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  1. 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 9:159

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2021 9:134

  2. This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacte...

    Authors: Anna Detman, Daniel Laubitz, Aleksandra Chojnacka, Pawel R. Kiela, Agnieszka Salamon, Albert Barberán, Yongjian Chen, Fei Yang, Mieczysław K. Błaszczyk and Anna Sikora

    Citation: Microbiome 2021 9:158

    Content type: Research

    Published on:

  3. Autism spectrum disorders (ASD) are associated with dysregulation of the microbiota-gut-brain axis, changes in microbiota composition as well as in the fecal, serum, and urine levels of microbial metabolites. ...

    Authors: Patricia Bermudez-Martin, Jérôme A. J. Becker, Nicolas Caramello, Sebastian P. Fernandez, Renan Costa-Campos, Juliette Canaguier, Susana Barbosa, Laura Martinez-Gili, Antonis Myridakis, Marc-Emmanuel Dumas, Aurélia Bruneau, Claire Cherbuy, Philippe Langella, Jacques Callebert, Jean-Marie Launay, Joëlle Chabry…

    Citation: Microbiome 2021 9:157

    Content type: Research

    Published on:

  4. Manufacturing and resource industries are the key drivers for economic growth with a huge environmental cost (e.g. discharge of industrial effluents and post-mining substrates). Pollutants from waste streams, ...

    Authors: Obulisamy Parthiba Karthikeyan, Thomas J. Smith, Shamsudeen Umar Dandare, Kamaludeen Sara Parwin, Heetasmin Singh, Hui Xin Loh, Mark R Cunningham, Paul Nicholas Williams, Tim Nichol, Avudainayagam Subramanian, Kumarasamy Ramasamy and Deepak Kumaresan

    Citation: Microbiome 2021 9:156

    Content type: Review

    Published on:

  7. Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members ...

    Authors: E. Lejal, J. Chiquet, J. Aubert, S. Robin, A. Estrada-Peña, O. Rue, C. Midoux, M. Mariadassou, X. Bailly, A. Cougoul, P. Gasqui, J. F. Cosson, K. Chalvet-Monfray, M. Vayssier-Taussat and T. Pollet

    Citation: Microbiome 2021 9:153

    Content type: Research

    Published on:

  8. The human microbiota plays several roles in health and disease but is often difficult to determine which part is in intimate relationships with the host vs. the occasional presence. During the Mars500 mission,...

    Authors: Giovanni Bacci, Alessio Mengoni, Giovanni Emiliani, Carolina Chiellini, Edoardo Giovanni Cipriani, Giovanna Bianconi, Francesco Canganella and Renato Fani

    Citation: Microbiome 2021 9:152

    Content type: Research

    Published on:

  9. Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genet...

    Authors: Shi Huang, Shuaiming Jiang, Dongxue Huo, Celeste Allaband, Mehrbod Estaki, Victor Cantu, Pedro Belda-Ferre, Yoshiki Vázquez-Baeza, Qiyun Zhu, Chenchen Ma, Congfa Li, Amir Zarrinpar, Yang-Yu Liu, Rob Knight and Jiachao Zhang

    Citation: Microbiome 2021 9:151

    Content type: Research

    Published on:

  10. Microbe–virus interactions have broad implications on the composition, function, and evolution of microbiomes. Elucidating the effects of environmental stresses on these interactions is critical to identify th...

    Authors: Dan Huang, Pingfeng Yu, Mao Ye, Cory Schwarz, Xin Jiang and Pedro J. J. Alvarez

    Citation: Microbiome 2021 9:150

    Content type: Research

    Published on:

  11. Since the prolonged use of insecticidal proteins has led to toxin resistance, it is important to search for novel insecticidal protein genes (IPGs) that are effective in controlling resistant insect population...

    Authors: Tatiana Dvorkina, Anton Bankevich, Alexei Sorokin, Fan Yang, Boahemaa Adu-Oppong, Ryan Williams, Keith Turner and Pavel A. Pevzner

    Citation: Microbiome 2021 9:149

    Content type: Research

    Published on:

  12. Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) exhibit changes in their gut microbiota and are experiencing a range of complications, including acute graft-versus-host disease (a...

    Authors: Anna Cäcilia Ingham, Katrine Kielsen, Hanne Mordhorst, Marianne Ifversen, Frank M. Aarestrup, Klaus Gottlob Müller and Sünje Johanna Pamp

    Citation: Microbiome 2021 9:148

    Content type: Research

    Published on:

  13. Leptin-deficient ob/ob mice and leptin receptor-deficient db/db mice are commonly used mice models mimicking the conditions of obesity and type 2 diabetes development. However, although ob/ob and db/db mice are s...

    Authors: Francesco Suriano, Sara Vieira-Silva, Gwen Falony, Martin Roumain, Adrien Paquot, Rudy Pelicaen, Marion Régnier, Nathalie M. Delzenne, Jeroen Raes, Giulio G. Muccioli, Matthias Van Hul and Patrice D. Cani

    Citation: Microbiome 2021 9:147

    Content type: Research

    Published on:

  14. The maternal microbiome has emerged as an important factor in gestational health and outcome and is associated with risk of preterm birth and offspring morbidity. Epidemiological evidence also points to succes...

    Authors: Alexander S. F. Berry, Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, Kevin O’Brien, Ying Chen, Samuel J. Murray, Lydia A. Ramharack, Robert N. Baldassano, Thomas D. Parsons and Daniel P. Beiting

    Citation: Microbiome 2021 9:146

    Content type: Research

    Published on:

  15. Modification of the gut microbiota has been reported to reduce the incidence of type 1 diabetes mellitus (T1D). We hypothesized that the gut microbiota shifts might also have an effect on cognitive functions i...

    Authors: Hong Zheng, Pengtao Xu, Qiaoying Jiang, Qingqing Xu, Yafei Zheng, Junjie Yan, Hui Ji, Jie Ning, Xi Zhang, Chen Li, Limin Zhang, Yuping Li, Xiaokun Li, Weihong Song and Hongchang Gao

    Citation: Microbiome 2021 9:145

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2021 9:164

  16. Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may t...

    Authors: David Pellow, Alvah Zorea, Maraike Probst, Ori Furman, Arik Segal, Itzhak Mizrahi and Ron Shamir

    Citation: Microbiome 2021 9:144

    Content type: Software article

    Published on:

  17. 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

  18. Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure cul...

    Authors: Patrick T. West, Samantha L. Peters, Matthew R. Olm, Feiqiao B. Yu, Haley Gause, Yue Clare Lou, Brian A. Firek, Robyn Baker, Alexander D. Johnson, Michael J. Morowitz, Robert L. Hettich and Jillian F. Banfield

    Citation: Microbiome 2021 9:142

    Content type: Research

    Published on:

  19. 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

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  42. 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:

  43. 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:

  44. 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:

  46. 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:

  47. 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:

  49. 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:

  50. 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:

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