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  1. Numerous microorganisms are found in aquaculture ponds, including several pathogenic bacteria. Infection of cultured animals by these pathogens results in diseases and metabolic dysregulation. However, changes...

    Authors: Zhongyan Wang, Jude Juventus Aweya, Defu Yao, Zhihong Zheng, Chuanqi Wang, Yongzhen Zhao, Shengkang Li and Yueling Zhang
    Citation: Microbiome 2022 10:213
  2. Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic dat...

    Authors: Hans-Joachim Ruscheweyh, Alessio Milanese, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Keller, Jakob Wirbel, Peer Bork, Daniel R. Mende, Georg Zeller and Shinichi Sunagawa
    Citation: Microbiome 2022 10:212
  3. The immature neonatal fecal microbiota substantially impacts the development of gut health and greatly increases the risk of disease. Developing effective strategies to modulate the development of neonatal fec...

    Authors: Gang Wang, Xinyu Wang, Yonghang Ma, Shuang Cai, Lijie Yang, Yuxin Fan, Xiangfang Zeng and Shiyan Qiao
    Citation: Microbiome 2022 10:211
  4. The accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing gaps in d...

    Authors: Lei Liu, Yu Yang, Yu Deng and Tong Zhang
    Citation: Microbiome 2022 10:209
  5. The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input tha...

    Authors: Cecilia Salazar, Matias Giménez, Nadia Riera, Andrés Parada, Josefina Puig, Antonio Galiana, Fabio Grill, Mariela Vieytes, Christopher E. Mason, Verónica Antelo, Bruno D’Alessandro, Jimena Risso and Gregorio Iraola
    Citation: Microbiome 2022 10:208
  6. Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus-like...

    Authors: Pratibha Panwar, Timothy J. Williams, Michelle A. Allen and Ricardo Cavicchioli
    Citation: Microbiome 2022 10:207
  7. Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but a...

    Authors: Jiaxian Shen, Alexander G. McFarland, Ryan A. Blaustein, Laura J. Rose, K. Allison Perry-Dow, Anahid A. Moghadam, Mary K. Hayden, Vincent B. Young and Erica M. Hartmann
    Citation: Microbiome 2022 10:206
  8. Mounting experimental evidence has shown that the gut microbiota plays a significant role in the pathogenesis of mastitis, and clinical investigations have found that the occurrence of mastitis is correlated w...

    Authors: Caijun Zhao, Xiaoyu Hu, Lijuan Bao, Keyi Wu, Yihong Zhao, Kaihe Xiang, Shuang Li, Ying Wang, Min Qiu, Lianjun Feng, Xiangyue Meng, Naisheng Zhang and Yunhe Fu
    Citation: Microbiome 2022 10:205
  9. A significant proportion of colorectal cancer (CRC) patients suffer from early recurrence and progression after surgical treatment. Although the gut microbiota is considered as a key player in the initiation a...

    Authors: Ji-Won Huh, Min Jung Kim, Jaesik Kim, Hyeon Gwon Lee, Seung-Bum Ryoo, Ja-Lok Ku, Seung-Yong Jeong, Kyu Joo Park, Dokyoon Kim, Jihyun F. Kim and Ji Won Park
    Citation: Microbiome 2022 10:203
  10. The establishment of the gut microbiota in early life is a critical process that influences the development and fitness of vertebrates. However, the relative influence of transmission from the early social env...

    Authors: Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski and Barbara A. Caspers
    Citation: Microbiome 2022 10:202
  11. A dominance of non-iners Lactobacillus species in the vaginal microbiome is optimal and strongly associated with gynecological and obstetric health, while the presence of diverse obligate or facultative anaerobic...

    Authors: Gautam Mahajan, Erin Doherty, Tania To, Arlene Sutherland, Jennifer Grant, Abidemi Junaid, Aakanksha Gulati, Nina LoGrande, Zohreh Izadifar, Sanjay Sharma Timilsina, Viktor Horváth, Roberto Plebani, Michael France, Indriati Hood-Pishchany, Seth Rakoff-Nahoum, Douglas S. Kwon…
    Citation: Microbiome 2022 10:201
  12. Intestinal inflammation disrupts the microbiota composition leading to an expansion of Enterobacteriaceae family members (dysbiosis). Associated with this shift in microbiota composition is a profound change i...

    Authors: Savannah J. Taylor, Maria G. Winter, Caroline C. Gillis, Laice Alves da Silva, Amanda L. Dobbins, Matthew K. Muramatsu, Angel G. Jimenez, Rachael B. Chanin, Luisella Spiga, Ernesto M. Llano, Vivian K. Rojas, Jiwoong Kim, Renato L. Santos, Wenhan Zhu and Sebastian E. Winter
    Citation: Microbiome 2022 10:200
  13. Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope pro...

    Authors: Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone and Jennifer Pett-Ridge
    Citation: Microbiome 2022 10:199
  14. Dysregulation of gut microbiota-associated tryptophan metabolism has been observed in patients with multiple sclerosis. However, defining direct mechanistic links between this apparent metabolic rewiring and i...

    Authors: Theresa L. Montgomery, Korin Eckstrom, Katarina H. Lile, Sydney Caldwell, Eamonn R. Heney, Karolyn G. Lahue, Angelo D’Alessandro, Matthew J. Wargo and Dimitry N. Krementsov
    Citation: Microbiome 2022 10:198
  15. Most previous studies attempting to prove the phenomenon of mother-to-infant microbiota transmission were observational, performed only at genus/species-level resolution, and relied entirely on non-culture-bas...

    Authors: Zhi Zhong, Hai Tang, Tingting Shen, Xinwei Ma, Feiyan Zhao, Lai-Yu Kwok, Zhihong Sun, Menghe Bilige and Heping Zhang
    Citation: Microbiome 2022 10:197
  16. The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted...

    Authors: Jingjing Chang, Lei Tian, Marcio F.A. Leite, Yu Sun, Shaohua Shi, Shangqi Xu, Jilin Wang, Hongping Chen, Dazhou Chen, Jianfeng Zhang, Chunjie Tian and Eiko E. Kuramae
    Citation: Microbiome 2022 10:196
  17. Vascular calcification is a major cause of the high morbidity and mortality of cardiovascular diseases and is closely associated with the intestinal microbiota. Short-chain fatty acids (SCFAs) are derived from...

    Authors: Jianlong Yan, Yanbin Pan, Wenming Shao, Caiping Wang, Rongning Wang, Yaqiong He, Min Zhang, Yongshun Wang, Tangzhiming Li, Zhefeng Wang, Wenxing Liu, Zhenmin Wang, Xin Sun and Shaohong Dong
    Citation: Microbiome 2022 10:195
  18. Seasonal breeding in mammals has been widely recognized to be regulated by photoperiod, but the association of gut microbiota with photoperiodic regulation of seasonal breeding has never been investigated.

    Authors: Hanyi Zhu, Guoliang Li, Jing Liu, Xiaoming Xu and Zhibin Zhang
    Citation: Microbiome 2022 10:194
  19. Fecal microbiota transplantation (FMT) effectively prevents the recurrence of Clostridioides difficile infection (CDI). Long-term engraftment of donor-specific microbial consortia may occur in the recipient, but ...

    Authors: Shaodong Wei, Marie Louise Jespersen, Simon Mark Dahl Baunwall, Pernille Neve Myers, Emilie Milton Smith, Jens Frederik Dahlerup, Simon Rasmussen, Henrik Bjørn Nielsen, Tine Rask Licht, Martin Iain Bahl and Christian Lodberg Hvas
    Citation: Microbiome 2022 10:193
  20. Symbionts provide a variety of reproductive, nutritional, and defensive resources to their hosts, but those resources can vary depending on symbiont community composition. As genetic techniques open our eyes t...

    Authors: Shelby E. McIlroy, Casey P. terHorst, Mark Teece and Mary Alice Coffroth
    Citation: Microbiome 2022 10:192
  21. Dioecious plants have coevolved with diverse plant microbiomes, which are crucial for the fitness and productivity of their host. Sexual dimorphism in morphology, physiology, or gene expression may relate to d...

    Authors: Qingxue Guo, Lin Liu, Jiantong Liu, Helena Korpelainen and Chunyang Li
    Citation: Microbiome 2022 10:191
  22. Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts’ metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensivel...

    Authors: Xiao-Qing Luo, Pandeng Wang, Jia-Ling Li, Manzoor Ahmad, Li Duan, Ling-Zi Yin, Qi-Qi Deng, Bao-Zhu Fang, Shan-Hui Li and Wen-Jun Li
    Citation: Microbiome 2022 10:190
  23. In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in special...

    Authors: Johanne Aubé, Marie-Anne Cambon-Bonavita, Lourdes Velo-Suárez, Valérie Cueff-Gauchard, Françoise Lesongeur, Marion Guéganton, Lucile Durand and Julie Reveillaud
    Citation: Microbiome 2022 10:189
  24. 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
  25. 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
  26. 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 Solemani, Zheng Chen, Zhimin Xu, Wenlong Gao, Bei Yan and Weimin Sun
    Citation: Microbiome 2022 10:186
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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

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

  45. 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
  46. 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

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

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