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  1. Viruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that i...

    Authors: Jing-Zhe Jiang, Yi-Fei Fang, Hong-Ying Wei, Peng Zhu, Min Liu, Wen-Guang Yuan, Li-Ling Yang, Ying-Xiang Guo, Tao Jin, Mang Shi, Tuo Yao, Jie Lu, Ling-Tong Ye, Shao-Kun Shi, Meng Wang, Ming Duan…
    Citation: Microbiome 2023 11:2
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2023 11:25

  2. Childhood cognitive development depends on neuroimmune interactions. Immunomodulation by early-life microbial exposure may influence neuropsychological function. In this study, we investigate the association b...

    Authors: Yinthe Dockx, Martin Täubel, Janneke Hogervorst, Leen Luyten, Martien Peusens, Leen Rasking, Hanne Sleurs, Katrien Witters, Michelle Plusquin, Maria Valkonen, Tim S. Nawrot and Lidia Casas
    Citation: Microbiome 2023 11:1
    Content type: Research Published on:

  3. The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune ...

    Authors: Yuan Huang, Wenlong Lu, Min Zeng, Xiaoyue Hu, Zhanhao Su, Yiwei Liu, Zeye Liu, Jianhui Yuan, Li Li, Xiaoling Zhang, Long Huang, Wanjin Hu, Xu Wang, Shoujun Li and Hao Zhang
    Citation: Microbiome 2022 10:245
    Content type: Research Published on:

  5. Alterations to the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous fact...

    Authors: B. J. Kunath, O. Hickl, P. Queirós, C. Martin-Gallausiaux, L. A. Lebrun, R. Halder, C. C. Laczny, T. S. B. Schmidt, M. R. Hayward, D. Becher, A. Heintz-Buschart, C. de Beaufort, P. Bork, P. May and P. Wilmes
    Citation: Microbiome 2022 10:243
    Content type: Research Published on:

  6. Considerable research has focussed on the importance of bacterial communities within the vertebrate gut microbiome (GM). However, studies investigating the significance of other microbial kingdoms, such as fun...

    Authors: Sarah F. Worsley, Charli S. Davies, Maria-Elena Mannarelli, Jan Komdeur, Hannah L. Dugdale and David S. Richardson
    Citation: Microbiome 2022 10:242
    Content type: Research Published on:

  7. When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich dive...

    Authors: Zhichao Zhou, Emily St. John, Karthik Anantharaman and Anna-Louise Reysenbach
    Citation: Microbiome 2022 10:241
    Content type: Research Published on:

  8. Early childhood caries (ECC)—dental caries (cavities) occurring in primary teeth up to age 6 years—is a prevalent childhood oral disease with a microbial etiology. Streptococcus mutans was previously considered a...

    Authors: Freida Blostein, Deesha Bhaumik, Elyse Davis, Elizabeth Salzman, Kerby Shedden, Melissa Duhaime, Kelly M. Bakulski, Daniel W. McNeil, Mary L. Marazita and Betsy Foxman
    Citation: Microbiome 2022 10:240
    Content type: Research Published on:

  9. The opportunistic pathogen Staphylococcus aureus is an asymptomatically carried member of the microbiome of about one third of the human population at any given point in time. Body sites known to harbor S. aureus

    Authors: Elisa J. M. Raineri, Sandra Maaß, Min Wang, Siobhan Brushett, Laura M. Palma Medina, Neus Sampol Escandell, Dania Altulea, Erwin Raangs, Anne de Jong, Elias Vera Murguia, Edward J. Feil, Alex W. Friedrich, Girbe Buist, Dörte Becher, Silvia García-Cobos, Natacha Couto…
    Citation: Microbiome 2022 10:239
    Content type: Research Published on:

  10. Aging is a natural process that an organism gradually loses its physical fitness and functionality. Great efforts have been made to understand and intervene in this deteriorating process. The gut microbiota af...

    Authors: Kwang H. Kim, Yusook Chung, Ji-Won Huh, Dong Jin Park, Yejin Cho, Yeseul Oh, Haengdueng Jeong, Jaekyung Yoon, Ju-Hee Kang, Hae-Sol Shin, Hyoung-Chin Kim, Soon-Kyeong Kwon, Kyoung Yul Seo, Seung Hyun Oh, Je Kyung Seong, Sang-Jun Ha…
    Citation: Microbiome 2022 10:238
    Content type: Research Published on:

  11. The Arctic Ocean receives massive freshwater input and a correspondingly large amount of humic-rich organic matter of terrestrial origin. Global warming, permafrost melt, and a changing hydrological cycle will...

    Authors: Thomas Grevesse, Céline Guéguen, Vera E. Onana and David A. Walsh
    Citation: Microbiome 2022 10:237
    Content type: Research Published on:

  12. The rapid and accurate identification of a minimal-size core set of representative microbial species plays an important role in the clustering of microbial community data and interpretation of clustering resul...

    Authors: Tung Dang, Kie Kumaishi, Erika Usui, Shungo Kobori, Takumi Sato, Yusuke Toda, Yuji Yamasaki, Hisashi Tsujimoto, Yasunori Ichihashi and Hiroyoshi Iwata
    Citation: Microbiome 2022 10:236
    Content type: Methodology Published on:

  14. Exposure to zearalenone (ZEN, a widespread Fusarium mycotoxin) causes reproductive toxicity and immunotoxicity in farm animals, and it then poses potential threats to human health through the food chain. A system...

    Authors: Shujin Wang, Wei Fu, Xueya Zhao, Xiaojiao Chang, Hujun Liu, Lin Zhou, Jian Li, Rui Cheng, Xin Wu, Xi Li and Changpo Sun
    Citation: Microbiome 2022 10:234
    Content type: Research Published on:

  15. Plant-microbe interactions dynamically affect plant growth, health, and development. The mechanisms underpinning these associations are—to a large extent—mediated by specialized host-derived secondary metaboli...

    Authors: Lanxiang Wang, Moxian Chen, Pui-Ying Lam, Francisco Dini-Andreote, Lei Dai and Zhong Wei
    Citation: Microbiome 2022 10:233
    Content type: Comment Published on:

  17. Rice-fish symbiosis, as an ecological and green aquaculture model, is an effective measure to relieve the environmental stress from intensive aquaculture. Compared with traditional aquaculture, the altered rea...

    Authors: Erlong Wang, Ya Zhou, Yue Liang, Fei Ling, Xiaoshu Xue, Xianlin He, Xuliang Zhai, Yang Xue, Chunlong Zhou, Guo Tang and Gaoxue Wang
    Citation: Microbiome 2022 10:231
    Content type: Research Published on:

  18. The gastrointestinal ecosystem is a highly complex environment with a profound influence on human health. Inflammation in the gut, linked to an altered gut microbiome, has been associated with the development ...

    Authors: Patrick G. Gavin, Ki Wook Kim, Maria E. Craig, Michelle M. Hill and Emma E. Hamilton-Williams
    Citation: Microbiome 2022 10:230
    Content type: Research Published on:

  19. Intestinal helminths are extremely prevalent among humans and animals. In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry. These p...

    Authors: Ankur Midha, Víctor Hugo Jarquín-Díaz, Friederike Ebner, Ulrike Löber, Rima Hayani, Arkadi Kundik, Alessio Cardilli, Emanuel Heitlinger, Sofia Kirke Forslund and Susanne Hartmann
    Citation: Microbiome 2022 10:229
    Content type: Research Published on:

  20. Authors: Fei Xie, Wei Jin, Huazhe Si, Yuan Yuan, Ye Tao, Junhua Liu, Xiaoxu Wang, Chengjian Yang, Qiushuang Li, Xiaoting Yan, Limei Lin, Qian Jiang, Lei Zhang, Changzheng Guo, Chris Greening, Rasmus Heller…
    Citation: Microbiome 2022 10:228
    Content type: Correction Published on:

    The original article was published in Microbiome 2021 9:137

  21. Ralstonia solanacearum (Rs) is a soilborne phytopathogen that causes bacterial wilt and substantial yield losses in many plants, such as tomatoes. A resistant tomato cultivar can recruit a beneficial microbiome f...

    Authors: Jiakang Yin, Ziliang Zhang, Chengcheng Zhu, Taotao Wang, Ruihong Wang and Lifang Ruan
    Citation: Microbiome 2022 10:227
    Content type: Research Published on:

  22. High intake of caffeoylquinic acid (CQA)-rich dietary supplements, such as green coffee bean extracts, offers health-promoting effects on maintaining metabolic homeostasis. Similar to many active herbal ingred...

    Authors: Yameng Liu, Xianchun Zhong, Suqin Lin, Hualing Xu, Xinyu Liang, Yibin Wang, Jingyi Xu, Kanglong Wang, Xiaozhen Guo, Jiawen Wang, Minjun Yu, Cuina Li and Cen Xie
    Citation: Microbiome 2022 10:226
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2023 11:182

  23. The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datas...

    Authors: Stephanie D. Jurburg, François Buscot, Antonis Chatzinotas, Narendrakumar M. Chaudhari, Adam T. Clark, Magda Garbowski, Matthias Grenié, Erik F. Y. Hom, Canan Karakoç, Susanne Marr, Steffen Neumann, Mika Tarkka, Nicole M. van Dam, Alexander Weinhold and Anna Heintz-Buschart
    Citation: Microbiome 2022 10:225
    Content type: Comment Published on:

  24. 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

  25. 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:

  26. 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:

  27. 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

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:
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