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  1. Peripheral neuropathy (PN) is a common complication in obesity, prediabetes, and type 2 diabetes, though its pathogenesis remains incompletely understood. In a murine high-fat diet (HFD) obesity model of PN, d...

    Authors: Kai Guo, Claudia Figueroa-Romero, Mohamed Noureldein, Lucy M. Hinder, Stacey A. Sakowski, Amy E. Rumora, Hayley Petit, Masha G. Savelieff, Junguk Hur and Eva L. Feldman
    Citation: Microbiome 2023 11:52
  2. Unrevealing the interplay between diet, the microbiome, and the health state could enable the design of personalized intervention strategies and improve the health and well-being of individuals. A common appro...

    Authors: Xiangnan Xu, Michal Lubomski, Andrew J. Holmes, Carolyn M. Sue, Ryan L. Davis, Samuel Muller and Jean Y. H. Yang
    Citation: Microbiome 2023 11:51
  3. The impact of host skin microbiome on horizontal transmission of tick-borne pathogens , and of pathogen associated transstadial and transovarial changes in tick microbiome are largely unknown, but are importan...

    Authors: Li-Feng Du, Ming-Zhu Zhang, Ting-Ting Yuan, Xue-Bing Ni, Wei Wei, Xiao-Ming Cui, Ning Wang, Tao Xiong, Jie Zhang, Yu-Sheng Pan, Dai-Yun Zhu, Liang-Jing Li, Luo-Yuan Xia, Tian-Hong Wang, Ran Wei, Hong-Bo Liu…
    Citation: Microbiome 2023 11:50
  4. Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogeni...

    Authors: Gustavo A. Ramírez, Rinat Bar-Shalom, Andrea Furlan, Roberto Romeo, Michelle Gavagnin, Gianluca Calabrese, Arkadiy I. Garber and Laura Steindler
    Citation: Microbiome 2023 11:49
  5. Root-knot nematodes (RKN) are among the most important root-damaging plant-parasitic nematodes, causing severe crop losses worldwide. The plant rhizosphere and root endosphere contain rich and diverse bacteria...

    Authors: Ye Li, Shaonan Lei, Zhiqiang Cheng, Lingyue Jin, Ting Zhang, Lian-Ming Liang, Linjie Cheng, Qinyi Zhang, Xiaohong Xu, Canhua Lan, Chaojun Lu, Minghe Mo, Ke-Qin Zhang, Jianping Xu and Baoyu Tian
    Citation: Microbiome 2023 11:48
  6. IL-22 is induced by aryl hydrocarbon receptor (AhR) signaling and plays a critical role in gastrointestinal barrier function through effects on antimicrobial protein production, mucus secretion, and epithelial...

    Authors: Jordan S. Mar, Naruhisa Ota, Nick D. Pokorzynski, Yutian Peng, Allan Jaochico, Dewakar Sangaraju, Elizabeth Skippington, Annemarie N. Lekkerkerker, Michael E. Rothenberg, Man-Wah Tan, Tangsheng Yi and Mary E. Keir
    Citation: Microbiome 2023 11:47
  7. Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, in...

    Authors: Laura de Nies, Valentina Galata, Camille Martin-Gallausiaux, Milena Despotovic, Susheel Bhanu Busi, Chantal J. Snoeck, Lea Delacour, Deepthi Poornima Budagavi, Cédric Christian Laczny, Janine Habier, Paula-Cristina Lupu, Rashi Halder, Joëlle V. Fritz, Taina Marques, Estelle Sandt, Marc Paul O’Sullivan…
    Citation: Microbiome 2023 11:46
  8. Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how ...

    Authors: Xia Li, Ruotong Zhao, Dandan Li, Guangzhou Wang, Shuikuan Bei, Xiaotang Ju, Ran An, Long Li, Thomas W. Kuyper, Peter Christie, Franz S. Bender, Ciska Veen, Marcel G. A. van der Heijden, Wim H. van der Putten, Fusuo Zhang, Klaus Butterbach-Bahl…
    Citation: Microbiome 2023 11:45
  9. Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established ...

    Authors: Juan Salvador Inda-Díaz, David Lund, Marcos Parras-Moltó, Anna Johnning, Johan Bengtsson-Palme and Erik Kristiansson
    Citation: Microbiome 2023 11:44
  10. The effects of fermented food consumption on the small intestine microbiome and its role on host homeostasis are largely uncharacterised as our knowledge on intestinal microbiota relies mainly on faecal sample...

    Authors: Edoardo Zaccaria, Tim Klaassen, Annick M. E. Alleleyn, Jos Boekhorst, Tamara Smokvina, Michiel Kleerebezem and Freddy J. Troost
    Citation: Microbiome 2023 11:43
  11. Microbes typically live in communities where individuals can interact with each other in numerous ways. However, knowledge on the importance of these interactions is limited and derives mainly from studies usi...

    Authors: Sarah Huet, Sana Romdhane, Marie-Christine Breuil, David Bru, Arnaud Mounier, Ayme Spor and Laurent Philippot
    Citation: Microbiome 2023 11:42
  12. Nutrition drives immunity and health in animals, and maternal immunity benefits offspring. In our previous study, a nutritional intervention strategy was found to promote the immunity of hens, which subsequent...

    Authors: Haizhou Gong, Taiping Wang, Min Wu, Qianran Chu, Hainan Lan, Wuying Lang, Lingyu Zhu, Yang Song, Yujie Zhou, Qiongyi Wen, Jing Yu, Baolin Wang and Xin Zheng
    Citation: Microbiome 2023 11:41
  13. Postpartum dairy cows experiencing excessive lipolysis are prone to severe immunosuppression. Despite the extensive understanding of the gut microbial regulation of host immunity and metabolism, its role durin...

    Authors: Fengfei Gu, Senlin Zhu, Yifan Tang, Xiaohan Liu, Minghui Jia, Nilusha Malmuthuge, Teresa G. Valencak, Joseph W. McFadden, Jian-Xin Liu and Hui-Zeng Sun
    Citation: Microbiome 2023 11:40
  14. Following viral infection, genetically manipulated mice lacking immunoregulatory function may develop colitis and dysbiosis in a strain-specific fashion that serves as a model for inflammatory bowel disease (I...

    Authors: Heather Armstrong, Mandana Rahbari, Heekuk Park, David Sharon, Aducio Thiesen, Naomi Hotte, Ning Sun, Hussain Syed, Hiatem Abofayed, Weiwei Wang, Karen Madsen, Eytan Wine and Andrew Mason
    Citation: Microbiome 2023 11:39
  15. The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context ...

    Authors: Jiarui Li, Qiuyu Jing, Jie Li, Mingxi Hua, Lin Di, Chuan Song, Yanyi Huang, Jianbin Wang, Chen Chen and Angela Ruohao Wu
    Citation: Microbiome 2023 11:38
  16. Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-in...

    Authors: Chuwen Zhang, Yun-Xin Fang, Xiuran Yin, Hongfei Lai, Zenggui Kuang, Tianxueyu Zhang, Xiang-Po Xu, Gunter Wegener, Jiang-Hai Wang and Xiyang Dong
    Citation: Microbiome 2023 11:37
  17. Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating ...

    Authors: Yue Clare Lou, Jordan Hoff, Matthew R. Olm, Jacob West-Roberts, Spencer Diamond, Brian A. Firek, Michael J. Morowitz and Jillian F. Banfield
    Citation: Microbiome 2023 11:36
  18. Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are co...

    Authors: Christoph Keuschnig, Timothy M. Vogel, Elena Barbaro, Andrea Spolaor, Krystyna Koziol, Mats P. Björkman, Christian Zdanowicz, Jean-Charles Gallet, Bartłomiej Luks, Rose Layton and Catherine Larose
    Citation: Microbiome 2023 11:35
  19. Microbiomes contribute to multiple ecosystem services by transforming organic matter in the soil. Extreme shifts in the environment, such as drying-rewetting cycles during drought, can impact the microbial met...

    Authors: Sneha P. Couvillion, Robert E. Danczak, Dan Naylor, Montana L. Smith, Kelly G. Stratton, Vanessa L. Paurus, Kent J. Bloodsworth, Yuliya Farris, Darren J. Schmidt, Rachel E. Richardson, Lisa M. Bramer, Sarah J. Fansler, Ernesto S. Nakayasu, Jason E. McDermott, Thomas O. Metz, Mary S. Lipton…
    Citation: Microbiome 2023 11:34
  20. Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which co...

    Authors: Mathijs J. P. Theelen, Roosmarijn E. C. Luiken, Jaap A. Wagenaar, Marianne M. Sloet van Oldruitenborgh-Oosterbaan, John W. A. Rossen, Femke J. W. C. Schaafstra, David A. van Doorn and Aldert L. Zomer
    Citation: Microbiome 2023 11:33
  21. Gamma-delta (γδ) T cells are a major cell population in the intestinal mucosa and are key mediators of mucosal tolerance and microbiota composition. Little is known about the mechanisms by which intestinal γδ ...

    Authors: Rafael M. Rezende, Laura M. Cox, Thais G. Moreira, Shirong Liu, Selma Boulenouar, Fyonn Dhang, Danielle S. LeServe, Brenda N. Nakagaki, Juliana R. Lopes, Bruna K. Tatematsu, Luisa Lemos, Julia Mayrink, Eduardo L. C. Lobo, Lydia Guo, Marilia G. Oliveira, Chantal Kuhn…
    Citation: Microbiome 2023 11:32
  22. Gut fungi are increasingly recognized as important contributors to host physiology, although most studies have focused on gut bacteria. Post-translational modifications (PTMs) of proteins play vital roles in c...

    Authors: Jun Hu, Jianwei Chen, Qiliang Hou, Xiaojian Xu, Jing Ren, Libao Ma and Xianghua Yan
    Citation: Microbiome 2023 11:31
  23. Gut homeostasis, including intestinal immunity and microbiome, is essential for cognitive function via the gut-brain axis. This axis is altered in high-fat diet (HFD)-induced cognitive impairment and is closel...

    Authors: Wei Pan, Jinxiu Zhao, Jiacheng Wu, Daxiang Xu, Xianran Meng, Pengfei Jiang, Hongli Shi, Xing Ge, Xiaoying Yang, Minmin Hu, Peng Zhang, Renxian Tang, Nathan Nagaratnam, Kuiyang Zheng, Xu-Feng Huang and Yinghua Yu
    Citation: Microbiome 2023 11:30

    The Correction to this article has been published in Microbiome 2023 11:55

  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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

    The original article was published in Microbiome 2023 11:12

  30. 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
  31. 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
  32. 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

    The original article was published in Microbiome 2022 10:221

  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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

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

  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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

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