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  1. Non-alcoholic liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome, and it can progress to non-alcoholic steatohepatitis (NASH). Alterations in the gut microbiome have been implicated in th...

    Authors: Ryo Aoki, Masayoshi Onuki, Koya Hattori, Masato Ito, Takahiro Yamada, Kohei Kamikado, Yun-Gi Kim, Nobuhiro Nakamoto, Ikuo Kimura, Julie M. Clarke, Takanori Kanai and Koji Hase

    Citation: Microbiome 2021 9:188

    Content type: Research

    Published on:

  2. The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficia...

    Authors: Min Gao, Chao Xiong, Cheng Gao, Clement K. M. Tsui, Meng-Meng Wang, Xin Zhou, Ai-Min Zhang and Lei Cai

    Citation: Microbiome 2021 9:187

    Content type: Research

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  3. Studies on the inhibition of inflammation by infection with helminth parasites have, until recently, overlooked a key determinant of health: the gut microbiota. Infection with helminths evokes changes in the c...

    Authors: Adam Shute, Blanca E. Callejas, ShuHua Li, Arthur Wang, Timothy S. Jayme, Christina Ohland, Ian A. Lewis, Brian T. Layden, André G. Buret and Derek M. McKay

    Citation: Microbiome 2021 9:186

    Content type: Research

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  4. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been suggested to prevent the development of metabolic disorders. However, their individual role in treating hyperglycemia and the mechanism of a...

    Authors: Pan Zhuang, Haoyu Li, Wei Jia, Qiyang Shou, Ya’er Zhu, Lei Mao, Wenqiao Wang, Fei Wu, Xiaoqian Chen, Xuzhi Wan, Yuqi Wu, Xiaohui Liu, Yin Li, Fanghuan Zhu, Lilin He, Jingnan Chen…

    Citation: Microbiome 2021 9:185

    Content type: Research

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  5. Alteration of the gut microbiota may contribute to the development of inflammatory bowel disease (IBD). Epigallocatechin-3-gallate (EGCG), a major bioactive constituent of green tea, is known to be beneficial ...

    Authors: Zhenhua Wu, Shimeng Huang, Tiantian Li, Na Li, Dandan Han, Bing Zhang, Zhenjiang Zech Xu, Shiyi Zhang, Jiaman Pang, Shilan Wang, Guolong Zhang, Jiangchao Zhao and Junjun Wang

    Citation: Microbiome 2021 9:184

    Content type: Research

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  6. P-glycoprotein (P-gp) plays a critical role in protection of the intestinal epithelia by mediating efflux of drugs/xenobiotics from the intestinal mucosa into the gut lumen. Recent studies bring to light that ...

    Authors: Sage E. Foley, Christine Tuohy, Merran Dunford, Michael J. Grey, Heidi De Luca, Caitlin Cawley, Rose L. Szabady, Ana Maldonado-Contreras, Jean Marie Houghton, Doyle V. Ward, Randall J. Mrsny and Beth A. McCormick

    Citation: Microbiome 2021 9:183

    Content type: Research

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  7. Deep-sea animals in hydrothermal vents often form endosymbioses with chemosynthetic bacteria. Endosymbionts serve essential biochemical and ecological functions, but the prokaryotic viruses (phages) that deter...

    Authors: Kun Zhou, Ying Xu, Rui Zhang and Pei-Yuan Qian

    Citation: Microbiome 2021 9:182

    Content type: Research

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  8. Identification of bacterial taxa associated with diseases, exposures, and other variables of interest offers a more comprehensive understanding of the role of microbes in many conditions. However, despite cons...

    Authors: Wodan Ling, Ni Zhao, Anna M. Plantinga, Lenore J. Launer, Anthony A. Fodor, Katie A. Meyer and Michael C. Wu

    Citation: Microbiome 2021 9:181

    Content type: Methodology

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  9. Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear.

    Authors: Yue Xiao, Chao Yang, Leilei Yu, Fengwei Tian, Yarong Wu, Jianxin Zhao, Hao Zhang, Ruifu Yang, Wei Chen, Colin Hill, Yujun Cui and Qixiao Zhai

    Citation: Microbiome 2021 9:180

    Content type: Research

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  10. The aquaculture sector now accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish feeds and feed additives t...

    Authors: Raminta Kazlauskaite, Bachar Cheaib, Chloe Heys, Umer Zeeshan Ijaz, Stephanie Connelly, William Sloan, Julie Russel, Laura Rubio, John Sweetman, Alex Kitts, Philip McGinnity, Philip Lyons and Martin Llewellyn

    Citation: Microbiome 2021 9:179

    Content type: Research

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  11. Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the s...

    Authors: Chhedi Lal Gupta, Shlomo E. Blum, Karuppasamy Kattusamy, Tali Daniel, Shelly Druyan, Roni Shapira, Oleg Krifucks, Yong-Guan Zhu, Xin-Yuan Zhou, Jian-Qiang Su and Eddie Cytryn

    Citation: Microbiome 2021 9:178

    Content type: Research

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  12. The microbiota in the cecum of laying hens is crucial for host digestion, metabolism, and odor gas production. The results of recent studies have suggested that host microRNAs (miRNAs) can regulate gene expres...

    Authors: Si-Cheng Xing, Chun-Bo Huang, Rui-Ting Wu, Yi-Wen Yang, Jing-Yuan Chen, Jian-Dui Mi, Yin-Bao Wu, Yan Wang and Xin-Di Liao

    Citation: Microbiome 2021 9:177

    Content type: Research

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  13. An Escherichia coli (E. coli) pathotype with invasive properties, first reported by Darfeuille-Michaud and termed adherent-invasive E. coli (AIEC), was shown to be prevalent in up to half the individuals with Cro...

    Authors: Grégoire Chevalier, Arnaud Laveissière, Guillaume Desachy, Nicolas Barnich, Adeline Sivignon, Marc Maresca, Cendrine Nicoletti, Eric Di Pasquale, Margarita Martinez-Medina, Kenneth William Simpson, Vijay Yajnik, Harry Sokol, Jonathan Plassais, Francesco Strozzi, Alessandra Cervino, Rachel Morra…

    Citation: Microbiome 2021 9:176

    Content type: Research

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  14. Excessive fat accumulation of pigs is undesirable, as it severely affects economic returns in the modern pig industry. Studies in humans and mice have examined the role of the gut microbiome in host energy met...

    Authors: Congying Chen, Shaoming Fang, Hong Wei, Maozhang He, Hao Fu, Xinwei Xiong, Yunyan Zhou, Jinyuan Wu, Jun Gao, Hui Yang and Lusheng Huang

    Citation: Microbiome 2021 9:175

    Content type: Research

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  15. The catabolic activity of the microbiota contributes to health by aiding in nutrition, immune education, and niche protection against pathogens. However, the nutrients consumed by common taxa within the gut mi...

    Authors: Connor R. Tiffany, Jee-Yon Lee, Andrew W. L. Rogers, Erin E. Olsan, Pavel Morales, Franziska Faber and Andreas J. Bäumler

    Citation: Microbiome 2021 9:174

    Content type: Research

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  16. The determination of taxon-specific composition of microbiomes by combining high-throughput sequencing of ribosomal genes with phyloinformatic analyses has become routine in microbiology and allied sciences. S...

    Authors: Luis Gonzalez-de-Salceda and Ferran Garcia-Pichel

    Citation: Microbiome 2021 9:173

    Content type: Research

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  17. 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

    Content type: Research

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  18. 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

    Content type: Research

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  19. 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

    Content type: Research

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  20. 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

    Content type: Research

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  21. 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

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2021 9:143

  22. 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

    Content type: Research

    Published on:

  23. 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

    Content type: Research

    Published on:

  24. 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

    Content type: Research

    Published on:

  25. 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

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2021 9:145

  26. 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. Ghebermichael and Douglas S. Kwon

    Citation: Microbiome 2021 9:163

    Content type: Research

    Published on:

  27. 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

    Content type: Review

    Published on:

  28. 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

    Content type: Research

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  29. 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

    Content type: Research

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  30. 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

  31. 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

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  32. 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

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  33. 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

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  34. 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

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  35. 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

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  36. 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

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  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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

  43. 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:

  44. 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

  45. 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:

  46. 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

  47. 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:

  48. 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:

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