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  1. Comparisons of the gut microbiome of lean and obese humans have revealed that obesity is associated with the gut microbiome plus changes in numerous environmental factors, including high-fat diet (HFD). Here, ...

    Authors: Gihyeon Kim, Youngmin Yoon, Jin Ho Park, Jae Won Park, Myung-guin Noh, Hyun Kim, Changho Park, Hyuktae Kwon, Jeong-hyeon Park, Yena Kim, Jinyoung Sohn, Shinyoung Park, Hyeonhui Kim, Sun-Kyoung Im, Yeongmin Kim, Ha Yung Chung…
    Citation: Microbiome 2022 10:188
    Content type: Research Published on:

  2. Gut microbiota (GM) dysregulation, known as dysbiosis, has been proposed as a crucial driver of obesity associated with “Western” diet (WD) consumption. Gut dysbiosis is associated with increased gut permeabil...

    Authors: Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian and Sookja Kim Chung
    Citation: Microbiome 2022 10:187
    Content type: Research Published on:

  3. Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plan...

    Authors: Yongbin Li, Rui Yang, Max M. Häggblom, Mengyan Li, Lifang Guo, Baoqin Li, Max Kolton, Zhiguo Cao, Mohsen Soleimani, Zheng Chen, Zhimin Xu, Wenlong Gao, Bei Yan and Weimin Sun
    Citation: Microbiome 2022 10:186
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:232

  4. Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct...

    Authors: Ilya B. Slizovskiy, Marco Oliva, Jonathen K. Settle, Lidiya V. Zyskina, Mattia Prosperi, Christina Boucher and Noelle R. Noyes
    Citation: Microbiome 2022 10:185
    Content type: Research Published on:

  6. Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological...

    Authors: Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro and Steven W. Singer
    Citation: Microbiome 2022 10:183
    Content type: Research Published on:

  8. The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-micr...

    Authors: George Muscatt, Sally Hilton, Sebastien Raguideau, Graham Teakle, Ian D. E. A. Lidbury, Elizabeth M. H. Wellington, Christopher Quince, Andrew Millard, Gary D. Bending and Eleanor Jameson
    Citation: Microbiome 2022 10:181
    Content type: Research Published on:

  9. As a widely used broad-spectrum antibiotic, chloramphenicol is prone to be released into environments, thus resulting in the disturbance of ecosystem stability as well as the emergence of antibiotic resistance...

    Authors: Jiayu Zhang, Xiaoyan Li, Uli Klümper, Huaxin Lei, Thomas U. Berendonk, Fangliang Guo, Ke Yu, Chao Yang and Bing Li
    Citation: Microbiome 2022 10:180
    Content type: Research Published on:

  10. Each year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on m...

    Authors: Amaranta Focardi, Lisa R. Moore, Jean-Baptiste Raina, Justin R. Seymour, Ian T. Paulsen and Sasha G. Tetu
    Citation: Microbiome 2022 10:179
    Content type: Research Published on:

  11. Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and thei...

    Authors: Yui Sato, Juliane Wippler, Cecilia Wentrup, Rebecca Ansorge, Miriam Sadowski, Harald Gruber-Vodicka, Nicole Dubilier and Manuel Kleiner
    Citation: Microbiome 2022 10:178
    Content type: Research Published on:

  12. Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the d...

    Authors: Tao Wen, Penghao Xie, C. Ryan Penton, Lauren Hale, Linda S. Thomashow, Shengdie Yang, Zhexu Ding, Yaqi Su, Jun Yuan and Qirong Shen
    Citation: Microbiome 2022 10:177
    Content type: Research Published on:

  13. Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to ...

    Authors: Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram and Falk Hildebrand
    Citation: Microbiome 2022 10:176
    Content type: Software Published on:

  14. The role of the pulmonary microbiome in sarcoidosis is unknown. The objectives of this study were the following: (1) examine whether the pulmonary fungal and bacterial microbiota differed in patients with sarc...

    Authors: Kristel S. Knudsen, Sverre Lehmann, Rune Nielsen, Solveig Tangedal, Andreu Paytuvi-Gallart, Walter Sanseverino, Einar M. H. Martinsen, Pieter S. Hiemstra and Tomas M. Eagan
    Citation: Microbiome 2022 10:175
    Content type: Research Published on:

  15. The gut microbiome plays an important role in autoimmunity including multiple sclerosis and its mouse model called experimental autoimmune encephalomyelitis (EAE). Prior studies have demonstrated that the mult...

    Authors: Paola Bianchimano, Graham J. Britton, David S. Wallach, Emma M. Smith, Laura M. Cox, Shirong Liu, Kacper Iwanowski, Howard L. Weiner, Jeremiah J. Faith, Jose C. Clemente and Stephanie K. Tankou
    Citation: Microbiome 2022 10:174
    Content type: Research Published on:

  16. Ixodes scapularis is the predominant tick vector of Borrelia burgdorferi, the agent of Lyme disease, in the USA. Molecular interactions between the tick and B. burgdorferi orchestrate the migration of spirochetes...

    Authors: Sukanya Narasimhan, Nallakkandi Rajeevan, Morven Graham, Ming-Jie Wu, Kathleen DePonte, Solenne Marion, Orlanne Masson, Anya J. O’Neal, Joao H. F. Pedra, Daniel E. Sonenshine and Erol Fikrig
    Citation: Microbiome 2022 10:173
    Content type: Research Published on:

  17. Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclu...

    Authors: Yuan-Guo Xie, Zhen-Hao Luo, Bao-Zhu Fang, Jian-Yu Jiao, Qi-Jun Xie, Xing-Ru Cao, Yan-Ni Qu, Yan-Lin Qi, Yang-Zhi Rao, Yu-Xian Li, Yong-Hong Liu, Andrew Li, Cale Seymour, Marike Palmer, Brian P. Hedlund, Wen-Jun Li…
    Citation: Microbiome 2022 10:172
    Content type: Research Published on:

  18. Faecal samples are frequently used to characterise the gut microbiota in health and disease, yet there is considerable debate about how representative faecal bacterial profiles are of the overall gut community...

    Authors: Indrani Mukhopadhya, Jennifer C. Martin, Sophie Shaw, Aileen J. McKinley, Silvia W. Gratz and Karen P. Scott
    Citation: Microbiome 2022 10:171
    Content type: Research Published on:

  19. Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates...

    Authors: Xiaofeng Chen, Kai Tang, Mu Zhang, Shujing Liu, Mingming Chen, Peiwen Zhan, Wei Fan, Chen-Tung Arthur Chen and Yao Zhang
    Citation: Microbiome 2022 10:170
    Content type: Research Published on:

  20. Chinese Lunar Palace 1 (LP1) is a ground-based bio-regenerative life support system (BLSS) test bed integrating highly efficient plant cultivation, animal protein production, urine nitrogen recycling, and bioc...

    Authors: Jianlou Yang, Zikai Hao, Lantao Zhang, Yuming Fu and Hong Liu
    Citation: Microbiome 2022 10:169
    Content type: Research Published on:

  21. Both the gut microbiota and chronic viral infections have profound effects on host immunity, but interactions between these influences have been only superficially explored. Cytomegalovirus (CMV), for example,...

    Authors: Ning Chin, Nicole R. Narayan, Gema Méndez-Lagares, Amir Ardeshir, W. L. William Chang, Jesse D. Deere, Justin H. Fontaine, Connie Chen, Hung T. Kieu, Wenze Lu, Peter A. Barry, Ellen E. Sparger and Dennis J. Hartigan-O’Connor
    Citation: Microbiome 2022 10:168
    Content type: Research Published on:

  22. The rumen is an ecosystem with a complex microbial microflora in which microbes initiate biofilm formation by attaching to plant surfaces for plant degradation and are capable of converting feed to nutrients a...

    Authors: Xiaozhen Liu, Qinmeng Liu, Sihuai Sun, Hengxi Sun, Yao Wang, Xihui Shen and Lei Zhang
    Citation: Microbiome 2022 10:167
    Content type: Research Published on:

  23. Healthier ruminant products can be achieved by adequate manipulation of the rumen microbiota to increase the flux of beneficial fatty acids reaching host tissues. Genomic selection to modify the microbiome fun...

    Authors: Marina Martínez-Álvaro, Jennifer Mattock, Marc Auffret, Ziqing Weng, Carol-Anne Duthie, Richard J. Dewhurst, Matthew A. Cleveland, Mick Watson and Rainer Roehe
    Citation: Microbiome 2022 10:166
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:184

  24. SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought ...

    Authors: Carter Merenstein, Frederic D. Bushman and Ronald G. Collman
    Citation: Microbiome 2022 10:165
    Content type: Comment Published on:

  25. Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircini...

    Authors: Joseph B. Kelly, David E. Carlson, Jun Siong Low and Robert W. Thacker
    Citation: Microbiome 2022 10:164
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:182

  27. Mammalian intestinal microbiomes are necessary for antagonizing systemic viral infections. However, very few studies have identified whether poultry commensal bacteria play a crucial role in protecting against...

    Authors: Hai-chang Yin, Zhen-dong Liu, Wei-wei Zhang, Qing-zhu Yang, Tian-fei Yu and Xin-jie Jiang
    Citation: Microbiome 2022 10:162
    Content type: Research Published on:

  28. Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis...

    Authors: Corey C. Holt, Vittorio Boscaro, Niels W. L. Van Steenkiste, Maria Herranz, Varsha Mathur, Nicholas A. T. Irwin, Gracy Buckholtz, Brian S. Leander and Patrick J. Keeling
    Citation: Microbiome 2022 10:161
    Content type: Research Published on:

  29. Although the lack of estrogen receptor β (ERβ) is a risk factor for the development of inflammatory bowel disease (IBD) and psychiatric disorders, the underlying cellular and molecular mechanisms are not fully...

    Authors: Yuanyuan Ma, Tianyao Liu, Xin Li, Anqi Kong, Rui Xiao, Ruxin Xie, Junwei Gao, Zhongke Wang, Yun Cai, Jiao Zou, Ling Yang, Lian Wang, Jinghui Zhao, Haiwei Xu, Warner Margaret, Xingshun Xu…
    Citation: Microbiome 2022 10:160
    Content type: Research Published on:

  30. Tooth decay is one of the most prevalent diseases worldwide, and efficient tooth brushing with a fluoride-containing dentifrice is considered fundamental to caries prevention. Fluoride-containing dentifrices h...

    Authors: Miguel Carda-Diéguez, Rebecca Moazzez and Alex Mira
    Citation: Microbiome 2022 10:159
    Content type: Research Published on:

  31. The intestinal microbiota fundamentally guides the development of a normal intestinal physiology, the education, and functioning of the mucosal immune system. The Citrobacter rodentium-carrier model in germ-free ...

    Authors: Rossana Romero, Agnieszka Zarzycka, Mathieu Preussner, Florence Fischer, Torsten Hain, Jan-Paul Herrmann, Katrin Roth, Corinna U. Keber, Kushal Suryamohan, Hartmann Raifer, Maik Luu, Hanna Leister, Wilhelm Bertrams, Matthias Klein, Hosam Shams-Eldin, Ralf Jacob…
    Citation: Microbiome 2022 10:158
    Content type: Research Published on:

  32. DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in c...

    Authors: Hoon Je Seong, Simon Roux, Chung Yeon Hwang and Woo Jun Sul
    Citation: Microbiome 2022 10:157
    Content type: Research Published on:

  33. Many insects house symbiotic intracellular bacteria (endosymbionts) that provide them with essential nutrients, thus promoting the usage of nutrient-poor habitats. Endosymbiont seclusion within host specialize...

    Authors: Mariana Galvão Ferrarini, Elisa Dell’Aglio, Agnès Vallier, Séverine Balmand, Carole Vincent-Monégat, Sandrine Hughes, Benjamin Gillet, Nicolas Parisot, Anna Zaidman-Rémy, Cristina Vieira, Abdelaziz Heddi and Rita Rebollo
    Citation: Microbiome 2022 10:156
    Content type: Research Published on:

  34. The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal...

    Authors: S. Teseo, S. Otani, C. Brinch, S. Leroy, P. Ruiz, M. Desvaux, E. Forano, F. M. Aarestrup and P. Sapountzis
    Citation: Microbiome 2022 10:155
    Content type: Research Published on:

  35. Complex interactions between the gut microbiome and immune cells in infancy are thought to be part of the pathogenesis for the marked rise in pediatric allergic diseases, particularly food allergies. Food prot...

    Authors: Victoria M. Martin, Yamini V. Virkud, Ehud Dahan, Hannah L. Seay, Dvir Itzkovits, Hera Vlamakis, Ramnik Xavier, Wayne G. Shreffler, Qian Yuan and Moran Yassour
    Citation: Microbiome 2022 10:154
    Content type: Research Published on:

  36. Infectious diseases have caused huge economic loss and food security issues in fish aquaculture. Current management and breeding strategies heavily rely on the knowledge of regulative mechanisms underlying dis...

    Authors: Qian Zhou, Xue Zhu, Yangzhen Li, Pengshuo Yang, Shengpeng Wang, Kang Ning and Songlin Chen
    Citation: Microbiome 2022 10:153
    Content type: Research Published on:

  37. Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage ...

    Authors: Oluwaseun Rume-Abiola Oyewole, Philipp Latzin, Silvio D. Brugger and Markus Hilty
    Citation: Microbiome 2022 10:152
    Content type: Research Published on:

  38. The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genom...

    Authors: Tina Keller-Costa, Lydia Kozma, Sandra G. Silva, Rodolfo Toscan, Jorge Gonçalves, Asunción Lago-Lestón, Nikos C. Kyrpides, Ulisses Nunes da Rocha and Rodrigo Costa
    Citation: Microbiome 2022 10:151
    Content type: Research Published on:

  39. Controlling excess biomass accumulation and clogging is important for maintaining the performance of gas biofilters and reducing energy consumption. Interruption of bacterial communication (quorum quenching) c...

    Authors: Yong-Chao Wang, Yu-Ting Lin, Can Wang, Zhen Tong, Xu-Rui Hu, Ya-Hui Lv, Guan-Yu Jiang, Meng-Fei Han, Ji-Guang Deng, Hsing-Cheng Hsi and Chung-Hak Lee
    Citation: Microbiome 2022 10:150
    Content type: Research Published on:

  40. The pathogenesis of inflammatory bowel diseases (IBD) is multifactorial, and diagnostic and treatment strategies for IBD remain to be developed. RhoB regulates multiple cell functions; however, its role in col...

    Authors: Jianming Yang, Geng Pei, Xuan Sun, Yawen Xiao, Chunhui Miao, Lu Zhou, Bangmao Wang, Liu Yang, Mingyu Yu, Zhi-Song Zhang, Evan T. Keller, Zhi Yao and Quan Wang
    Citation: Microbiome 2022 10:149
    Content type: Research Published on:

  41. In nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which playe...

    Authors: Francesco Maria Calabrese, Hana Ameur, Olga Nikoloudaki, Giuseppe Celano, Mirco Vacca, Wilson JFLemos Junior, Caterina Manzari, Fabienne Vertè, Raffaella Di Cagno, Graziano Pesole, Maria De Angelis and Marco Gobbetti
    Citation: Microbiome 2022 10:148
    Content type: Research Published on:

  42. The human gut is home to a largely underexplored microbiome component, the archaeome. Little is known of the impact of geography, urbanization, ethnicity, and diet on the gut archaeome in association with host...

    Authors: Xiaowu Bai, Yang Sun, Yue Li, Maojuan Li, Zhirui Cao, Ziyu Huang, Feng Zhang, Ping Yan, Lan Wang, Juan Luo, Jing Wu, Dejun Fan, Hongxia Chen, Min Zhi, Ping Lan, Zhong Zeng…
    Citation: Microbiome 2022 10:147
    Content type: Research Published on:

  43. Enteric methane emissions from dairy cows are an environmental problem as well as a gross feed energy loss to the animal. Methane is generated in the rumen by methanogenic archaea from hydrogen (H2) + carbon diox...

    Authors: Dipti W. Pitta, Nagaraju Indugu, Audino Melgar, Alexander Hristov, Krishna Challa, Bonnie Vecchiarelli, Meagan Hennessy, Kapil Narayan, Stephane Duval, Maik Kindermann and Nicola Walker
    Citation: Microbiome 2022 10:146
    Content type: Research Published on:

  44. The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth—teeth, tongue dorsum, and keratinized and non-...

    Authors: Viviana Morillo-Lopez, Alexandra Sjaarda, Imon Islam, Gary G. Borisy and Jessica L. Mark Welch
    Citation: Microbiome 2022 10:145
    Content type: Research Published on:

  45. Authors: Xingyu Ma, Tengxu Wang, Zhou Shi, Nona R. Chiariello, Kathryn Docherty, Christopher B. Field, Jessica Gutknecht, Qun Gao, Yunfu Gu, Xue Guo, Bruce A. Hungate, Jiesi Lei, Audrey Niboyet, Xavier Le Roux, Mengting Yuan, Tong Yuan…
    Citation: Microbiome 2022 10:144
    Content type: Correction Published on:

    The original article was published in Microbiome 2022 10:112

  48. Women with a cervicovaginal microbiota dominated by Lactobacillus spp. are at reduced risk of acquiring sexually transmitted infections including HIV, but the biological mechanisms involved remain poorly defined....

    Authors: David Jose Delgado-Diaz, Brianna Jesaveluk, Joshua A. Hayward, David Tyssen, Arghavan Alisoltani, Matthys Potgieter, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Imane Allali, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien, Jonathan M. Blackburn, Nicola Mulder, Steven B. Smith…
    Citation: Microbiome 2022 10:141
    Content type: Research Published on:

  49. Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts’ health. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same s...

    Authors: Yujie Meng, Shuang Li, Chong Zhang and Hao Zheng
    Citation: Microbiome 2022 10:140
    Content type: Research Published on:

  50. Post-weaning diarrhea in piglets reduces growth performance and increases mortality, thereby causing serious economic losses. The intestinal epithelial cells and microbiota reciprocally regulate each other in ...

    Authors: Bing Xia, Ruqing Zhong, Weida Wu, Chengzeng Luo, Qingshi Meng, Qingtao Gao, Yong Zhao, Liang Chen, Sheng Zhang, Xin Zhao and Hongfu Zhang
    Citation: Microbiome 2022 10:139
    Content type: Research Published on:
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