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  1. Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, s...

    Authors: Dandan Zhang, Huang Yu, Yuchun Yang, Fei Liu, Mingyue Li, Jie Huang, Yuhe Yu, Cheng Wang, Feng Jiang, Zhili He and Qingyun Yan
    Citation: Microbiome 2023 11:82
  2. A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies sug...

    Authors: Tiantian Yu, Weichao Wu, Wenyue Liang, Yinzhao Wang, Jialin Hou, Yunru Chen, Marcus Elvert, Kai-Uwe Hinrichs and Fengping Wang
    Citation: Microbiome 2023 11:81
  3. Understanding human genetic influences on the gut microbiota helps elucidate the mechanisms by which genetics may influence health outcomes. Typical microbiome genome-wide association studies (GWAS) marginally...

    Authors: Hongjiao Liu, Wodan Ling, Xing Hua, Jee-Young Moon, Jessica S. Williams-Nguyen, Xiang Zhan, Anna M. Plantinga, Ni Zhao, Angela Zhang, Rob Knight, Qibin Qi, Robert D. Burk, Robert C. Kaplan and Michael C. Wu
    Citation: Microbiome 2023 11:80
  4. While the rootstock genotype (belowground part of a plant) can impact rhizosphere microbial communities, few studies have examined the relationships between rootstock genotype-based recruitment of active rhizo...

    Authors: Antonio Castellano-Hinojosa, Ute Albrecht and Sarah L. Strauss
    Citation: Microbiome 2023 11:79
  5. Mastitis is one of the most severe diseases in humans and animals, especially on dairy farms. Mounting evidence indicates that gastrointestinal dysbiosis caused by induction of subacute ruminal acidosis (SARA)...

    Authors: Caijun Zhao, Xiaoyu Hu, Min Qiu, Lijuan Bao, Keyi Wu, Xiangyue Meng, Yihong Zhao, Lianjun Feng, Shiyu Duan, Yuhong He, Naisheng Zhang and Yunhe Fu
    Citation: Microbiome 2023 11:78
  6. Blooms of marine microalgae play a pivotal role in global carbon cycling. Such blooms entail successive blooms of specialized clades of planktonic bacteria that collectively remineralize gigatons of algal biom...

    Authors: Chandni Sidhu, Inga V. Kirstein, Cédric L. Meunier, Johannes Rick, Vera Fofonova, Karen H. Wiltshire, Nicola Steinke, Silvia Vidal-Melgosa, Jan-Hendrik Hehemann, Bruno Huettel, Thomas Schweder, Bernhard M. Fuchs, Rudolf I. Amann and Hanno Teeling
    Citation: Microbiome 2023 11:77
  7. Ruminants can utilize urea as a dietary nitrogen source owing to their ability to recycle urea-N back to the rumen where numerous ureolytic bacteria hydrolyze urea into ammonia, which is used by numerous bacte...

    Authors: Sijia Liu, Zhongtang Yu, Huiyue Zhong, Nan Zheng, Sharon Huws, Jiaqi Wang and Shengguo Zhao
    Citation: Microbiome 2023 11:76
  8. Captive koala breeding programmes are essential for long-term species management. However, breeding efficacy is frequently impacted by high neonatal mortality rates in otherwise healthy females. Loss of pouch ...

    Authors: Toby I. Maidment, Emily R. Bryan, Michael Pyne, Michele Barnes, Sarah Eccleston, Samantha Cunningham, Emma Whitlock, Kelsie Redman, Vere Nicolson, Kenneth W. Beagley and Elise Pelzer
    Citation: Microbiome 2023 11:75
  9. Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of...

    Authors: Haoyu Liang, Zhi-Man Song, Zheng Zhong, Dengwei Zhang, Wei Yang, Le Zhou, Ethan A. Older, Jie Li, Huan Wang, Zhirui Zeng and Yong-Xin Li
    Citation: Microbiome 2023 11:74
  10. Effects of antibiotics on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the fungal microbiota (mycobiota). It is commonly believed that fungal loa...

    Authors: Madeleine Spatz, Gregory Da Costa, Rebecka Ventin-Holmberg, Julien Planchais, Chloé Michaudel, Yazhou Wang, Camille Danne, Alexia Lapiere, Marie-Laure Michel, Kaija-Leena Kolho, Philippe Langella, Harry Sokol and Mathias L. Richard
    Citation: Microbiome 2023 11:73
  11. Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove w...

    Authors: Lu Qian, Xiaoli Yu, Hang Gu, Fei Liu, Yijun Fan, Cheng Wang, Qiang He, Yun Tian, Yisheng Peng, Longfei Shu, Shanquan Wang, Zhijian Huang, Qingyun Yan, Jianguo He, Guangli Liu, Qichao Tu…
    Citation: Microbiome 2023 11:71
  12. The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication build...

    Authors: Hong Yue, Wenjie Yue, Shuo Jiao, Hyun Kim, Yong-Hwan Lee, Gehong Wei, Weining Song and Duntao Shu
    Citation: Microbiome 2023 11:70
  13. Dental erosion is a disease of the oral cavity where acids cause a loss of tooth enamel and is defined as having no bacterial involvement. The tooth surface is protected from acid attack by salivary proteins t...

    Authors: Leanne M. Cleaver, Miguel Carda-Diéguez, Rebeca Moazzez and Guy H. Carpenter
    Citation: Microbiome 2023 11:69
  14. Many animals and plants acquire their coevolved symbiotic partners shortly post-embryonic development. Thus, during embryogenesis, cellular features must be developed that will promote both symbiont colonizati...

    Authors: Tara Essock-Burns, Susannah Lawhorn, Leo Wu, Sawyer McClosky, Silvia Moriano-Gutierrez, Edward G. Ruby and Margaret J. McFall-Ngai
    Citation: Microbiome 2023 11:68
  15. The majority of studies characterizing female genital tract microbiota have focused on luminal organisms, while the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood...

    Authors: Gabriella Edfeldt, Vilde Kaldhusdal, Paulo Czarnewski, Frideborg Bradley, Sofia Bergström, Julie Lajoie, Jiawu Xu, Anna Månberg, Joshua Kimani, Julius Oyugi, Peter Nilsson, Annelie Tjernlund, Keith R. Fowke, Douglas S. Kwon and Kristina Broliden
    Citation: Microbiome 2023 11:67
  16. Crohn’s disease (CD) is associated with changes in the microbiota, and murine models of CD-like ileo-colonic inflammation depend on the presence of microbial triggers. Increased abundance of unknown Clostridia...

    Authors: Amira Metwaly, Jelena Jovic, Nadine Waldschmitt, Sevana Khaloian, Helena Heimes, Deborah Häcker, Mohamed Ahmed, Nassim Hammoudi, Lionel Le Bourhis, Aida Mayorgas, Kolja Siebert, Marijana Basic, Tobias Schwerd, Matthieu Allez, Julian Panes, Azucena Salas…
    Citation: Microbiome 2023 11:66
  17. The COVID-19 pandemic has highlighted the extent to which the public transportation environment, such as in subways, may be important for the transmission of potential pathogenic microbes among humans, with th...

    Authors: Maria D’Accolti, Irene Soffritti, Francesca Bini, Eleonora Mazziga, Carolina Cason, Manola Comar, Antonella Volta, Matteo Bisi, Daniele Fumagalli, Sante Mazzacane and Elisabetta Caselli
    Citation: Microbiome 2023 11:64
  18. Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult bec...

    Authors: Hiroaki Fujita, Masayuki Ushio, Kenta Suzuki, Masato S. Abe, Masato Yamamichi, Koji Iwayama, Alberto Canarini, Ibuki Hayashi, Keitaro Fukushima, Shinji Fukuda, E. Toby Kiers and Hirokazu Toju
    Citation: Microbiome 2023 11:63
  19. Dysbiotic gut microbiome, genetically predisposed or chemically disrupted, has been linked with insulin-dependent diabetes (IDD) including autoimmune type 1 diabetes (T1D) in both humans and animal models. How...

    Authors: Xin Yang, Zhiyi Wang, Junling Niu, Rui Zhai, Xinhe Xue, Guojun Wu, Yuanyuan Fang, Guangxun Meng, Huijuan Yuan, Liping Zhao and Chenhong Zhang
    Citation: Microbiome 2023 11:62
  20. The medicinal material quality of Citrus reticulata ‘Chachi’ differs depending on the bioactive components influenced by the planting area. Environmental factors, such as soil nutrients, the plant-associated micr...

    Authors: Jianmu Su, Yayu Wang, Mei Bai, Tianhua Peng, Huisi Li, Hui-Juan Xu, Guifang Guo, Haiyi Bai, Ning Rong, Sunil Kumar Sahu, Hanjun He, Xiangxiu Liang, Canzhi Jin, Wei Liu, Mikael Lenz Strube, Lone Gram…
    Citation: Microbiome 2023 11:61
  21. In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less kn...

    Authors: Mark Paul Selda Rivarez, Anja Pecman, Katarina Bačnik, Olivera Maksimović, Ana Vučurović, Gabrijel Seljak, Nataša Mehle, Ion Gutiérrez-Aguirre, Maja Ravnikar and Denis Kutnjak
    Citation: Microbiome 2023 11:60
  22. Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, ...

    Authors: Alba Regueira-Iglesias, Lara Vázquez-González, Carlos Balsa-Castro, Nicolás Vila-Blanco, Triana Blanco-Pintos, Javier Tamames, Maria José Carreira and Inmaculada Tomás
    Citation: Microbiome 2023 11:58
  23. In microbiome fields of study, meta-analyses have proven to be a valuable tool for identifying the technical drivers of variation among studies and results of investigations in several diseases, such as those ...

    Authors: David Broderick, Robyn Marsh, David Waite, Naveen Pillarisetti, Anne B. Chang and Michael W. Taylor
    Citation: Microbiome 2023 11:57
  24. Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts...

    Authors: Yulin Wang, Yulin Zhang, Yu Hu, Lei Liu, Shuang-Jiang Liu and Tong Zhang
    Citation: Microbiome 2023 11:56
  25. 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 11:55

    The original article was published in Microbiome 2023 11:30

  26. Bacterial vaginosis (BV) is a disease caused by vaginal microbiota dysbiosis. Here, we propose the use of synthetic bacterial consortia transplantation (SBCT) for the treatment of Gardnerella vaginalis-induced BV...

    Authors: Yunxia Li, Wei Zhu, Yan Jiang, Duncan James Lessing and Weihua Chu
    Citation: Microbiome 2023 11:54
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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

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