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out ...

    Authors: Dieter M. Tourlousse, Koji Narita, Takamasa Miura, Mitsuo Sakamoto, Akiko Ohashi, Keita Shiina, Masami Matsuda, Daisuke Miura, Mamiko Shimamura, Yoshifumi Ohyama, Atsushi Yamazoe, Yoshihito Uchino, Keishi Kameyama, Shingo Arioka, Jiro Kataoka, Takayoshi Hisada…
    Citation: Microbiome 2021 9:95
    Content type: Methodology Published on:

  48. Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stim...

    Authors: Javier A. Ceja-Navarro, Yuan Wang, Daliang Ning, Abelardo Arellano, Leila Ramanculova, Mengting Maggie Yuan, Alyssa Byer, Kelly D. Craven, Malay C. Saha, Eoin L. Brodie, Jennifer Pett-Ridge and Mary K. Firestone
    Citation: Microbiome 2021 9:96
    Content type: Research Published on:

  50. 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 Published on:
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