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  1. Cystic Fibrosis (CF) is a genetic condition characterized by neutrophilic inflammation and recurrent infection of the airways. How these processes are initiated and perpetuated in CF remains largely unknown. W...

    Authors: Jose A. Caparrós-Martín, Montserrat Saladie, S. Patricia Agudelo-Romero, F. Jerry Reen, Robert S. Ware, Peter D. Sly, Stephen M. Stick and Fergal O’Gara
    Citation: Microbiome 2023 11:132
  2. Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active (“viable”) communi...

    Authors: Ya Wang, Kelsey N. Thompson, Yan Yan, Meghan I. Short, Yancong Zhang, Eric A. Franzosa, Jiaxian Shen, Erica M. Hartmann and Curtis Huttenhower
    Citation: Microbiome 2023 11:131
  3. Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiot...

    Authors: Mária Džunková, James J. La Clair, Tomáš Tyml, Devin Doud, Frederik Schulz, Samuel Piquer-Esteban, Dafne Porcel Sanchis, Andrew Osborn, David Robinson, Katherine B. Louie, Ben P. Bowen, Robert M. Bowers, Janey Lee, Vicente Arnau, Wladimiro Díaz-Villanueva, Ramunas Stepanauskas…
    Citation: Microbiome 2023 11:130
  4. Humans emit approximately 30 million microbial cells per hour into their immediate vicinity. However, sampling of aerosolized microbial taxa (aerobiome) remains largely uncharacterized due to the complexity an...

    Authors: Jarrad T. Hampton-Marcell, Aritra Ghosh, Mohamad Jafari Gukeh and Constantine M. Megaridis
    Citation: Microbiome 2023 11:129
  5. Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about mi...

    Authors: M. Laura Rolon, Xiaoqing Tan, Taejung Chung, Narjol Gonzalez-Escalona, Yi Chen, Dumitru Macarisin, Luke F. LaBorde and Jasna Kovac
    Citation: Microbiome 2023 11:128
  6. Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countr...

    Authors: Shantelle Claassen-Weitz, Sugnet Gardner-Lubbe, Yao Xia, Kilaza S. Mwaikono, Stephanie Harris Mounaud, William C. Nierman, Lesley Workman, Heather J. Zar and Mark P. Nicol
    Citation: Microbiome 2023 11:127
  7. Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequenc...

    Authors: De-Chen Lu, Feng-Qing Wang, Rudolf I. Amann, Hanno Teeling and Zong-Jun Du
    Citation: Microbiome 2023 11:126
  8. Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the mi...

    Authors: Nitin K. Singh, Jason M. Wood, Jose Patane, Livia Maria Silva Moura, Jonathan Lombardino, João Carlos Setubal and Kasthuri Venkateswaran
    Citation: Microbiome 2023 11:125
  9. The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiome...

    Authors: Marcus H. Y. Leung, Xinzhao Tong, Zhiyong Shen, Shicong Du, Philippe Bastien, Brice M. R. Appenzeller, Richard J. Betts, Sakina Mezzache, Nasrine Bourokba, Nukhet Cavusoglu, Luc Aguilar, Namita Misra, Cécile Clavaud and Patrick K. H. Lee
    Citation: Microbiome 2023 11:124
  10. Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by t...

    Authors: Yuan Liu, Scott G. Daniel, Hye-Eun Kim, Hyun Koo, Jonathan Korostoff, Flavia Teles, Kyle Bittinger and Geelsu Hwang
    Citation: Microbiome 2023 11:123
  11. 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 11:122

    The original article was published in Microbiome 2023 11:90

  12. The gut microbiome regulates host energy balance and adiposity-related metabolic consequences, but it remains unknown how the gut microbiome modulates body weight response to physical activity (PA).

    Authors: Kai Wang, Raaj S. Mehta, Wenjie Ma, Long H. Nguyen, Dong D. Wang, Andrew R. Ghazi, Yan Yan, Laila Al-Shaar, Yiqing Wang, Dong Hang, Benjamin C. Fu, Shuji Ogino, Eric B. Rimm, Frank B. Hu, Rachel N. Carmody, Wendy S. Garrett…
    Citation: Microbiome 2023 11:121
  13. Metformin, a type 2 diabetes treatment, improves the cognitive function of aged mice; however, whether the protective effects of metformin on cognitive function in aged mice are associated with the gut microbi...

    Authors: Xiaoqi Zhu, Junyan Shen, Shengyu Feng, Ce Huang, Hao Wang, Fengjiao Huo and Hailiang Liu
    Citation: Microbiome 2023 11:120
  14. Alterations in gut microbiota have been implicated in HIV infection and cardiovascular disease. However, how gut microbial alterations relate to host inflammation and metabolite profiles, and their relationshi...

    Authors: Zheng Wang, Brandilyn A. Peters, MacKenzie Bryant, David B. Hanna, Tara Schwartz, Tao Wang, Christopher C. Sollecito, Mykhaylo Usyk, Evan Grassi, Fanua Wiek, Lauren St. Peter, Wendy S. Post, Alan L. Landay, Howard N. Hodis, Kathleen M. Weber, Audrey French…
    Citation: Microbiome 2023 11:119
  15. Viruses play important roles in the ocean’s biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors ...

    Authors: Felipe H. Coutinho, Cynthia B. Silveira, Marta Sebastián, Pablo Sánchez, Carlos M. Duarte, Dolors Vaqué, Josep M. Gasol and Silvia G. Acinas
    Citation: Microbiome 2023 11:118
  16. The advent of culture-independent, next-generation DNA sequencing has led to the discovery of distinct lung bacterial communities. Studies of lung microbiome taxonomy often reveal only subtle differences betwe...

    Authors: Daniel G. Dunlap, Libing Yang, Shulin Qin, Kelvin Li, Adam Fitch, Laurence Huang, Bryan J. McVerry, Timothy W. Hand, Barbara A. Methé and Alison Morris
    Citation: Microbiome 2023 11:117
  17. Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities unde...

    Authors: Yang Liu, Hao Wang, Xun Qian, Jie Gu, Weimin Chen, Xihui Shen, Shiheng Tao, Shuo Jiao and Gehong Wei
    Citation: Microbiome 2023 11:109
  18. The insect hemolymph (blood-equivalent fluid), composed of a large number of hemocytes (blood cells) and a variety of soluble immune effectors, is hostile for pathogens including fungi. In order to survive in ...

    Authors: Jia-Lin Wang, Jing Sun, Ya-Jing Song, Huan-Huan Zheng, Gui-Jie Wang, Wen-Xia Luo, Li Li and Xu-Sheng Liu
    Citation: Microbiome 2023 11:116
  19. Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. Howe...

    Authors: Rubing Du, Wu Xiong, Lei Xu, Yan Xu and Qun Wu
    Citation: Microbiome 2023 11:115
  20. The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disr...

    Authors: Ikaia Leleiwi, Josué Rodriguez-Ramos, Michael Shaffer, Anice Sabag-Daigle, Katherine Kokkinias, Rory M. Flynn, Rebecca A. Daly, Linnea F. M. Kop, Lindsey M. Solden, Brian M. M. Ahmer, Mikayla A. Borton and Kelly C. Wrighton
    Citation: Microbiome 2023 11:114
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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

  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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

  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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

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