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  1. The observation that the intestinal microbiota is  central in the development of IBD suggests that dietary fiber, the microbiota’s primary source of nourishment, could play a central role in these diseases. Ac...

    Authors: Erica Bonazzi, Alexis Bretin, Lucile Vigué, Fuhua Hao, Andrew D. Patterson, Andrew T. Gewirtz and Benoit Chassaing
    Citation: Microbiome 2024 12:5
  2. The overgrowth of Desulfovibrio, an inflammation promoting flagellated bacteria, has been found in ulcerative colitis (UC) patients. However, the molecular mechanism in promoting colitis remains unestablished.

    Authors: Runxiang Xie, Yu Gu, Mengfan Li, Lingfeng Li, Yunwei Yang, Yue Sun, Bingqian Zhou, Tianyu Liu, Sinan Wang, Wentian Liu, Rongcun Yang, Xiaomin Su, Weilong Zhong, Bangmao Wang and Hailong Cao
    Citation: Microbiome 2024 12:4
  3. In anoxic coastal and marine sediments, degradation of methylated compounds is the major route to the production of methane, a powerful greenhouse gas. Dimethylsulphide (DMS) is the most abundant biogenic orga...

    Authors: S. L. Tsola, Y. Zhu, Y. Chen, I. A. Sanders, C. K. Economou, V. Brüchert and Ö. Eyice
    Citation: Microbiome 2024 12:3
  4. Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in t...

    Authors: Ming Li, Hui Liang, Hongwei Yang, Qianwen Ding, Rui Xia, Jie Chen, Wenhao Zhou, Yalin Yang, Zhen Zhang, Yuanyuan Yao, Chao Ran and Zhigang Zhou
    Citation: Microbiome 2024 12:2
  5. The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenc...

    Authors: Abdelrahman Alahmad, Mourad Harir, Sylvain Fochesato, Joris Tulumello, Alesia Walker, Mohamed Barakat, Papa Mamadou Sitor Ndour, Philippe Schmitt-Kopplin, Laurent Cournac, Laurent Laplaze, Thierry Heulin and Wafa Achouak
    Citation: Microbiome 2024 12:1
  6. Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (A...

    Authors: Rachel M. Bleich, Chuang Li, Shan Sun, Ju-Hyun Ahn, Belgin Dogan, Cassandra J. Barlogio, Christopher A. Broberg, Adrienne R. Franks, Emily Bulik-Sullivan, Ian M. Carroll, Kenneth W. Simpson, Anthony A. Fodor and Janelle C. Arthur
    Citation: Microbiome 2023 11:277
  7. Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. Howeve...

    Authors: Danrui Wang, Jiangtao Li, Lei Su, Wenli Shen, Kai Feng, Xi Peng, Zhujun Wang, Bo Zhao, Zheng Zhang, Zhaojing Zhang, Étienne Yergeau and Ye Deng
    Citation: Microbiome 2023 11:276
  8. The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in ...

    Authors: Zixuan Xie, Aleix Canalda-Baltrons, Christophe d’Enfert and Chaysavanh Manichanh
    Citation: Microbiome 2023 11:275
  9. Insects living in nutritionally poor environments often establish long-term relationships with intracellular bacteria that supplement their diets and improve their adaptive and invasive powers. Even though the...

    Authors: Mariana Galvão Ferrarini, Agnès Vallier, Carole Vincent-Monégat, Elisa Dell’Aglio, Benjamin Gillet, Sandrine Hughes, Ophélie Hurtado, Guy Condemine, Anna Zaidman-Rémy, Rita Rebollo, Nicolas Parisot and Abdelaziz Heddi
    Citation: Microbiome 2023 11:274
  10. Oral infection with cysts is the main transmission route of Toxoplasma gondii (T. gondii), which leads to lethal intestinal inflammation. It has been widely recognized that T. gondii infection alters the composit...

    Authors: Jing Yang, Songhao Liu, Qian Zhao, Xiaobing Li and Kangfeng Jiang
    Citation: Microbiome 2023 11:273
  11. Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them re...

    Authors: Meng Li, Mubashar Raza, Shuang Song, Lingwei Hou, Zhi-Feng Zhang, Min Gao, Jun-En Huang, Fang Liu and Lei Cai
    Citation: Microbiome 2023 11:272
  12. Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs)...

    Authors: Camille Prioux, Romie Tignat-Perrier, Ophélie Gervais, Tristan Estaque, Quentin Schull, Stéphanie Reynaud, Eric Béraud, Bastien Mérigot, Anaïs Beauvieux, Maria-Isabelle Marcus, Justine Richaume, Olivier Bianchimani, Adrien Cheminée, Denis Allemand and Christine Ferrier-Pagès
    Citation: Microbiome 2023 11:271
  13. Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecos...

    Authors: Wenchao Deng, Zihao Zhao, Yufang Li, Rongguang Cao, Mingming Chen, Kai Tang, Deli Wang, Wei Fan, Anyi Hu, Guangcheng Chen, Chen-Tung Arthur Chen and Yao Zhang
    Citation: Microbiome 2023 11:270
  14. Ileal pouch-anal anastomosis (IPAA) is the standard of care after total proctocolectomy for ulcerative colitis (UC). Around 50% of patients will experience pouchitis, an idiopathic inflammatory condition. Anti...

    Authors: Zhi-Luo Deng, Dietmar H. Pieper, Andreas Stallmach, Arndt Steube, Marius Vital, Michael Reck and Irene Wagner-Döbler
    Citation: Microbiome 2023 11:269
  15. Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and...

    Authors: Marcell Costa de Medeiros, Stephanie The, Emily Bellile, Nickole Russo, Ligia Schmitd, Erika Danella, Priyanka Singh, Rajat Banerjee, Christine Bassis, George R. Murphy III, Maureen A. Sartor, Isabelle Lombaert, Thomas M. Schmidt, Avi Eisbruch, Carol Anne Murdoch-Kinch, Laura Rozek…
    Citation: Microbiome 2023 11:268
  16. A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microb...

    Authors: Johanna B. Holm, Michael T. France, Pawel Gajer, Bing Ma, Rebecca M. Brotman, Michelle Shardell, Larry Forney and Jacques Ravel
    Citation: Microbiome 2023 11:259

    The Correction to this article has been published in Microbiome 2024 12:21

  17. Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship...

    Authors: Datao Lin, Jinni Hong, Benjamin Sanogo, Shuling Du, Suoyu Xiang, Jerome Ho-Lam Hui, Tao Ding, Zhongdao Wu and Xi Sun
    Citation: Microbiome 2023 11:267
  18. Many studies have investigated how nanoplastics (NPs) exposure mediates nerve and intestinal toxicity through a dysregulated brain-gut axis interaction, but there are few studies aimed at alleviating those eff...

    Authors: Miaomiao Teng, Yunxia Li, Xiaoli Zhao, Jason C. White, Lihui Zhao, Jiaqi Sun, Wentao Zhu and Fengchang Wu
    Citation: Microbiome 2023 11:266
  19. The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genom...

    Authors: Yanting Liu, Thorsten Brinkhoff, Martine Berger, Anja Poehlein, Sonja Voget, Lucas Paoli, Shinichi Sunagawa, Rudolf Amann and Meinhard Simon
    Citation: Microbiome 2023 11:265
  20. Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systemati...

    Authors: Kait F. Al, Benjamin R. Joris, Brendan A. Daisley, John A. Chmiel, Jennifer Bjazevic, Gregor Reid, Gregory B. Gloor, John D. Denstedt, Hassan Razvi and Jeremy P. Burton
    Citation: Microbiome 2023 11:263
  21. Diet-induced dyslipidemia is linked to the gut microbiota, but the causality of microbiota-host interaction affecting lipid metabolism remains controversial. Here, the humanized dyslipidemia mice model was suc...

    Authors: Hongtao Xu, Fang Fang, Kaizhang Wu, Jiangping Song, Yaqian Li, Xingyu Lu, Juncheng Liu, Liuyang Zhou, Wenqing Yu, Fei Yu and Jie Gao
    Citation: Microbiome 2023 11:262
  22. Declines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So fa...

    Authors: Siqi Tao, G. F. (Ciska) Veen, Naili Zhang, Tianhe Yu and Laiye Qu
    Citation: Microbiome 2023 11:261
  23. The modulation of immune responses by probiotics is crucial for local and systemic immunity. Recent studies have suggested a correlation between gut microbiota and lung immunity, known as the gut–lung axis. Ho...

    Authors: Seungil Kim, Sohyeon Lee, Tae-Young Kim, Su-Hyun Lee, Sang-Uk Seo and Mi-Na Kweon
    Citation: Microbiome 2023 11:260
  24. While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental...

    Authors: Javad Sadeghi, Subba Rao Chaganti, Timothy B. Johnson and Daniel D. Heath
    Citation: Microbiome 2023 11:258
  25. The microbiota of multicellular organisms undergoes considerable changes during host ontogeny but the general mechanisms that control community assembly and succession are poorly understood. Here, we use bacte...

    Authors: H. Domin, J. Zimmermann, J. Taubenheim, G. Fuentes Reyes, L. Saueressig, D. Prasse, M. Höppner, R. A. Schmitz, U. Hentschel, C. Kaleta and S. Fraune
    Citation: Microbiome 2023 11:257
  26. Intestinal epithelial cell (IEC) mitochondrial dysfunction involvement in inflammatory bowel diseases (IBD), including Crohn’s disease affecting the small intestine, is emerging in recent studies. As the inter...

    Authors: Kibrom M. Alula, Alexander S. Dowdell, Brittany LeBere, J. Scott Lee, Cassandra L. Levens, Kristine A. Kuhn, Benny A. Kaipparettu, Winston E. Thompson, Richard S. Blumberg, Sean P. Colgan and Arianne L. Theiss
    Citation: Microbiome 2023 11:256
  27. Parkinson’s disease (PD) is a common chronic neurological disorder with a high risk of disability and no cure. Periodontitis is an infectious bacterial disease occurring in periodontal supporting tissues. Stud...

    Authors: Xue-Bing Bai, Shuo Xu, Lu-Jun Zhou, Xiao-Qian Meng, Yu-Lin Li, Yan-Lin Chen, Yi-Han Jiang, Wen-Zhen Lin, Bo-Yan Chen, Lin-Juan Du, Guo-Cai Tian, Yan Liu, Sheng-Zhong Duan and Ya-Qin Zhu
    Citation: Microbiome 2023 11:254
  28. The within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intr...

    Authors: Yan Sun, Minxiao Wang, Lei Cao, Inge Seim, Li Zhou, Jianwei Chen, Hao Wang, Zhaoshan Zhong, Hao Chen, Lulu Fu, Mengna Li, Chaolun Li and Song Sun
    Citation: Microbiome 2023 11:253
  29. Reports regarding the presence of bacteria in the fetal environment remain limited and controversial. Recently, extracellular vesicles secreted by the human gut microbiota have emerged as a novel mechanism for...

    Authors: Anna Kaisanlahti, Jenni Turunen, Nadiya Byts, Anatoliy Samoylenko, Genevieve Bart, Nikke Virtanen, Mysore V. Tejesvi, Artem Zhyvolozhnyi, Sonia Sarfraz, Sohvi Kumpula, Jenni Hekkala, Sonja Salmi, Olga Will, Johanna Korvala, Niko Paalanne, Pande Putu Erawijantari…
    Citation: Microbiome 2023 11:249
  30. Perturbations of animal-associated microbiomes from chemical stress can affect host physiology and health. While dysbiosis induced by antibiotic treatments and disease is well known, chemical, nonantibiotic dr...

    Authors: Rebecca J. Stevick, Bianca Audrain, Sébastien Bedu, Nicolas Dray, Jean-Marc Ghigo and David Pérez-Pascual
    Citation: Microbiome 2023 11:252
  31. Alterations of the uterine microbiome are closely associated with various intrauterine diseases and physiological conditions, which are well-established in mammals. However, as representative oviparous animals...

    Authors: Dong Dai, Jing Wang, Haijun Zhang, Shugeng Wu and Guanghai Qi
    Citation: Microbiome 2023 11:251
  32. Ticks are major vectors of diseases affecting humans such as Lyme disease or domestic animals such as anaplasmosis. Cross-alteration of the vertebrate host skin microbiome and the tick microbiome may be essent...

    Authors: Nathalie Boulanger, Jean-Louis-Marie Insonere, Sebastian Van Blerk, Cathy Barthel, Céline Serres, Olivier Rais, Alain Roulet, Florence Servant, Olivier Duron and Benjamin Lelouvier
    Citation: Microbiome 2023 11:250
  33. Perioperative neurocognitive disorders (PND) are the most common postoperative complications with few therapeutic options. Gut microbial dysbiosis is associated with neurological diseases; however, the mechani...

    Authors: Cailong Pan, Huiwen Zhang, Lingyuan Zhang, Lu Chen, Lu Xu, Ning Xu, Xue Liu, Qinghai Meng, Xiaoliang Wang and Zhi-Yuan Zhang
    Citation: Microbiome 2023 11:248
  34. The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonizati...

    Authors: Anna Hakobyan, Stefanie Velte, Wiebke Sickel, Dietmar Quandt, Alexandra Stoll and Claudia Knief
    Citation: Microbiome 2023 11:246
  35. Autism spectrum disorder (ASD) has been associated with intrauterine growth restriction (IUGR), but the underlying mechanisms are unclear.

    Authors: Tingting Wang, Beidi Chen, Mingcui Luo, Lulu Xie, Mengxi Lu, Xiaoqian Lu, Shuai Zhang, Liyi Wei, Xinli Zhou, Baozhen Yao, Hui Wang and Dan Xu
    Citation: Microbiome 2023 11:245
  36. The true bugs (Heteroptera) occupy nearly all of the known ecological niches of insects. Among them, as a group containing more than 30,000 species, the phytophagous true bugs are making increasing impacts on ...

    Authors: Zi-Wen Yang, Jiu-Yang Luo, Yu Men, Zhi-Hui Liu, Zi-Kai Zheng, Yan-Hui Wang and Qiang Xie
    Citation: Microbiome 2023 11:244
  37. The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial So...

    Authors: Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard and Rayan Chikhi
    Citation: Microbiome 2023 11:243
  38. Authors: Yao Fu, Songyang Yao, Tiankun Wang, Yongqiang Lu, Huigang Han, Xuening Liu, Dongying Lv, Xiao Ma, Shengyu Guan, Yujun Yao, Yunjie Liu, Haiying Yu, Shengli Li, Ning Yang and Guoshi Liu
    Citation: Microbiome 2023 11:242

    The original article was published in Microbiome 2023 11:196

  39. The mechanism of microbiota assembly is one of the main problems in microbiome research, which is also the primary theoretical basis for precise manipulation of microbial communities. Bacterial quorum sensing ...

    Authors: Ying Su, Ming-ying Xu, Ying Cui, Run-zhi Chen, Li-xiang Xie, Jing-xiang Zhang, Yong-qiu Chen and Tao Ding
    Citation: Microbiome 2023 11:241
  40. Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in...

    Authors: Yorick Minnebo, Karen Delbaere, Valerie Goethals, Jeroen Raes, Tom Van de Wiele and Kim De Paepe
    Citation: Microbiome 2023 11:240
  41. Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for ene...

    Authors: Abhishek Srivastava, Daniele De Corte, Juan A. L. Garcia, Brandon K. Swan, Ramunas Stepanauskas, Gerhard J. Herndl and Eva Sintes
    Citation: Microbiome 2023 11:239
  42. Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly de...

    Authors: Yanjiao Li, Kang Mao, Yitian Zang, Guwei Lu, Qinghua Qiu, Kehui Ouyang, Xianghui Zhao, Xiaozhen Song, Lanjiao Xu, Huan Liang and Mingren Qu
    Citation: Microbiome 2023 11:238
  43. The widespread nature of plastic pollution has given rise to wide scientific and social concern regarding the capacity of these materials to serve as vectors for pathogenic bacteria and reservoirs for Antimicr...

    Authors: Vinko Zadjelovic, Robyn J. Wright, Chiara Borsetto, Jeannelle Quartey, Tyler N. Cairns, Morgan G. I. Langille, Elizabeth M. H. Wellington and Joseph A. Christie-Oleza
    Citation: Microbiome 2023 11:225
  44. Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distr...

    Authors: Clement Coclet, Patrick O. Sorensen, Ulas Karaoz, Shi Wang, Eoin L. Brodie, Emiley A. Eloe-Fadrosh and Simon Roux
    Citation: Microbiome 2023 11:237
  45. Modern dairy diets have shifted from being forage-based to grain and energy dense. However, feeding high-starch diets can lead to a metabolic disturbance that is linked to dysregulation of the gastrointestinal...

    Authors: Yuchao Zhao, Shiqiang Yu, Huiying Zhao, Liuxue Li, Yuqin Li, Ming Liu and Linshu Jiang
    Citation: Microbiome 2023 11:236
  46. Companion animals can contribute to the physical and mental health of people and often live in very close association with their owners. However, the antibiotic resistome carried by companion animals and the i...

    Authors: Yiwen Yang, Xinwen Hu, Shuang Cai, Nan Hu, Yilin Yuan, Yinbao Wu, Yan Wang, Jiandui Mi and Xindi Liao
    Citation: Microbiome 2023 11:235
  47. Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential ...

    Authors: Mirja Thomsen, Axel Künstner, Inken Wohlers, Michael Olbrich, Tim Lenfers, Takafumi Osumi, Yotaro Shimazaki, Koji Nishifuji, Saleh M. Ibrahim, Adrian Watson, Hauke Busch and Misa Hirose
    Citation: Microbiome 2023 11:232

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