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  1. Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean’s interior. SAR324 is a ubiquitous but poorly understood...

    Authors: Dominique Boeuf, John M. Eppley, Daniel R. Mende, Rex R. Malmstrom, Tanja Woyke and Edward F. DeLong
    Citation: Microbiome 2021 9:172
  2. Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop mi...

    Authors: Chao Xiong, Brajesh K. Singh, Ji-Zheng He, Yan-Lai Han, Pei-Pei Li, Li-Hua Wan, Guo-Zhong Meng, Si-Yi Liu, Jun-Tao Wang, Chuan-Fa Wu, An-Hui Ge and Li-Mei Zhang
    Citation: Microbiome 2021 9:171
  3. Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology an...

    Authors: Wisnu Adi Wicaksono, Tomislav Cernava, Christian Berg and Gabriele Berg
    Citation: Microbiome 2021 9:170
  4. Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case ...

    Authors: Tilman E. Klassert, Rasmus Leistner, Cristina Zubiria-Barrera, Magdalena Stock, Mercedes López, Robert Neubert, Dominik Driesch, Petra Gastmeier and Hortense Slevogt
    Citation: Microbiome 2021 9:169
  5. 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 9:168

    The original article was published in Microbiome 2021 9:143

  6. The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the ...

    Authors: Alexandra J. Roth-Schulze, Megan A. S. Penno, Katrina M. Ngui, Helena Oakey, Esther Bandala-Sanchez, Alannah D. Smith, Theo R. Allnutt, Rebecca L. Thomson, Peter J. Vuillermin, Maria E. Craig, William D. Rawlinson, Elizabeth A. Davis, Mark Harris, Georgia Soldatos, Peter G. Colman, John M. Wentworth…
    Citation: Microbiome 2021 9:167
  7. Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, i...

    Authors: Pil Soo Kim, Na-Ri Shin, Jae-Bong Lee, Min-Soo Kim, Tae Woong Whon, Dong-Wook Hyun, Ji-Hyun Yun, Mi-Ja Jung, Joon Yong Kim and Jin-Woo Bae
    Citation: Microbiome 2021 9:166
  8. A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have be...

    Authors: Pranvera Hiseni, Knut Rudi, Robert C. Wilson, Finn Terje Hegge and Lars Snipen
    Citation: Microbiome 2021 9:165
  9. 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 9:164

    The original article was published in Microbiome 2021 9:145

  10. Cervicovaginal bacterial communities composed of diverse anaerobes with low Lactobacillus abundance are associated with poor reproductive outcomes such as preterm birth, infertility, cervicitis, and risk of sexua...

    Authors: Alexander Munoz, Matthew R. Hayward, Seth M. Bloom, Muntsa Rocafort, Sinaye Ngcapu, Nomfuneko A. Mafunda, Jiawu Xu, Nondumiso Xulu, Mary Dong, Krista L. Dong, Nasreen Ismail, Thumbi Ndung’u, Musie S. Ghebremichael and Douglas S. Kwon
    Citation: Microbiome 2021 9:163

    The Correction to this article has been published in Microbiome 2021 9:206

  11. Feelings of hunger and satiety are the key determinants for maintaining the life of humans and animals. Disturbed appetite control may disrupt the metabolic health of the host and cause various metabolic disor...

    Authors: Hui Han, Bao Yi, Ruqing Zhong, Mengyu Wang, Shunfen Zhang, Jie Ma, Yulong Yin, Jie Yin, Liang Chen and Hongfu Zhang
    Citation: Microbiome 2021 9:162
  12. A foodborne pathogen, Vibrio vulnificus, encounters normal microflora inhabiting the gut environments prior to causing fatal septicemia or gastroenteritis and should overcome the barriers derived from the gut com...

    Authors: Jeong-A Kim, Bo-Ram Jang, Yu-Ra Kim, You-Chul Jung, Kun-Soo Kim and Kyu-Ho Lee
    Citation: Microbiome 2021 9:161
  13. Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approache...

    Authors: Zhi-Ping Zhong, Funing Tian, Simon Roux, M. Consuelo Gazitúa, Natalie E. Solonenko, Yueh-Fen Li, Mary E. Davis, James L. Van Etten, Ellen Mosley-Thompson, Virginia I. Rich, Matthew B. Sullivan and Lonnie G. Thompson
    Citation: Microbiome 2021 9:160
  14. 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

    The original article was published in Microbiome 2021 9:134

  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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

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

  27. 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
  28. 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

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

  29. 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
  30. 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

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

  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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

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

  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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

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