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  1. Planktonic microbial communities have critical impacts on the pelagic food web and water quality status in freshwater ecosystems, yet no general model of bacterial community assembly linked to higher trophic l...

    Authors: Hongjae Park, Tanja Shabarova, Michaela M. Salcher, Lenka Kosová, Pavel Rychtecký, Indranil Mukherjee, Karel Šimek, Petr Porcal, Jaromír Seďa, Petr Znachor and Vojtěch Kasalický
    Citation: Microbiome 2023 11:112
  2. Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem, the interact...

    Authors: Quentin Lamy-Besnier, Amaury Bignaud, Julian R. Garneau, Marie Titecat, Devon E. Conti, Alexandra Von Strempel, Marc Monot, Bärbel Stecher, Romain Koszul, Laurent Debarbieux and Martial Marbouty
    Citation: Microbiome 2023 11:111
  3. Understanding the ecological and environmental functions of phototrophic biofilms in the biological crust is crucial for improving metal(loid) (e.g. Cd, As) bioremediation in mining ecosystems. In this study, in ...

    Authors: Guobao Wang, Xiuran Yin, Zekai Feng, Chiyu Chen, Daijie Chen, Bo Wu, Chong Liu, Jean Louis Morel, Yuanyuan Jiang, Hang Yu, Huan He, Yuanqing Chao, Yetao Tang, Rongliang Qiu and Shizhong Wang
    Citation: Microbiome 2023 11:110
  4. Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen dep...

    Authors: Alison Gallet, Sébastien Halary, Charlotte Duval, Hélène Huet, Sébastien Duperron and Benjamin Marie
    Citation: Microbiome 2023 11:108
  5. The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that ...

    Authors: Shun Yao, Tianzhi Jin, Lu Zhang, Yong Zhang, Rui Chen, Qian Wang, Mingjie Lv, Chuxiao Hu, Ting Ma and Wenjie Xia
    Citation: Microbiome 2023 11:107
  6. Marine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to...

    Authors: Michelle A. Hauer, Corinna Breusing, Elizabeth Trembath-Reichert, Julie A. Huber and Roxanne A. Beinart
    Citation: Microbiome 2023 11:106
  7. Over the past years, sequencing technologies have expanded our ability to examine novel microbial metabolisms and diversity previously obscured by isolation approaches. Long-read sequencing promises to revolut...

    Authors: Luis H. Orellana, Karen Krüger, Chandni Sidhu and Rudolf Amann
    Citation: Microbiome 2023 11:105
  8. Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, the...

    Authors: Adrien Vigneron, Perrine Cruaud, Connie Lovejoy and Warwick F. Vincent
    Citation: Microbiome 2023 11:104
  9. Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have b...

    Authors: Cassandra L. Ettinger, Morgan Saunders, Laura Selbmann, Manuel Delgado-Baquerizo, Claudio Donati, Davide Albanese, Simon Roux, Susannah Tringe, Christa Pennacchio, Tijana G. del Rio, Jason E. Stajich and Claudia Coleine
    Citation: Microbiome 2023 11:103
  10. The intestinal epithelial barrier confers protection against the intestinal invasion by pathogens and exposure to food antigens and toxins. Growing studies have linked the gut microbiota to the intestinal epit...

    Authors: Jun Hu, Jianwei Chen, Xiaojian Xu, Qiliang Hou, Jing Ren and Xianghua Yan
    Citation: Microbiome 2023 11:102

    The Correction to this article has been published in Microbiome 2023 11:113

  11. The pathogenic viruses transmitted by mosquitoes cause a variety of animal and human diseases and public health concerns. Virome surveillance is important for the discovery, and control of mosquito-borne patho...

    Authors: Qing Liu, Feng Cui, Xiang Liu, Yumei Fu, Wenjing Fang, Xun Kang, Hong Lu, Siping Li, Biao Liu, Wei Guo, Qianfeng Xia, Le Kang and Feng Jiang
    Citation: Microbiome 2023 11:101
  12. The gut microbiota is implicated in the pathogenesis of colorectal cancer (CRC). We aimed to map the CRC mucosal microbiota and metabolome and define the influence of the tumoral microbiota on oncological outc...

    Authors: James L. Alexander, Joram M. Posma, Alasdair Scott, Liam Poynter, Sam E. Mason, M. Luisa Doria, Lili Herendi, Lauren Roberts, Julie A. K. McDonald, Simon Cameron, David J. Hughes, Vaclav Liska, Simona Susova, Pavel Soucek, Verena Horneffer-van der Sluis, Maria Gomez-Romero…
    Citation: Microbiome 2023 11:100
  13. During the course of history, various important lifestyle changes have caused profound transitions of the gut microbiome. These include the introduction of agriculture and animal husbandry, a shift from a noma...

    Authors: Eduard W. J. van der Vossen, Mark Davids, Lucas R. F. Bresser, Henrike Galenkamp, Bert-Jan H. van den Born, Aeilko H. Zwinderman, Evgeni Levin, Max Nieuwdorp and Marcus C. de Goffau
    Citation: Microbiome 2023 11:99
  14. Some insects can degrade both natural and synthetic plastic polymers, their host and gut microbes play crucial roles in this process. However, there is still a scientific gap in understanding how the insect ad...

    Authors: Tursunay Mamtimin, Huawen Han, Aman Khan, Pengya Feng, Qing Zhang, Xiaobiao Ma, Yitian Fang, Pu Liu, Saurabh Kulshrestha, Toshiro Shigaki and Xiangkai Li
    Citation: Microbiome 2023 11:98
  15. Tetramates or tetramic acid-containing compounds (TACs) are a group of bioactive natural products featuring a pyrrolidine-2,4-dione ring acknowledged being closed via Dieckmann cyclization. The cariogenic Strepto...

    Authors: Yuwei Zhang, Ge Liao, Min Wang, Zhao Zhang, Liwei Liu, Yuqin Song, Dacheng Wang, Tingting Hao, Jie Feng, Bin Xia, Yixiang Wang, Xiaoyu Tang and Yihua Chen
    Citation: Microbiome 2023 11:97
  16. The Western dietary pattern, characterized by high consumption of fats and sugars, has been strongly associated with an increased risk of developing Crohn’s disease (CD). However, the potential impact of mater...

    Authors: Chongyang Huang, Huishi Tan, Mengyao Song, Ke Liu, Hongbin Liu, Jun Wang, Yanqiang Shi, Fengyi Hou, Qian Zhou, Ruo Huang, Binghai Shen, Xinlong Lin, Xiaoming Qin and Fachao Zhi
    Citation: Microbiome 2023 11:96
  17. For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cyc...

    Authors: Lingyue Zhu, Yan Chen, Ruibo Sun, Jiabao Zhang, Lauren Hale, Kenneth Dumack, Stefan Geisen, Ye Deng, Yinghua Duan, Bo Zhu, Yan Li, Wenzhao Liu, Xiaoyue Wang, Bryan S. Griffiths, Michael Bonkowski, Jizhong Zhou…
    Citation: Microbiome 2023 11:95
  18. Excessive hedonic consumption is one of the main drivers for weight gain. Identifying contributors of this dysregulation would help to tackle obesity. The gut microbiome is altered during obesity and regulates...

    Authors: Alice de Wouters d’Oplinter, Marko Verce, Sabrina J. P. Huwart, Jacob Lessard-Lord, Clara Depommier, Matthias Van Hul, Yves Desjardins, Patrice D. Cani and Amandine Everard
    Citation: Microbiome 2023 11:94
  19. Microbiome alterations have been associated with depression, and fecal transfer of depressed patients’ microbiomes is sufficient to enhance despair behaviors in rodents. Yet little is known about the potential...

    Authors: Eva M. Medina-Rodriguez, Jowan Watson, Juliana Reyes, Madhukar Trivedi and Eléonore Beurel
    Citation: Microbiome 2023 11:92
  20. Lactic acid bacteria (LAB) produce various bioactive secondary metabolites (SMs), which endow LAB with a protective role for the host. However, the biosynthetic potentials of LAB-derived SMs remain elusive, pa...

    Authors: Dengwei Zhang, Jian Zhang, Shanthini Kalimuthu, Jing Liu, Zhi-Man Song, Bei-bei He, Peiyan Cai, Zheng Zhong, Chenchen Feng, Prasanna Neelakantan and Yong-Xin Li
    Citation: Microbiome 2023 11:91
  21. The continuous proliferation of intestinal stem cells followed by their tightly regulated differentiation to epithelial cells is essential for the maintenance of the gut epithelial barrier and its functions. H...

    Authors: Renan Oliveira Corrêa, Pollyana Ribeiro Castro, José Luís Fachi, Vinícius Dias Nirello, Salma El-Sahhar, Shinya Imada, Gabriel Vasconcelos Pereira, Laís Passariello Pral, Nathália Vitoria Pereira Araújo, Mariane Font Fernandes, Valquíria Aparecida Matheus, Jaqueline de Souza Felipe, Arilson Bernardo dos Santos Pereira Gomes, Sarah de Oliveira, Vinícius de Rezende Rodovalho, Samantha Roberta Machado de Oliveira…
    Citation: Microbiome 2023 11:90

    The Correction to this article has been published in Microbiome 2023 11:122

  22. Coral meta-organisms consist of the coral, and its associated Symbiodiniaceae (dinoflagellate algae), bacteria, and other microbes. Corals can acquire photosynthates from Symbiodiniaceae, whilst Symbiodiniacea...

    Authors: Haoya Tong, Fang Zhang, Jin Sun, Shelby E. McIlroy, Weipeng Zhang, Yan Wang, Hui Huang, Guowei Zhou and Pei-Yuan Qian
    Citation: Microbiome 2023 11:89
  23. Psychological health risk is one of the most severe and complex risks in manned deep-space exploration and long-term closed environments. Recently, with the in-depth research of the microbiota–gut–brain axis, ...

    Authors: Zikai Hao, Chen Meng, Leyuan Li, Siyuan Feng, Yinzhen Zhu, Jianlou Yang, Liangzhe Han, Leilei Sun, Weifeng Lv, Daniel Figeys and Hong Liu
    Citation: Microbiome 2023 11:88
  24. Dairy cows are susceptible to postpartum systemic oxidative stress (OS), which leads to significant production loss and metabolic disorders. The gut microbiota has been linked to host health and stress levels....

    Authors: Fengfei Gu, Senlin Zhu, Jinxiu Hou, Yifan Tang, Jian-Xin Liu, Qingbiao Xu and Hui-Zeng Sun
    Citation: Microbiome 2023 11:87
  25. We aimed to identify mucin-microbiome signatures shaping the tumor microenvironment in gastric adenocarcinomas and clinical outcomes.

    Authors: Baptiste Oosterlinck, Hannah Ceuleers, Wout Arras, Joris G. De Man, Karen Geboes, Heiko De Schepper, Marc Peeters, Sarah Lebeer, Jurgita Skieceviciene, Georgina L. Hold, Juozas Kupcinskas, Alexander Link, Benedicte Y. De Winter and Annemieke Smet
    Citation: Microbiome 2023 11:86
  26. Plants sustain intimate relationships with diverse microbes. It is well-recognized that these plant-associated microbiota shape individual performance and fitness of host plants, but much remains to be explore...

    Authors: Zhiqiang Pang, Xinyu Mao, Shaoqun Zhou, Sheng Yu, Guizhou Liu, Chengkai Lu, Jinpeng Wan, Lingfei Hu and Peng Xu
    Citation: Microbiome 2023 11:85
  27. The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-...

    Authors: Siu Fung Stanley Ho, Nicole E. Wheeler, Andrew D. Millard and Willem van Schaik
    Citation: Microbiome 2023 11:84
  28. Microbial interactions are fundamental for Earth’s ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in ...

    Authors: Ina Maria Deutschmann, Anders K. Krabberød, Francisco Latorre, Erwan Delage, Cèlia Marrasé, Vanessa Balagué, Josep M. Gasol, Ramon Massana, Damien Eveillard, Samuel Chaffron and Ramiro Logares
    Citation: Microbiome 2023 11:83
  29. Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, s...

    Authors: Dandan Zhang, Huang Yu, Yuchun Yang, Fei Liu, Mingyue Li, Jie Huang, Yuhe Yu, Cheng Wang, Feng Jiang, Zhili He and Qingyun Yan
    Citation: Microbiome 2023 11:82
  30. A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies sug...

    Authors: Tiantian Yu, Weichao Wu, Wenyue Liang, Yinzhao Wang, Jialin Hou, Yunru Chen, Marcus Elvert, Kai-Uwe Hinrichs and Fengping Wang
    Citation: Microbiome 2023 11:81
  31. Understanding human genetic influences on the gut microbiota helps elucidate the mechanisms by which genetics may influence health outcomes. Typical microbiome genome-wide association studies (GWAS) marginally...

    Authors: Hongjiao Liu, Wodan Ling, Xing Hua, Jee-Young Moon, Jessica S. Williams-Nguyen, Xiang Zhan, Anna M. Plantinga, Ni Zhao, Angela Zhang, Rob Knight, Qibin Qi, Robert D. Burk, Robert C. Kaplan and Michael C. Wu
    Citation: Microbiome 2023 11:80
  32. While the rootstock genotype (belowground part of a plant) can impact rhizosphere microbial communities, few studies have examined the relationships between rootstock genotype-based recruitment of active rhizo...

    Authors: Antonio Castellano-Hinojosa, Ute Albrecht and Sarah L. Strauss
    Citation: Microbiome 2023 11:79
  33. Mastitis is one of the most severe diseases in humans and animals, especially on dairy farms. Mounting evidence indicates that gastrointestinal dysbiosis caused by induction of subacute ruminal acidosis (SARA)...

    Authors: Caijun Zhao, Xiaoyu Hu, Min Qiu, Lijuan Bao, Keyi Wu, Xiangyue Meng, Yihong Zhao, Lianjun Feng, Shiyu Duan, Yuhong He, Naisheng Zhang and Yunhe Fu
    Citation: Microbiome 2023 11:78
  34. Blooms of marine microalgae play a pivotal role in global carbon cycling. Such blooms entail successive blooms of specialized clades of planktonic bacteria that collectively remineralize gigatons of algal biom...

    Authors: Chandni Sidhu, Inga V. Kirstein, Cédric L. Meunier, Johannes Rick, Vera Fofonova, Karen H. Wiltshire, Nicola Steinke, Silvia Vidal-Melgosa, Jan-Hendrik Hehemann, Bruno Huettel, Thomas Schweder, Bernhard M. Fuchs, Rudolf I. Amann and Hanno Teeling
    Citation: Microbiome 2023 11:77
  35. Ruminants can utilize urea as a dietary nitrogen source owing to their ability to recycle urea-N back to the rumen where numerous ureolytic bacteria hydrolyze urea into ammonia, which is used by numerous bacte...

    Authors: Sijia Liu, Zhongtang Yu, Huiyue Zhong, Nan Zheng, Sharon Huws, Jiaqi Wang and Shengguo Zhao
    Citation: Microbiome 2023 11:76
  36. Captive koala breeding programmes are essential for long-term species management. However, breeding efficacy is frequently impacted by high neonatal mortality rates in otherwise healthy females. Loss of pouch ...

    Authors: Toby I. Maidment, Emily R. Bryan, Michael Pyne, Michele Barnes, Sarah Eccleston, Samantha Cunningham, Emma Whitlock, Kelsie Redman, Vere Nicolson, Kenneth W. Beagley and Elise Pelzer
    Citation: Microbiome 2023 11:75
  37. Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of...

    Authors: Haoyu Liang, Zhi-Man Song, Zheng Zhong, Dengwei Zhang, Wei Yang, Le Zhou, Ethan A. Older, Jie Li, Huan Wang, Zhirui Zeng and Yong-Xin Li
    Citation: Microbiome 2023 11:74
  38. Effects of antibiotics on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the fungal microbiota (mycobiota). It is commonly believed that fungal loa...

    Authors: Madeleine Spatz, Gregory Da Costa, Rebecka Ventin-Holmberg, Julien Planchais, Chloé Michaudel, Yazhou Wang, Camille Danne, Alexia Lapiere, Marie-Laure Michel, Kaija-Leena Kolho, Philippe Langella, Harry Sokol and Mathias L. Richard
    Citation: Microbiome 2023 11:73
  39. Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove w...

    Authors: Lu Qian, Xiaoli Yu, Hang Gu, Fei Liu, Yijun Fan, Cheng Wang, Qiang He, Yun Tian, Yisheng Peng, Longfei Shu, Shanquan Wang, Zhijian Huang, Qingyun Yan, Jianguo He, Guangli Liu, Qichao Tu…
    Citation: Microbiome 2023 11:71
  40. The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication build...

    Authors: Hong Yue, Wenjie Yue, Shuo Jiao, Hyun Kim, Yong-Hwan Lee, Gehong Wei, Weining Song and Duntao Shu
    Citation: Microbiome 2023 11:70
  41. Dental erosion is a disease of the oral cavity where acids cause a loss of tooth enamel and is defined as having no bacterial involvement. The tooth surface is protected from acid attack by salivary proteins t...

    Authors: Leanne M. Cleaver, Miguel Carda-Diéguez, Rebeca Moazzez and Guy H. Carpenter
    Citation: Microbiome 2023 11:69
  42. Many animals and plants acquire their coevolved symbiotic partners shortly post-embryonic development. Thus, during embryogenesis, cellular features must be developed that will promote both symbiont colonizati...

    Authors: Tara Essock-Burns, Susannah Lawhorn, Leo Wu, Sawyer McClosky, Silvia Moriano-Gutierrez, Edward G. Ruby and Margaret J. McFall-Ngai
    Citation: Microbiome 2023 11:68
  43. The majority of studies characterizing female genital tract microbiota have focused on luminal organisms, while the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood...

    Authors: Gabriella Edfeldt, Vilde Kaldhusdal, Paulo Czarnewski, Frideborg Bradley, Sofia Bergström, Julie Lajoie, Jiawu Xu, Anna Månberg, Joshua Kimani, Julius Oyugi, Peter Nilsson, Annelie Tjernlund, Keith R. Fowke, Douglas S. Kwon and Kristina Broliden
    Citation: Microbiome 2023 11:67
  44. Crohn’s disease (CD) is associated with changes in the microbiota, and murine models of CD-like ileo-colonic inflammation depend on the presence of microbial triggers. Increased abundance of unknown Clostridia...

    Authors: Amira Metwaly, Jelena Jovic, Nadine Waldschmitt, Sevana Khaloian, Helena Heimes, Deborah Häcker, Mohamed Ahmed, Nassim Hammoudi, Lionel Le Bourhis, Aida Mayorgas, Kolja Siebert, Marijana Basic, Tobias Schwerd, Matthieu Allez, Julian Panes, Azucena Salas…
    Citation: Microbiome 2023 11:66
  45. The COVID-19 pandemic has highlighted the extent to which the public transportation environment, such as in subways, may be important for the transmission of potential pathogenic microbes among humans, with th...

    Authors: Maria D’Accolti, Irene Soffritti, Francesca Bini, Eleonora Mazziga, Carolina Cason, Manola Comar, Antonella Volta, Matteo Bisi, Daniele Fumagalli, Sante Mazzacane and Elisabetta Caselli
    Citation: Microbiome 2023 11:64
  46. Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult bec...

    Authors: Hiroaki Fujita, Masayuki Ushio, Kenta Suzuki, Masato S. Abe, Masato Yamamichi, Koji Iwayama, Alberto Canarini, Ibuki Hayashi, Keitaro Fukushima, Shinji Fukuda, E. Toby Kiers and Hirokazu Toju
    Citation: Microbiome 2023 11:63
  47. Dysbiotic gut microbiome, genetically predisposed or chemically disrupted, has been linked with insulin-dependent diabetes (IDD) including autoimmune type 1 diabetes (T1D) in both humans and animal models. How...

    Authors: Xin Yang, Zhiyi Wang, Junling Niu, Rui Zhai, Xinhe Xue, Guojun Wu, Yuanyuan Fang, Guangxun Meng, Huijuan Yuan, Liping Zhao and Chenhong Zhang
    Citation: Microbiome 2023 11:62

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