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  1. The metabolic interactions of microbes significantly affect the assembly of microbial communities that play important roles in biogeochemical processes. However, most interspecies interactions between microorg...

    Authors: Huan Du, Jie Pan, Dayu Zou, Yuhan Huang, Yang Liu and Meng Li
    Citation: Microbiome 2022 10:224
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:244

  2. It has been hypothesised that the gut microbiota causally affects obesity via its capacity to extract energy from the diet. Yet, evidence elucidating the role of particular human microbial community structures...

    Authors: Jos Boekhorst, Naomi Venlet, Nicola Procházková, Mathias L. Hansen, Christian B. Lieberoth, Martin I. Bahl, Lotte Lauritzen, Oluf Pedersen, Tine Rask Licht, Michiel Kleerebezem and Henrik M. Roager
    Citation: Microbiome 2022 10:223
    Content type: Brief Report Published on:

  3. The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that oc...

    Authors: Xiaoting Yan, Huazhe Si, Yuhang Zhu, Songze Li, Yu Han, Hanlu Liu, Rui Du, Phillip B. Pope, Qiang Qiu and Zhipeng Li
    Citation: Microbiome 2022 10:222
    Content type: Research Published on:

  4. After millions of years of coevolution, symbiotic microbiota has become an integral part of the host and plays an important role in host immunity, metabolism, and health. Vaccination, as an effective means of ...

    Authors: Zhenbing Wu, Qianqian Zhang, Jicheng Yang, Jinyong Zhang, Jie Fu, Chenyuan Dang, Mansen Liu, Shuyi Wang, Yaoyao Lin, Jingwen Hao, Meiqi Weng, Derong Xie and Aihua Li
    Citation: Microbiome 2022 10:221
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2023 11:20

  5. Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of En...

    Authors: Keigo Ide, Yohei Nishikawa, Toru Maruyama, Yuko Tsukada, Masato Kogawa, Hiroki Takeda, Haruka Ito, Ryota Wagatsuma, Rimi Miyaoka, Yoshikatsu Nakano, Koji Kinjo, Michihiro Ito, Masahito Hosokawa, Kei Yura, Shoichiro Suda and Haruko Takeyama
    Citation: Microbiome 2022 10:220
    Content type: Research Published on:

  6. Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth’s largest reservoirs of ARGs, which...

    Authors: Manuel Delgado-Baquerizo, Hang-Wei Hu, Fernando T. Maestre, Carlos A. Guerra, Nico Eisenhauer, David J. Eldridge, Yong-Guan Zhu, Qing-Lin Chen, Pankaj Trivedi, Shuai Du, Thulani P. Makhalanyane, Jay Prakash Verma, Beatriz Gozalo, Victoria Ochoa, Sergio Asensio, Ling Wang…
    Citation: Microbiome 2022 10:219
    Content type: Research Published on:

  7. Monitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an...

    Authors: Braden T. Tierney, Nitin K. Singh, Anna C. Simpson, Andrea M. Hujer, Robert A. Bonomo, Christopher E. Mason and Kasthuri Venkateswaran
    Citation: Microbiome 2022 10:210
    Content type: Research Published on:

  8. The gut microbiome promotes specific immune responses, and in turn, the immune system has a hand in shaping the microbiome. Cancer and autoimmune diseases are two major disease families that result from the co...

    Authors: Md Zohorul Islam, Melissa Tran, Tao Xu, Braden T. Tierney, Chirag Patel and Aleksandar David Kostic
    Citation: Microbiome 2022 10:218
    Content type: Research Published on:

  9. From a theoretical ecology point of view, microbiomes are far more complex than expected. Besides competition and competitive exclusion, cooperative microbe-microbe interactions have to be carefully considered...

    Authors: Victor Mataigne, Nathan Vannier, Philippe Vandenkoornhuyse and Stéphane Hacquard
    Citation: Microbiome 2022 10:217
    Content type: Research Published on:

  10. Plants and their associated microbiota constitute an assemblage of species known as holobionts. The plant seed microbiome plays an important role in nutrient uptake and stress attenuation. However, the core ve...

    Authors: Xiaoxia Zhang, Yi-Nan Ma, Xing Wang, Kaiji Liao, Shanwen He, Xia Zhao, Hebao Guo, Dongfang Zhao and Hai-Lei Wei
    Citation: Microbiome 2022 10:216
    Content type: Research Published on:

  11. Mount Everest and the Mariana Trench represent the highest and deepest places on Earth, respectively. They are geographically separated, with distinct extreme environmental parameters that provide unique habit...

    Authors: Yongqin Liu, Zhihao Zhang, Mukan Ji, Aoran Hu, Jing Wang, Hongmei Jing, Keshao Liu, Xiang Xiao and Weishu Zhao
    Citation: Microbiome 2022 10:215
    Content type: Research Published on:

  12. While microbiomes in industrialized societies are well characterized, indigenous populations with traditional lifestyles have microbiomes that are more akin to those of ancient humans. However, metagenomic dat...

    Authors: Mian Zi Tee, Yi Xian Er, Alice V. Easton, Nan Jiun Yap, Ii Li Lee, Joseph Devlin, Ze Chen, Kee Seong Ng, Poorani Subramanian, Angelina Angelova, Oyebola Oyesola, Shushan Sargsian, Romano Ngui, Daniel P. Beiting, Christopher Chiong Meng Boey, Kek Heng Chua…
    Citation: Microbiome 2022 10:214
    Content type: Research Published on:

  13. 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
    Content type: Research Published on:

  14. 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
    Content type: Software Published on:

  15. 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
    Content type: Research Published on:

  16. 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
    Content type: Brief Report Published on:

  17. 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
    Content type: Research Published on:

  18. 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
    Content type: Research Published on:

  19. 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
    Content type: Research Published on:

  20. 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
    Content type: Research Published on:

  22. 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
    Content type: Research Published on:

  23. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  26. 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
    Content type: Research Published on:

  27. 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
    Content type: Research Published on:

  28. 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
    Content type: Research Published on:

  29. 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
    Content type: Research Published on:

  30. 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
    Content type: Research Published on:

  31. 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
    Content type: Research Published on:

  32. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  34. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  37. 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:

  38. 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:

  39. 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

  40. 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:

  42. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:
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