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  1. The virome of lung transplant recipients (LTRs) under immunosuppressive therapy is dominated by non-pathogenic Anelloviridae and further includes several pathogenic viruses such as Herpesviruses or respiratory vi...

    Authors: Stefanie Widder, Irene Görzer, Benjamin Friedel, Nina Rahimi, Stefan Schwarz, Peter Jaksch, Sylvia Knapp and Elisabeth Puchhammer-Stöckl
    Citation: Microbiome 2022 10:66
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:81

  2. Critically ill 2019 coronavirus disease (COVID-19) patients under invasive mechanical ventilation (IMV) are 10 to 40 times more likely to die than the general population. Although progression from mild to seve...

    Authors: Jairo R. Temerozo, Natalia Fintelman-Rodrigues, Monique Cristina dos Santos, Eugenio D. Hottz, Carolina Q. Sacramento, Aline de Paula Dias da Silva, Samuel Coelho Mandacaru, Emilly Caroline dos Santos Moraes, Monique R. O. Trugilho, João S. M. Gesto, Marcelo Alves Ferreira, Felipe Betoni Saraiva, Lohanna Palhinha, Remy Martins-Gonçalves, Isaclaudia Gomes Azevedo-Quintanilha, Juliana L. Abrantes…
    Citation: Microbiome 2022 10:65
    Content type: Research Published on:

  3. Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Microbial sul...

    Authors: Patricia G. Wolf, Elise S. Cowley, Adam Breister, Sarah Matatov, Luke Lucio, Paige Polak, Jason M. Ridlon, H. Rex Gaskins and Karthik Anantharaman
    Citation: Microbiome 2022 10:64
    Content type: Research Published on:

  4. It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental ris...

    Authors: Jiajin Song, Tongxin Li, Zhiruo Zheng, Wenjie Fu, Zhengnan Long, Nan Shi, Yuling Han, Luqing Zhang, Yunlong Yu and Hua Fang
    Citation: Microbiome 2022 10:63
    Content type: Research Published on:

  5. Chronic cerebral hypoperfusion (CCH) underlies secondary brain injury following certain metabolic disorders and central nervous system (CNS) diseases. Dysregulation of the microbiota-gut-brain axis can exacerb...

    Authors: Weiping Xiao, Jiabin Su, Xinjie Gao, Heng Yang, Ruiyuan Weng, Wei Ni and Yuxiang Gu
    Citation: Microbiome 2022 10:62
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:70

  6. Access to antiretroviral therapy (ART) during pregnancy and breastfeeding for mothers with HIV has resulted in fewer children acquiring HIV peri- and postnatally, resulting in an increase in the number of chil...

    Authors: Silvia Grant-Beurmann, Jibreel Jumare, Nicaise Ndembi, Olayemi Matthew, Ashley Shutt, Augustine Omoigberale, Olivia A. Martin, Claire M. Fraser and Man Charurat
    Citation: Microbiome 2022 10:61
    Content type: Research Published on:

  7. Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife.

    Authors: Tongling Shan, Shixing Yang, Haoning Wang, Hao Wang, Ju Zhang, Ga Gong, Yuqing Xiao, Jie Yang, Xiaolong Wang, Juan Lu, Min Zhao, Zijun Yang, Xiang Lu, Ziyuan Dai, Yumin He, Xu Chen…
    Citation: Microbiome 2022 10:60
    Content type: Research Published on:

  8. The potential role of the gut microbiome as a predictor of immune-mediated HIV-1 control in the absence of antiretroviral therapy (ART) is still unknown. In the BCN02 clinical trial, which combined the MVA.HIV...

    Authors: Alessandra Borgognone, Marc Noguera-Julian, Bruna Oriol, Laura Noël-Romas, Marta Ruiz-Riol, Yolanda Guillén, Mariona Parera, Maria Casadellà, Clara Duran, Maria C. Puertas, Francesc Català-Moll, Marlon De Leon, Samantha Knodel, Kenzie Birse, Christian Manzardo, José M. Miró…
    Citation: Microbiome 2022 10:59
    Content type: Research Published on:

  10. Caloric restriction can delay the development of metabolic diseases ranging from insulin resistance to type 2 diabetes and is linked to both changes in the composition and metabolic function of the gut microbi...

    Authors: Julia Sbierski-Kind, Sophia Grenkowitz, Stephan Schlickeiser, Arvid Sandforth, Marie Friedrich, Désirée Kunkel, Rainer Glauben, Sebastian Brachs, Knut Mai, Andrea Thürmer, Aleksandar Radonić, Oliver Drechsel, Peter J. Turnbaugh, Jordan E. Bisanz, Hans-Dieter Volk, Joachim Spranger…
    Citation: Microbiome 2022 10:57
    Content type: Research Published on:

  11. Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, ...

    Authors: Pu-Dong Li, Zeng-Rong Zhu, Yunzeng Zhang, Jianping Xu, Hongkai Wang, Zhengyi Wang and Hongye Li
    Citation: Microbiome 2022 10:56
    Content type: Research Published on:

  14. The understanding of how microbiomes assemble, function, and evolve requires metagenomic tools that can resolve microbiota compositions at the strain level. However, the identification and tracking of microbia...

    Authors: Daniel Podlesny, Cesar Arze, Elisabeth Dörner, Sandeep Verma, Sudhir Dutta, Jens Walter and W. Florian Fricke
    Citation: Microbiome 2022 10:53
    Content type: Research Published on:

  15. The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. He...

    Authors: Bin Liu, Heike Sträuber, João Saraiva, Hauke Harms, Sandra Godinho Silva, Jonas Coelho Kasmanas, Sabine Kleinsteuber and Ulisses Nunes da Rocha
    Citation: Microbiome 2022 10:48
    Content type: Research Published on:

  16. Elucidating the spatial structure of host-associated microbial communities is essential for understanding taxon-taxon interactions within the microbiota and between microbiota and host. Macroalgae are colonize...

    Authors: S. Tabita Ramírez-Puebla, Brooke L. Weigel, Loretha Jack, Cathleen Schlundt, Catherine A. Pfister and Jessica L. Mark Welch
    Citation: Microbiome 2022 10:52
    Content type: Research Published on:

  17. Cryoconite granules are mineral–microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier eco...

    Authors: Takumi Murakami, Nozomu Takeuchi, Hiroshi Mori, Yuu Hirose, Arwyn Edwards, Tristram Irvine-Fynn, Zhongqin Li, Satoshi Ishii and Takahiro Segawa
    Citation: Microbiome 2022 10:50
    Content type: Research Published on:

  19. Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of...

    Authors: Ann C. Gregory, Kenji Gerhardt, Zhi-Ping Zhong, Benjamin Bolduc, Ben Temperton, Konstantinos T. Konstantinidis and Matthew B. Sullivan
    Citation: Microbiome 2022 10:49
    Content type: Software article Published on:

  20. The gut microbiota can affect neurologic disease by shaping microglia, the primary immune cell in the central nervous system (CNS). While antibiotics improve models of Alzheimer’s disease, Parkinson’s disease,...

    Authors: Laura M. Cox, Narghes Calcagno, Christian Gauthier, Charlotte Madore, Oleg Butovsky and Howard L. Weiner
    Citation: Microbiome 2022 10:47
    Content type: Short report Published on:

  21. Clustering the metagenomic contigs into potential genomes is a key step to investigate the functional roles of microbial populations. Existing algorithms have achieved considerable success with simulated or re...

    Authors: Cong-Cong Liu, Shan-Shan Dong, Jia-Bin Chen, Chen Wang, Pan Ning, Yan Guo and Tie-Lin Yang
    Citation: Microbiome 2022 10:46
    Content type: Methodology Published on:

  22. The causative agent of Chagas disease, Trypanosoma cruzi, and its nonpathogenic relative, Trypanosoma rangeli, are transmitted by haematophagous triatomines and undergo a crucial ontogenetic phase in the insect’s...

    Authors: Fanny E. Eberhard, Sven Klimpel, Alessandra A. Guarneri and Nicholas J. Tobias
    Citation: Microbiome 2022 10:45
    Content type: Research Published on:

  23. The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of

    Authors: Kieran A. Bates, Ulf Sommer, Kevin P. Hopkins, Jennifer M. G. Shelton, Claudia Wierzbicki, Christopher Sergeant, Benjamin Tapley, Christopher J. Michaels, Dirk S. Schmeller, Adeline Loyau, Jaime Bosch, Mark R. Viant, Xavier A. Harrison, Trenton W. J. Garner and Matthew C. Fisher
    Citation: Microbiome 2022 10:44
    Content type: Research Published on:

  24. The human intestinal microbiome is a complex community that contributes to host health and disease. In addition to normal microbiota, pathogens like carbapenem-resistant Enterobacteriaceae may be asymptomatically...

    Authors: Choon K. Sim, Sara Saheb Kashaf, Apollo Stacy, Diana M. Proctor, Alexandre Almeida, Nicolas Bouladoux, Mark Chen, Robert D. Finn, Yasmine Belkaid, Sean Conlan and Julia A. Segre
    Citation: Microbiome 2022 10:43
    Content type: Research Published on:

  25. Authors: Arghavan Alisoltani, Monalisa T. Manhanzva, Matthys Potgieter, Christina Balle, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Michelle du Plessis, Nina Radzey, Zac McDonald, Bridget Calder, Imane Allali, Nicola Mulder, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien…
    Citation: Microbiome 2022 10:42
    Content type: Correction Published on:

    The original article was published in Microbiome 2020 8:165

  26. The gut microbiome (GM) can influence many biological processes in the host, impacting its health and survival, but the GM can also be influenced by the host’s traits. In vertebrates, Major Histocompatibility...

    Authors: Charli S. Davies, Sarah F. Worsley, Kathryn H. Maher, Jan Komdeur, Terry Burke, Hannah L. Dugdale and David S. Richardson
    Citation: Microbiome 2022 10:41
    Content type: Research Published on:

  28. Antimicrobial resistance (AMR) has been regarded as a major threat to global health. Pigs are considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of large-sc...

    Authors: Yunyan Zhou, Hao Fu, Hui Yang, Jinyuan Wu, Zhe Chen, Hui Jiang, Min Liu, Qin Liu, Lusheng Huang, Jun Gao and Congying Chen
    Citation: Microbiome 2022 10:39
    Content type: Research Published on:

  29. Intestinal ischemia/reperfusion (I/R) injury has high morbidity and mortality rates. Gut microbiota is a potential key factor affecting intestinal I/R injury. Populations exhibit different sensitivities to int...

    Authors: Jingjuan Hu, Fan Deng, Bingcheng Zhao, Zebin Lin, Qishun Sun, Xiao Yang, Mei Wu, Shida Qiu, Yu Chen, Zhengzheng Yan, Sidan Luo, Jin Zhao, Weifeng Liu, Cai Li and Ke Xuan Liu
    Citation: Microbiome 2022 10:38
    Content type: Research Published on:

  30. Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in...

    Authors: Jose L. Rolando, Max Kolton, Tianze Song and Joel E. Kostka
    Citation: Microbiome 2022 10:37
    Content type: Research Published on:

  31. Soil microbiomes are considered a cornerstone of the next green revolution, and plant growth-promoting bacteria (PGPB) are critical for microbiome engineering. However, taking plant-beneficial microorganisms f...

    Authors: Chen Chen, Miao Wang, Jingzhi Zhu, Yongwei Tang, Hanchao Zhang, Qiming Zhao, Minyu Jing, Yahua Chen, Xihui Xu, Jiandong Jiang and Zhenguo Shen
    Citation: Microbiome 2022 10:36
    Content type: Research Published on:

  32. Gut microbiota contributes to colorectal cancer (CRC) pathogenesis through microbes and their metabolites. The importance of microbiota-associated metabolites in colorectal carcinogenesis highlights the need t...

    Authors: Olabisi Oluwabukola Coker, Changan Liu, William Ka Kei Wu, Sunny Hei Wong, Wei Jia, Joseph J. Y. Sung and Jun Yu
    Citation: Microbiome 2022 10:35
    Content type: Research Published on:

  33. There is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear tha...

    Authors: Céline Pattaroni, Matthew Macowan, Roxanne Chatzis, Carmel Daunt, Adnan Custovic, Michael D. Shields, Ultan F. Power, Jonathan Grigg, Graham Roberts, Peter Ghazal, Jürgen Schwarze, Mindy Gore, Steve Turner, Andrew Bush, Sejal Saglani, Clare M. Lloyd…
    Citation: Microbiome 2022 10:34
    Content type: Research Published on:

  34. Establishing fecal microbiota transplantation (FMT) to prevent multifactorial diarrhea in calves is challenging because of the differences in farm management practices, the lack of optimal donors, and recipien...

    Authors: Jahidul Islam, Masae Tanimizu, Yu Shimizu, Yoshiaki Goto, Natsuki Ohtani, Kentaro Sugiyama, Eriko Tatezaki, Masumi Sato, Eiji Makino, Toru Shimada, Chise Ueda, Ayumi Matsuo, Yoshihisa Suyama, Yoshifumi Sakai, Mutsumi Furukawa, Katsuki Usami…
    Citation: Microbiome 2022 10:31
    Content type: Research Published on:

  35. Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-c...

    Authors: Zhichao Zhou, Patricia Q. Tran, Adam M. Breister, Yang Liu, Kristopher Kieft, Elise S. Cowley, Ulas Karaoz and Karthik Anantharaman
    Citation: Microbiome 2022 10:33
    Content type: Methodology Published on:

  36. As the global population continues to grow, competition for resources between humans and livestock has been intensifying. Increasing milk protein production and improving feed efficiency are becoming increasin...

    Authors: Ming-Yuan Xue, Yun-Yi Xie, Yifan Zhong, Xiao-Jiao Ma, Hui-Zeng Sun and Jian-Xin Liu
    Citation: Microbiome 2022 10:32
    Content type: Research Published on:

  38. Chronic diarrhea is a common disease causing morbidity and mortality of captive rhesus macaques (RMs, Macaca mulatta). Chronic diarrhea in RMs is typically characterized by long-term diarrhea and a weak response ...

    Authors: Shengzhi Yang, Yu Liu, Nan Yang, Yue Lan, Weiqi Lan, Jinyi Feng, Bisong Yue, Miao He, Liang Zhang, Anyun Zhang, Megan Price, Jing Li and Zhenxin Fan
    Citation: Microbiome 2022 10:29
    Content type: Research Published on:

  39. Various aspects of sociality can benefit individuals’ health. The host social environment and its relative contributions to the host-microbiome relationship have emerged as key topics in microbial research. Ye...

    Authors: Katja Rudolph, Dominik Schneider, Claudia Fichtel, Rolf Daniel, Michael Heistermann and Peter M. Kappeler
    Citation: Microbiome 2022 10:28
    Content type: Research Published on:

  41. A human spaceflight to Mars is scheduled for the next decade. In preparation for this unmatched endeavor, a plethora of challenges must be faced prior to the actual journey to Mars. Mission success will depend...

    Authors: Torben Kuehnast, Carmel Abbott, Manuela R. Pausan, David A. Pearce, Christine Moissl-Eichinger and Alexander Mahnert
    Citation: Microbiome 2022 10:26
    Content type: Commentary Published on:

  43. There is a growing interest in using gut commensal bacteria as “next generation” probiotics. However, this approach is still hampered by the fact that there are few or no strains available for specific species...

    Authors: Samuel Bellais, Mélanie Nehlich, Maryne Ania, Aurore Duquenoy, Wilfrid Mazier, Ger van den Engh, Jan Baijer, Nicole Simone Treichel, Thomas Clavel, Ilia Belotserkovsky and Vincent Thomas
    Citation: Microbiome 2022 10:24
    Content type: Research Published on:

  44. It is of critical importance to understand how anammox consortia respond to disturbance events and fluctuations in the wastewater treatment reactors. Although the responses of anammox consortia to operational ...

    Authors: Dou Wang, Yulin Wang, Lei Liu, Yiqiang Chen, Chunxiao Wang, Yu-You Li and Tong Zhang
    Citation: Microbiome 2022 10:23
    Content type: Research Published on:

  45. Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limi...

    Authors: Shan Zhang, Weizhi Song, Louis-Félix Nothias, Sneha P. Couvillion, Nicole Webster and Torsten Thomas
    Citation: Microbiome 2022 10:22
    Content type: Research Published on:

  46. Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. He...

    Authors: Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen and Morten Tønsberg Limborg
    Citation: Microbiome 2022 10:21
    Content type: Research Published on:

  47. There is concern that the microbially rich activated sludge environment of wastewater treatment plants (WWTPs) may contribute to the dissemination of antibiotic resistance genes (ARGs). We applied long-read (n...

    Authors: Dongjuan Dai, Connor Brown, Helmut Bürgmann, D. G. Joakim Larsson, Indumathi Nambi, Tong Zhang, Carl-Fredrik Flach, Amy Pruden and Peter J. Vikesland
    Citation: Microbiome 2022 10:20
    Content type: Research Published on:

  48. Threats of antimicrobial resistance (AMR) to human health are on the rise worldwide. Airborne fine particulate matter (PM2.5), especially those emitted from hospitals, could serve as a substantial yet lesser-know...

    Authors: Dong Wu, Ling Jin, Jiawen Xie, Hang Liu, Jue Zhao, Dan Ye and Xiang-dong Li
    Citation: Microbiome 2022 10:19
    Content type: Research Published on:

  49. Given the lack of genetic background, the source tracking unknown individuals of fish species with both farmed and wild populations often cannot be robustly achieved. The gut microbiome, which is shaped by bot...

    Authors: Jun Zhu, Hao Li, Ze Zhou Jing, Wei Zheng, Yuan Rong Luo, Shi Xi Chen and Feng Guo
    Citation: Microbiome 2022 10:18
    Content type: Research Published on:

  50. Authors: Anneliek M. ter Horst, Christian Santos-Medellín, Jackson W. Sorensen, Laura A. Zinke, Rachel M. Wilson, Eric R. Johnston, Gareth Trubl, Jennifer Pett-Ridge, Steven J. Blazewicz, Paul J. Hanson, Jeffrey P. Chanton, Christopher W. Schadt, Joel E. Kostka and Joanne B. Emerson
    Citation: Microbiome 2022 10:17
    Content type: Correction Published on:

    The original article was published in Microbiome 2021 9:233

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