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  1. 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
    Content type: Research Published on:

  2. 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
    Content type: Research Published on:

  3. 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
    Content type: Research Published on:

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

  4. 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
    Content type: Research Published on:

  5. 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
    Content type: Research Published on:

  6. 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
    Content type: Research Published on:

  8. 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
    Content type: Research Published on:

  9. 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
    Content type: Research Published on:

  10. 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
    Content type: Research Published on:

  11. 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
    Content type: Research Published on:

  12. 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
    Content type: Research Published on:

  13. 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
    Content type: Research Published on:

  14. 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
    Content type: Research Published on:

  16. 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
    Content type: Research Published on:

  17. 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
    Content type: Research Published on:

  18. 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
    Content type: Research Published on:

  19. 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
    Content type: Research Published on:

  20. 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
    Content type: Research Published on:

  21. 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
    Content type: Research Published on:

  22. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  26. 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
    Content type: Research Published on:

  27. 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
    Content type: Methodology Published on:

  28. 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
    Content type: Correction Published on:

    The original article was published in Microbiome 2023 11:196

  29. 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
    Content type: Research Published on:

  30. 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
    Content type: Research Published on:

  31. 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
    Content type: Research Published on:

  32. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  34. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  37. Activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. Howe...

    Authors: Xiangyu Fan, Mengzhi Ji, Dashuai Mu, Xianghe Zeng, Zhen Tian, Kaili Sun, Rongfeng Gao, Yang Liu, Xinyuan He, Linwei Wu and Qiang Li
    Citation: Microbiome 2023 11:234
    Content type: Research Published on:

  38. Respiratory mucosal host defense relies on the production of secretory IgA (sIgA) antibodies, but we currently lack a fundamental understanding of how sIgA is induced by contact with microbes and how such immu...

    Authors: Rob van Dalen, Ahmed M. A. Elsherbini, Mareike Harms, Svenja Alber, Regine Stemmler and Andreas Peschel
    Citation: Microbiome 2023 11:233
    Content type: Research Published on:

  39. 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
    Content type: Research Published on:

  40. With the emergence of metagenomic data, multiple links between the gut microbiome and the host health have been shown. Deciphering these complex interactions require evolved analysis methods focusing on the mi...

    Authors: Simon Labarthe, Sandra Plancade, Sebastien Raguideau, Florian Plaza Oñate, Emmanuelle Le Chatelier, Marion Leclerc and Beatrice Laroche
    Citation: Microbiome 2023 11:231
    Content type: Research Published on:

  41. Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported that the gut bacterial community induced ...

    Authors: Haipeng Guo, Xuezhi Fu, Jikun He, Ruoyu Wang, Mengchen Yan, Jing Wang, Pengsheng Dong, Lei Huang and Demin Zhang
    Citation: Microbiome 2023 11:230
    Content type: Research Published on:

  42. Ruminant livestock production is a considerable source of enteric methane (CH4) emissions. In a previous study, we found that dietary inclusions of Bacillus subtilis (BS) and Macleaya cordata extract (MCE) increa...

    Authors: Peng Jia, Li-feng Dong, Yan Tu and Qi-yu Diao
    Citation: Microbiome 2023 11:229
    Content type: Research Published on:

  44. Following descriptive studies on skin microbiota in health and disease, mechanistic studies on the interplay between skin and microbes are on the rise, for which experimental models are in great demand. Here, ...

    Authors: Gijs Rikken, Luca D. Meesters, Patrick A. M. Jansen, Diana Rodijk-Olthuis, Ivonne M. J. J. van Vlijmen-Willems, Hanna Niehues, Jos P. H. Smits, Peter Oláh, Bernhard Homey, Joost Schalkwijk, Patrick L. J. M. Zeeuwen and Ellen H. van den Bogaard
    Citation: Microbiome 2023 11:227
    Content type: Methodology Published on:

  45. Mammalian mucosal barriers secrete antimicrobial peptides (AMPs) as critical, host-derived regulators of the microbiota. However, mechanisms that support microbiota homeostasis in response to inflammatory stim...

    Authors: Ahmed Abdelgawad, Teodora Nicola, Isaac Martin, Brian A. Halloran, Kosuke Tanaka, Comfort Y. Adegboye, Pankaj Jain, Changchun Ren, Charitharth V. Lal, Namasivayam Ambalavanan, Amy E. O’Connell, Tamás Jilling and Kent A. Willis
    Citation: Microbiome 2023 11:226
    Content type: Research Published on:

  46. Plastic-degrading microbial isolates offer great potential to degrade, transform, and upcycle plastic waste. Tandem chemical and biological processing of plastic wastes has been shown to substantially increase...

    Authors: Laura Schaerer, Lindsay Putman, Isaac Bigcraft, Emma Byrne, Daniel Kulas, Ali Zolghadr, Sulihat Aloba, Rebecca Ong, David Shonnard and Stephen Techtmann
    Citation: Microbiome 2023 11:224
    Content type: Research Published on:

  47. Identification of pathogenic bacteria from clinical specimens and evaluating their antimicrobial resistance (AMR) are laborious tasks that involve in vitro cultivation, isolation, and susceptibility testing. R...

    Authors: Pieter-Jan Van Camp, V. B. Surya Prasath, David B. Haslam and Aleksey Porollo
    Citation: Microbiome 2023 11:223
    Content type: Methodology Published on:

  48. Host genetics can shape microbiome composition, but to what extent it does, remains unclear. Like any other complex trait, this important question can be addressed by estimating the heritability (h2) of the micro...

    Authors: Marjolein Bruijning, Julien F. Ayroles, Lucas P. Henry, Britt Koskella, Kyle M. Meyer and C. Jessica E. Metcalf
    Citation: Microbiome 2023 11:222
    Content type: Research Published on:

  49. The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of thre...

    Authors: Guangping Huang, Wenyu Shi, Le Wang, Qingyue Qu, Zhenqiang Zuo, Jinfeng Wang, Fangqing Zhao and Fuwen Wei
    Citation: Microbiome 2023 11:221
    Content type: Research Published on:

  50. The gut microbiota is modulated by a combination of diet, host genetics, and sex effects. The magnitude of these effects and interactions among them is important to understanding inter-individual variability i...

    Authors: Anna C. Salvador, M. Nazmul Huda, Danny Arends, Ahmed M. Elsaadi, C. Anthony Gacasan, Gudrun A. Brockmann, William Valdar, Brian J. Bennett and David W. Threadgill
    Citation: Microbiome 2023 11:220
    Content type: Research Published on:
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