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  1. Cognitive impairment, an increasing mental health issue, is a core feature of the aging brain and neurodegenerative diseases. Industrialized nations especially, have experienced a marked decrease in dietary fi...

    Authors: Hongli Shi, Xing Ge, Xi Ma, Mingxuan Zheng, Xiaoying Cui, Wei Pan, Peng Zheng, Xiaoying Yang, Peng Zhang, Minmin Hu, Tao Hu, Renxian Tang, Kuiyang Zheng, Xu-Feng Huang and Yinghua Yu
    Citation: Microbiome 2021 9:223
  2. Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and betw...

    Authors: Eva Lena F. Estensmo, Luis Morgado, Sundy Maurice, Pedro M. Martin-Sanchez, Ingeborg B. Engh, Johan Mattsson, Håvard Kauserud and Inger Skrede
    Citation: Microbiome 2021 9:220
  3. Fructo-oligosaccharides (FOS), inulin, and galacto-oligosaccharides (GOS) are widely recognized prebiotics that profoundly affect the intestinal microbiota, including stimulation of bifidobacteria and lactobac...

    Authors: Jori Fuhren, Markus Schwalbe, Jos Boekhorst, Christiane Rösch, Henk A. Schols and Michiel Kleerebezem
    Citation: Microbiome 2021 9:218
  4. Plant health and growth are negatively affected by pathogen invasion; however, plants can dynamically modulate their rhizosphere microbiome and adapt to such biotic stresses. Although plant-recruited protectiv...

    Authors: Zhefei Li, Xiaoli Bai, Shuo Jiao, Yanmei Li, Peirong Li, Yan Yang, Hui Zhang and Gehong Wei
    Citation: Microbiome 2021 9:217
  5. Microbial acquisition and development of the gut microbiota impact the establishment of a healthy host-microbes symbiosis. Compared with other animals, the eusocial bumblebees and honeybees possess a simple, r...

    Authors: Qinzhi Su, Qinglin Wang, Xiaohuan Mu, Hao Chen, Yujie Meng, Xue Zhang, Li Zheng, Xiaosong Hu, Yifan Zhai and Hao Zheng
    Citation: Microbiome 2021 9:216
  6. The gut microbiome is altered in patients with inflammatory bowel disease, yet how these alterations contribute to intestinal inflammation is poorly understood. Murine models have demonstrated the importance o...

    Authors: Amy M. Tsou, Jeremy A. Goettel, Bin Bao, Amlan Biswas, Yu Hui Kang, Naresh S. Redhu, Kaiyue Peng, Gregory G. Putzel, Jeffrey Saltzman, Ryan Kelly, Jordan Gringauz, Jared Barends, Mai Hatazaki, Sandra M. Frei, Rohini Emani, Ying Huang…
    Citation: Microbiome 2021 9:215
  7. Upper gastrointestinal (GI) disorders and abdominal pain afflict between 12 and 30% of the worldwide population and research suggests these conditions are linked to the gut microbiome. Although large-intestine...

    Authors: Jacob T. Barlow, Gabriela Leite, Anna E. Romano, Rashin Sedighi, Christine Chang, Shreya Celly, Ali Rezaie, Ruchi Mathur, Mark Pimentel and Rustem F. Ismagilov
    Citation: Microbiome 2021 9:214
  8. Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in ...

    Authors: Xinzhao Tong, Marcus H. Y. Leung, Zhiyong Shen, Justin Y. Y. Lee, Christopher E. Mason and Patrick K. H. Lee
    Citation: Microbiome 2021 9:213
  9. Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental co...

    Authors: Zhiwen Luo, Qiuping Zhong, Xingguo Han, Ruiwen Hu, Xingyu Liu, Wenjun Xu, Yongjie Wu, Weiming Huang, Zhengyuan Zhou, Wei Zhuang, Qingyun Yan, Zhili He and Cheng Wang
    Citation: Microbiome 2021 9:212
  10. The magnitude of microbiota perturbations after exposure to antibiotics varies among individuals. It has been suggested that the composition of pre-treatment microbiota underpins personalized responses to anti...

    Authors: Armin Rashidi, Maryam Ebadi, Tauseef Ur Rehman, Heba Elhusseini, Harika Nalluri, Thomas Kaiser, Shernan G. Holtan, Alexander Khoruts, Daniel J. Weisdorf and Christopher Staley
    Citation: Microbiome 2021 9:211
  11. The intestinal microbiota plays an important role in regulating gastrointestinal (GI) physiology in part through interactions with the enteric nervous system (ENS). Alterations in the gut microbiome frequently...

    Authors: Fernando A. Vicentini, Catherine M. Keenan, Laurie E. Wallace, Crystal Woods, Jean-Baptiste Cavin, Amanda R. Flockton, Wendy B. Macklin, Jaime Belkind-Gerson, Simon A. Hirota and Keith A. Sharkey
    Citation: Microbiome 2021 9:210
  12. Microbes can grow in indoor environments if moisture is available, and we need an improved understanding of how this growth contributes to emissions of microbial volatile organic compounds (mVOCs). The goal of...

    Authors: Sarah R. Haines, Emma C. Hall, Katarzyna Marciniak, Pawel K. Misztal, Allen H. Goldstein, Rachel I. Adams and Karen C. Dannemiller
    Citation: Microbiome 2021 9:209

    The Correction to this article has been published in Microbiome 2021 9:219

  13. Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling vi...

    Authors: Gareth Trubl, Jeffrey A. Kimbrel, Jose Liquet-Gonzalez, Erin E. Nuccio, Peter K. Weber, Jennifer Pett-Ridge, Janet K. Jansson, Mark P. Waldrop and Steven J. Blazewicz
    Citation: Microbiome 2021 9:208
  14. Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bact...

    Authors: Zhao-Jie Teng, Qi-Long Qin, Weipeng Zhang, Jian Li, Hui-Hui Fu, Peng Wang, Musheng Lan, Guangfu Luo, Jianfeng He, Andrew McMinn, Min Wang, Xiu-Lan Chen, Yu-Zhong Zhang, Yin Chen and Chun-Yang Li
    Citation: Microbiome 2021 9:207

    The Correction to this article has been published in Microbiome 2021 9:221

  15. 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 9:206

    The original article was published in Microbiome 2021 9:163

  16. Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain...

    Authors: Lei Liu, Yulin Wang, Yu Yang, Depeng Wang, Suk Hang Cheng, Chunmiao Zheng and Tong Zhang
    Citation: Microbiome 2021 9:205
  17. The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-re...

    Authors: José F. Cobo-Díaz, Adrián Alvarez-Molina, Elena A. Alexa, Calum J. Walsh, Oscar Mencía-Ares, Paula Puente-Gómez, Eleni Likotrafiti, Paula Fernández-Gómez, Bernardo Prieto, Fiona Crispie, Lorena Ruiz, Montserrat González-Raurich, Mercedes López, Miguel Prieto, Paul Cotter and Avelino Alvarez-Ordóñez
    Citation: Microbiome 2021 9:204
  18. Obtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite improvements in ...

    Authors: Koji Arikawa, Keigo Ide, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Taruho Endoh, Ayumi Matsuhashi, Haruko Takeyama and Masahito Hosokawa
    Citation: Microbiome 2021 9:202
  19. Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close r...

    Authors: Benoît Paix, Nicolas Layglon, Christophe Le Poupon, Sébastien D’Onofrio, Benjamin Misson, Cédric Garnier, Gérald Culioli and Jean-François Briand
    Citation: Microbiome 2021 9:201
  20. The development of suppressive soils is a promising strategy to protect plants against soil-borne diseases in a sustainable and viable manner. The use of crop rotation and the incorporation of plant residues i...

    Authors: Xianfu Yuan, Shan Hong, Wu Xiong, Waseem Raza, Zongzhuan Shen, Beibei Wang, Rong Li, Yunze Ruan, Qirong Shen and Francisco Dini-Andreote
    Citation: Microbiome 2021 9:200
  21. Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between stat...

    Authors: Yulin Wang, Jun Ye, Feng Ju, Lei Liu, Joel A. Boyd, Yu Deng, Donovan H. Parks, Xiaotao Jiang, Xiaole Yin, Ben J. Woodcroft, Gene W. Tyson, Philip Hugenholtz, Martin F. Polz and Tong Zhang
    Citation: Microbiome 2021 9:199
  22. Intestinal Peyer’s patches (PPs) form unique niches for bacteria-immune cell interactions that direct host immunity and shape the microbiome. Here we investigate how peroral administration of probiotic bacterium

    Authors: Hao-Yu Liu, Antoine Giraud, Cedric Seignez, David Ahl, Feilong Guo, John Sedin, Tomas Walden, Jee-Hwan Oh, Jan Peter van Pijkeren, Lena Holm, Stefan Roos, Stefan Bertilsson and Mia Phillipson
    Citation: Microbiome 2021 9:198
  23. Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding o...

    Authors: Lena Granehäll, Kun D. Huang, Adrian Tett, Paolo Manghi, Alice Paladin, Niall O’Sullivan, Omar Rota-Stabelli, Nicola Segata, Albert Zink and Frank Maixner
    Citation: Microbiome 2021 9:197
  24. The ubiquitous gut microbiotas acquired from the environment contribute to host health. The gut microbiotas of soil invertebrates are gradually assembled from the microecological region of the soil ecosystem w...

    Authors: Qi Zhang, Zhenyan Zhang, Tao Lu, Yitian Yu, Josep Penuelas, Yong-Guan Zhu and Haifeng Qian
    Citation: Microbiome 2021 9:196
  25. Soil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is u...

    Authors: Virginie Jouffret, Guylaine Miotello, Karen Culotta, Sophie Ayrault, Olivier Pible and Jean Armengaud
    Citation: Microbiome 2021 9:195
  26. Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria—their microbiome. However, the nature of the relationship between Microcystis and its microbiome ...

    Authors: Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laisa Corrêa Braga Marques, Nathalie Fortin and B. Jesse Shapiro
    Citation: Microbiome 2021 9:194
  27. Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been ...

    Authors: Christina Kumpitsch, Florian Ph. S. Fischmeister, Alexander Mahnert, Sonja Lackner, Marilena Wilding, Corina Sturm, Anna Springer, Tobias Madl, Sandra Holasek, Christoph Högenauer, Ivan A. Berg, Veronika Schoepf and Christine Moissl-Eichinger
    Citation: Microbiome 2021 9:193
  28. Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effect...

    Authors: Le Wang, Guangping Huang, Rong Hou, Dunwu Qi, Qi Wu, Yonggang Nie, Zhenqiang Zuo, Rui Ma, Wenliang Zhou, Yingjie Ma, Yibo Hu, Zhisong Yang, Li Yan and Fuwen Wei
    Citation: Microbiome 2021 9:192
  29. Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 1...

    Authors: Christina N. Nikolova, Umer Zeeshan Ijaz, Clayton Magill, Sara Kleindienst, Samantha B. Joye and Tony Gutierrez
    Citation: Microbiome 2021 9:191
  30. Coastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutri...

    Authors: Hwee Sze Tee, David Waite, Gavin Lear and Kim Marie Handley
    Citation: Microbiome 2021 9:190
  31. Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing lar...

    Authors: Dong Zhu, Manuel Delgado-Baquerizo, Jing Ding, Michael R. Gillings and Yong-Guan Zhu
    Citation: Microbiome 2021 9:189
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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

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