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  1. Long-term azithromycin (AZM) treatment reduces the frequency of acute respiratory exacerbation in children and adolescents with HIV-associated chronic lung disease (HCLD). However, the impact of this treatment...

    Authors: Regina E. Abotsi, Felix S. Dube, Andrea M. Rehman, Shantelle Claassen-Weitz, Yao Xia, Victoria Simms, Kilaza S. Mwaikono, Sugnet Gardner-Lubbe, Grace McHugh, Lucky G. Ngwira, Brenda Kwambana-Adams, Robert S. Heyderman, Jon Ø. Odland, Rashida A. Ferrand and Mark P. Nicol
    Citation: Microbiome 2023 11:29
    Content type: Research Published on:

  2. Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and qua...

    Authors: Christian Ayala-Ortiz, Nathalia Graf-Grachet, Viviana Freire-Zapata, Jane Fudyma, Gina Hildebrand, Roya AminiTabrizi, Cristina Howard-Varona, Yuri E. Corilo, Nancy Hess, Melissa B. Duhaime, Matthew B. Sullivan and Malak M. Tfaily
    Citation: Microbiome 2023 11:28
    Content type: Software Published on:

  3. The correlation between the physical performance of athletes and their gut microbiota has become of growing interest in the past years, since new evidences have emerged regarding the importance of the gut micr...

    Authors: Federico Fontana, Giulia Longhi, Chiara Tarracchini, Leonardo Mancabelli, Gabriele Andrea Lugli, Giulia Alessandri, Francesca Turroni, Christian Milani and Marco Ventura
    Citation: Microbiome 2023 11:27
    Content type: Research Published on:

  4. Bioactive lipids produced by human cells or by the gut microbiota might play an important role in health and disease. Dietary intakes are key determinants of the gut microbiota, its production of short-chain (...

    Authors: Isabelle Bourdeau-Julien, Sophie Castonguay-Paradis, Gabrielle Rochefort, Julie Perron, Benoît Lamarche, Nicolas Flamand, Vincenzo Di Marzo, Alain Veilleux and Frédéric Raymond
    Citation: Microbiome 2023 11:26
    Content type: Research Published on:

  6. Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approac...

    Authors: Manuel Kleiner, Angela Kouris, Marlene Violette, Grace D’Angelo, Yihua Liu, Abigail Korenek, Nikola Tolić, Timo Sachsenberg, Janine McCalder, Mary S. Lipton and Marc Strous
    Citation: Microbiome 2023 11:24
    Content type: Methodology Published on:

  7. Authors: Guillaume Dalmasso, Racha Beyrouthy, Sandrine Brugiroux, Etienne Ruppé, Laurent Guillouard, Virginie Bonnin, Pierre Saint-Sardos, Amine Ghozlane, Vincent Gaumet, Nicolas Barnich, Julien Delmas and Richard Bonnet
    Citation: Microbiome 2023 11:23
    Content type: Correction Published on:

    The original article was published in Microbiome 2023 11:12

  8. Wolbachia belong to highly abundant bacteria which are frequently found in invertebrate microbiomes and manifest by a broad spectrum of lifestyles from parasitism to mutualism. Wolbachia supergroup F is a particu...

    Authors: Sazzad Mahmood, Eva Nováková, Jana Martinů, Oldřich Sychra and Václav Hypša
    Citation: Microbiome 2023 11:22
    Content type: Research Published on:

  9. Vitamin B12 supplements typically contain doses that far exceed the recommended daily amount, and high exposures are generally considered safe. Competitive and syntrophic interactions for B12 exist between mic...

    Authors: Andrew J. Forgie, Deanna M. Pepin, Tingting Ju, Stephanie Tollenaar, Consolato M. Sergi, Samantha Gruenheid and Benjamin P. Willing
    Citation: Microbiome 2023 11:21
    Content type: Research Published on:

  10. 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 2023 11:20
    Content type: Correction Published on:

    The original article was published in Microbiome 2022 10:221

  11. Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial c...

    Authors: Keming Yang, Xiaofang Wang, Rujiao Hou, Chunxia Lu, Zhe Fan, Jingxuan Li, Shuo Wang, Yangchun Xu, Qirong Shen, Ville-Petri Friman and Zhong Wei
    Citation: Microbiome 2023 11:16
    Content type: Research Published on:

  12. Low birth weight (LBW) is associated with intestinal inflammation and dysbiosis after birth. However, the underlying mechanism remains largely unknown.

    Authors: Yu Pi, Yujun Wu, Xiangyu Zhang, Dongdong Lu, Dandan Han, Jiangchao Zhao, Xiaojiao Zheng, Shiyi Zhang, Hao Ye, Shuai Lian, Yu Bai, Zhenyu Wang, Shiyu Tao, Dongjiao Ni, Xinhua Zou, Wei Jia…
    Citation: Microbiome 2023 11:19
    Content type: Research Published on:

  13. Narrow host range is a major limitation for phage applications, but phages can evolve expanded host range through adaptations in the receptor-binding proteins.

    Authors: Li Sun, Jiajia You, Donghang Li, Zhiqiang Zhang, Xuying Qin, Wenjing Pang, Peize Li, Qingzhu Han, Yueying Li, Zhiwei Huang, Xixi Zhang, Mengxin Gong and Hongjiang Yang
    Citation: Microbiome 2023 11:18
    Content type: Research Published on:

  14. Sleep loss is a serious global health concern. Consequences include memory deficits and gastrointestinal dysfunction. Our previous research showed that melatonin can effectively improve cognitive impairment an...

    Authors: Xintong Wang, Zixu Wang, Jing Cao, Yulan Dong and Yaoxing Chen
    Citation: Microbiome 2023 11:17
    Content type: Research Published on:

  15. The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assem...

    Authors: Vinicius S. Kavagutti, Paul-Adrian Bulzu, Cecilia M. Chiriac, Michaela M. Salcher, Indranil Mukherjee, Tanja Shabarova, Vesna Grujčić, Maliheh Mehrshad, Vojtěch Kasalický, Adrian-Stefan Andrei, Jitka Jezberová, Jaromir Seďa, Pavel Rychtecký, Petr Znachor, Karel Šimek and Rohit Ghai
    Citation: Microbiome 2023 11:15
    Content type: Research Published on:

  16. Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Rece...

    Authors: Alexander L. Jaffe, Corinne Bardot, Anne-Hélène Le Jeune, Jett Liu, Jonathan Colombet, Fanny Perrière, Hermine Billard, Cindy J. Castelle, Anne-Catherine Lehours and Jillian F. Banfield
    Citation: Microbiome 2023 11:14
    Content type: Research Published on:

  17. It is well-known that the microbiome produces a myriad of specialised metabolites with diverse functions. To better characterise their structures and identify their producers in complex samples, integrative ge...

    Authors: Joris J. R. Louwen, Marnix H. Medema and Justin J. J. van der Hooft
    Citation: Microbiome 2023 11:13
    Content type: Software Published on:

  18. The plasmid-mediated resistance gene mcr-1 confers colistin resistance in Escherichia coli and paves the way for the evolution to pan-drug resistance. We investigated the impact of mcr-1 in gut colonization in th...

    Authors: Guillaume Dalmasso, Racha Beyrouthy, Sandrine Brugiroux, Etienne Ruppé, Laurent Guillouard, Virginie Bonnin, Pierre Saint-Sardos, Amine Ghozlane, Vincent Gaumet, Nicolas Barnich, Julien Delmas and Richard Bonnet
    Citation: Microbiome 2023 11:12
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2023 11:23

  19. Paederus fuscipes is medically the most famous rove beetle, which causes dermatitis or conjunctivitis in humans, as well as gastrointestinal toxicosis in livestock, via releasing toxic hemolymph containing pederi...

    Authors: Bahar Chamankar, Naseh Maleki-Ravasan, Mohsen Karami, Esmaeil Forouzan, Fateh Karimian, Sabah Naeimi and Nayyereh Choobdar
    Citation: Microbiome 2023 11:11
    Content type: Research Published on:

  20. Dairy cattle (Bos taurus), especially Holstein cows, which are the highest-producing dairy animals and are widely bred to provide milk products to humans, rely critically on their associated gastrointestinal trac...

    Authors: Limei Lin, Zheng Lai, Jiyou Zhang, Weiyun Zhu and Shengyong Mao
    Citation: Microbiome 2023 11:10
    Content type: Research Published on:

  21. Celiac disease (CD) is an autoimmune disorder triggered by gluten consumption. Almost all CD patients possess human leukocyte antigen (HLA) DQ2/DQ8 haplotypes; however, only a small subset of individuals carry...

    Authors: Khyati Girdhar, Yusuf Dogus Dogru, Qian Huang, Yi Yang, Vladimir Tolstikov, Amol Raisingani, Martina Chrudinova, Jaewon Oh, Kristina Kelley, Jonas F. Ludvigsson, Michael A. Kiebish, Noah W. Palm, Johnny Ludvigsson and Emrah Altindis
    Citation: Microbiome 2023 11:9
    Content type: Research Published on:

  22. The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential...

    Authors: Maria Berihu, Tracey S. Somera, Assaf Malik, Shlomit Medina, Edoardo Piombo, Ofir Tal, Matan Cohen, Alon Ginatt, Maya Ofek-Lalzar, Adi Doron-Faigenboim, Mark Mazzola and Shiri Freilich
    Citation: Microbiome 2023 11:8
    Content type: Research Published on:

  23. As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in t...

    Authors: Cunyuan Li, Xiaoyue Li, Rongjun Guo, Wei Ni, Kaiping Liu, Zhuang Liu, Jihong Dai, Yueren Xu, Shamshidin Abduriyim, Zhuangyuan Wu, Yaqi Zeng, Bingbing Lei, Yunfeng Zhang, Yue Wang, Weibin Zeng, Qiang Zhang…
    Citation: Microbiome 2023 11:7
    Content type: Research Published on:

  24. The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our unders...

    Authors: Nannan Li, Cixiu Li, Tao Hu, Juan Li, Hong Zhou, Jingkai Ji, Jiangli Wu, Weipeng Kang, Edward C. Holmes, Weifeng Shi and Shufa Xu
    Citation: Microbiome 2023 11:6
    Content type: Research Published on:

  25. Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior st...

    Authors: Jonathan P. Jacobs, Venu Lagishetty, Megan C. Hauer, Jennifer S. Labus, Tien S. Dong, Ryan Toma, Momchilo Vuyisich, Bruce D. Naliboff, Jeffrey M. Lackner, Arpana Gupta, Kirsten Tillisch and Emeran A. Mayer
    Citation: Microbiome 2023 11:5
    Content type: Research Published on:

  26. Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD usi...

    Authors: V. Bay, A. Gillespie, E. Ganda, N. J. Evans, S. D. Carter, L. Lenzi, A. Lucaci, S. Haldenby, M. Barden, B. E. Griffiths, E. Sánchez-Molano, R. Bicalho, G. Banos, A. Darby and G. Oikonomou
    Citation: Microbiome 2023 11:4
    Content type: Research Published on:

  27. Chronic kidney disease (CKD) is a severe public health problem associated with a disordered gut microbiome. However, the functional alterations of microbiota and their cross talk with metabolism pathways based...

    Authors: Haichao Wang, Aisima Ainiwaer, Yaxiang Song, Ling Qin, Ai Peng, Hui Bao and Huanlong Qin
    Citation: Microbiome 2023 11:3
    Content type: Research Published on:

  28. 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

  29. 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:

  30. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  41. 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:

  42. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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

  48. 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:

  49. 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:

  50. 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:
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