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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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

    The original article was published in Microbiome 2020 8:165

  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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

    The original article was published in Microbiome 2021 9:233

  29. Our interconnected world and the ability of bacteria to quickly swap antibiotic resistance genes (ARGs) make it particularly important to establish the epidemiological links of multidrug resistance (MDR) trans...

    Authors: You Che, Xiaoqing Xu, Yu Yang, Karel Břinda, William Hanage, Chao Yang and Tong Zhang
    Citation: Microbiome 2022 10:16
  30. Immunoglobulin A (IgA) plays an important role in maintaining a healthy intestinal microbiome, but little is known about the interaction between local immunoglobulins and the vaginal microbiome. We assessed im...

    Authors: Annelot C. Breedveld, Heleen J. Schuster, Robin van Houdt, Rebecca C. Painter, Reina E. Mebius, Charlotte van der Veer, Sylvia M. Bruisten, Paul H. M. Savelkoul and Marjolein van Egmond
    Citation: Microbiome 2022 10:15
  31. Early gut microbial colonization is important for postnatal growth and immune development of the chicken. However, at present, commercial chickens are hatched and raised without adult hens, thus are cut off fr...

    Authors: Xiaobing Li, Ran Bi, Kangpeng Xiao, Ayan Roy, Zhipeng Zhang, Xiaoyuan Chen, Jinyu Peng, Ruichen Wang, Rou Yang, Xuejuan Shen, David M. Irwin and Yongyi Shen
    Citation: Microbiome 2022 10:14
  32. IL-35–producing Bregs and Treg cells critically regulate chronic illnesses worldwide via mechanisms related to disrupting the gut microbiota composition. However, whether the gut microbiota regulates these IL-35+

    Authors: Xiaomin Su, Minying Zhang, Houbao Qi, Yunhuan Gao, Yazheng Yang, Huan Yun, Qianjing Zhang, Xiaorong Yang, Yuan Zhang, Jiangshan He, Yaqi Fan, Yuxue Wang, Pei Guo, Chunze Zhang and Rongcun Yang
    Citation: Microbiome 2022 10:13
  33. Understanding how elevated atmospheric CO2 (eCO2) impacts on phosphorus (P) transformation in plant rhizosphere is critical for maintaining ecological sustainability in response to climate change, especially in a...

    Authors: Jian Jin, Christian Krohn, Ashley E. Franks, Xiaojuan Wang, Jennifer L. Wood, Steve Petrovski, Malcolm McCaskill, Steven Batinovic, Zhihuang Xie and Caixian Tang
    Citation: Microbiome 2022 10:12
  34. Dairy cows utilize human-inedible, low-value plant biomass to produce milk, a low-cost product with rich nutrients and high proteins. This process largely relies on rumen microbes that ferment lignocellulose a...

    Authors: Ming-Yuan Xue, Jia-Jin Wu, Yun-Yi Xie, Sen-Lin Zhu, Yi-Fan Zhong, Jian-Xin Liu and Hui-Zeng Sun
    Citation: Microbiome 2022 10:11
  35. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Imane Allali, Regina E. Abotsi, Lemese Ah. Tow, Lehana Thabane, Heather J. Zar, Nicola M. Mulder and Mark P. Nicol
    Citation: Microbiome 2022 10:10

    The original article was published in Microbiome 2021 9:241

  36. Short-chain fatty acids (SCFAs) produced by the gut microbiota have beneficial anti-inflammatory and gut homeostasis effects and prevent type 1 diabetes (T1D) in mice. Reduced SCFA production indicates a loss ...

    Authors: Kirstine J. Bell, Sonia Saad, Bree J. Tillett, Helen M. McGuire, Sara Bordbar, Yu Anne Yap, Long T. Nguyen, Marc R. Wilkins, Susan Corley, Shannon Brodie, Sussan Duong, Courtney J. Wright, Stephen Twigg, Barbara Fazekas de St Groth, Leonard C. Harrison, Charles R. Mackay…
    Citation: Microbiome 2022 10:9
  37. Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the...

    Authors: Jie Pan, Wei Xu, Zhichao Zhou, Zongze Shao, Chunming Dong, Lirui Liu, Zhuhua Luo and Meng Li
    Citation: Microbiome 2022 10:8

    The Correction to this article has been published in Microbiome 2022 10:40

  38. Coronal sulcus (CS) anaerobe abundance and IL-8 levels are linked to HIV acquisition, and are dramatically reduced after penile circumcision (PC). The distal urethra may be the site of some HIV acquisition bef...

    Authors: Ronald M. Galiwango, Daniel E. Park, Sanja Huibner, Abigail Onos, Maliha Aziz, Kelsey Roach, Aggrey Anok, James Nnamutete, Yahaya Isabirye, John Bosco Wasswa, Deo Male, Godfrey Kigozi, Aaron A. R. Tobian, Jessica L. Prodger, Cindy M. Liu and Rupert Kaul
    Citation: Microbiome 2022 10:7
  39. The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic...

    Authors: Boahemaa Adu-Oppong, Robert Thänert, Meghan A. Wallace, Carey-Ann D. Burnham and Gautam Dantas
    Citation: Microbiome 2022 10:6
  40. Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface eco...

    Authors: Kaela K. Amundson, Mikayla A. Borton, Rebecca A. Daly, David W. Hoyt, Allison Wong, Elizabeth Eder, Joseph Moore, Kenneth Wunch, Kelly C. Wrighton and Michael J. Wilkins
    Citation: Microbiome 2022 10:5

    The Correction to this article has been published in Microbiome 2022 10:30

  41. Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity...

    Authors: Pauliina Rajala, Dong-Qiang Cheng, Scott A. Rice and Federico M. Lauro
    Citation: Microbiome 2022 10:4
  42. Host tp53 mutations are frequently found during the early stages of colitis-associated colorectal cancer (CAC), but whether such mutations induce gut microbiota dysbiosis and chronic intestinal inflammation that ...

    Authors: Jae-Geun Lee, Soohyun Lee, Juhee Jeon, Hyun Gi Kong, Hyun-Ju Cho, Jong-Hwan Kim, Seon-Young Kim, Myung Jin Oh, Daum Lee, Nari Seo, Ki Hun Park, Kweon Yu, Hyun Joo An, Choong-Min Ryu and Jeong-Soo Lee
    Citation: Microbiome 2022 10:3
  43. In ecology, population density is a key feature of community analysis. Yet in studies of the gut microbiome, bacterial density is rarely reported. Studies of hospitalized patients commonly use rectal swabs for...

    Authors: Rishi Chanderraj, Christopher A. Brown, Kevin Hinkle, Nicole Falkowski, Robert J. Woods and Robert P. Dickson
    Citation: Microbiome 2022 10:2
  44. Previous evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whet...

    Authors: Inmaculada Moreno, Iolanda Garcia-Grau, David Perez-Villaroya, Marta Gonzalez-Monfort, Mustafa Bahçeci, Marcelo J. Barrionuevo, Sagiri Taguchi, Elena Puente, Michael Dimattina, Mei Wei Lim, Georgina Meneghini, Mira Aubuchon, Mark Leondires, Alexandra Izquierdo, Martina Perez-Olgiati, Alejandro Chavez…
    Citation: Microbiome 2022 10:1
  45. Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delight...

    Authors: Tim Van Den Bossche, Magnus Ø. Arntzen, Dörte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Céline Henry, Pratik D. Jagtap, Nico Jehmlich, Catherine Juste, Benoit J. Kunath, Bart Mesuere, Thilo Muth, Phillip B. Pope, Jana Seifert, Alessandro Tanca, Sergio Uzzau…
    Citation: Microbiome 2021 9:243

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