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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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

  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive s...

    Authors: Yanhong Cao, Tong Feng, Yingjian Wu, Yixue Xu, Li Du, Teng Wang, Yuhong Luo, Yan Wang, Zhipeng Li, Zeyi Xuan, Shaomei Chen, Na Yao, Na L. Gao, Qian Xiao, Kongwei Huang, Xiaobo Wang…
    Citation: Microbiome 2023 11:219
  32. Major advances over the past decade in molecular ecology are providing access to soil fungal diversity in forest ecosystems worldwide, but the diverse functions and metabolic capabilities of this microbial com...

    Authors: Qingchao Zeng, Annie Lebreton, Lucas Auer, Xiaowu Man, Liukun Jia, Gengshen Wang, Sai Gong, Vincent Lombard, Marc Buée, Gang Wu, Yucheng Dai, Zhuliang Yang and Francis M. Martin
    Citation: Microbiome 2023 11:217
  33. High-copper diets have been widely used to promote growth performance of pigs, but excess copper supplementation can also produce negative effects on ecosystem stability and organism health. High-copper supple...

    Authors: Yang Wen, Luqing Yang, Zhenyu Wang, Xiaoyi Liu, Meng Gao, Yunhui Zhang, Junjun Wang and Pingli He
    Citation: Microbiome 2023 11:218
  34. Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic a...

    Authors: Niuniu Ji, Di Liang, Lindsay V. Clark, Erik J. Sacks and Angela D. Kent
    Citation: Microbiome 2023 11:216
  35. The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the earl...

    Authors: Dangdang Wang, Luyu Chen, Guangfu Tang, Junjian Yu, Jie Chen, Zongjun Li, Yangchun Cao, Xinjian Lei, Lu Deng, Shengru Wu, Le Luo Guan and Junhu Yao
    Citation: Microbiome 2023 11:215
  36. Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in...

    Authors: Daniel Garrido-Sanz, Senka Čaušević, Jordan Vacheron, Clara M. Heiman, Vladimir Sentchilo, Jan Roelof van der Meer and Christoph Keel
    Citation: Microbiome 2023 11:214
  37. Aging-related fertility decline is a prevalent concern globally. Male reproductive system aging is mainly characterized by a decrease in sperm quality and fertility. While it is known that intestinal physiolog...

    Authors: Zirun Jin, Yuzhuo Yang, Yalei Cao, Qi Wen, Yu Xi, Jianxing Cheng, Qiancheng Zhao, Jiaming Weng, Kai Hong, Hui Jiang, Jing Hang and Zhe Zhang
    Citation: Microbiome 2023 11:212
  38. Ocean warming is a leading cause of increasing episodes of coral bleaching, the dissociation between coral hosts and their dinoflagellate algal symbionts in the family Symbiodiniaceae. While the diversity and ...

    Authors: Chenying Wang, Xinqing Zheng, Hagit Kvitt, Huaxia Sheng, Danye Sun, Gaofeng Niu, Dan Tchernov and Tuo Shi
    Citation: Microbiome 2023 11:211
  39. The terrestrial subsurface is home to a significant proportion of the Earth’s microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and po...

    Authors: Carl-Eric Wegner, Raphaela Stahl, Irina Velsko, Alex Hübner, Zandra Fagernäs, Christina Warinner, Robert Lehmann, Thomas Ritschel, Kai U. Totsche and Kirsten Küsel
    Citation: Microbiome 2023 11:210
  40. The existence of the gut microbiota produces an “individual drug reaction.” As members of the intestinal microbiota, probiotics, although they have prebiotic functions, may accelerate the degradation of drugs,...

    Authors: Siyuan Shen, Jun Wang, Chenchen Ma, Yanni Chen, Hao Ding and Jiachao Zhang
    Citation: Microbiome 2023 11:209
  41. The gut microbiota contributes to macrophage-mediated inflammation in adipose tissue with consumption of an obesogenic diet, thus driving the development of metabolic syndrome. There is a need to identify and ...

    Authors: N. K. Newman, Y. Zhang, J. Padiadpu, C. L. Miranda, A. A. Magana, C. P. Wong, K. A. Hioki, J. W. Pederson, Z. Li, M. Gurung, A. M. Bruce, K. Brown, G. Bobe, T. J. Sharpton, N. Shulzhenko, C. S. Maier…
    Citation: Microbiome 2023 11:208
  42. Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and a...

    Authors: Molly Mills, Seungjun Lee, Barbara A. Piperata, Rebecca Garabed, Boseung Choi and Jiyoung Lee
    Citation: Microbiome 2023 11:207
  43. Authors: Yacine Amar, Danielle Rogner, Rafaela L. Silva, Bärbel U. Foesel, Minhaz Ud‑Dean, Ilias Lagkouvardos, Susanne A. Steimle‑Grauer, Sebastian Niedermeier, Susanne Kublik, Manja Jargosch, Matthias Heinig, Jenny Thomas, Stefanie Eyerich, Jakob D. Wikström, Michael Schloter, Kilian Eyerich…
    Citation: Microbiome 2023 11:206

    The original article was published in Microbiome 2023 11:162

  44. In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic was...

    Authors: Francesca De Filippis, Marco Bonelli, Daniele Bruno, Giuseppina Sequino, Aurora Montali, Marcella Reguzzoni, Edoardo Pasolli, Davide Savy, Silvana Cangemi, Vincenza Cozzolino, Gianluca Tettamanti, Danilo Ercolini, Morena Casartelli and Silvia Caccia
    Citation: Microbiome 2023 11:205
  45. Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7–8% salini...

    Authors: Elisse Magnuson, Ianina Altshuler, Nastasia J. Freyria, Richard J. Leveille and Lyle G. Whyte
    Citation: Microbiome 2023 11:203
  46. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease that carries mutations in NOTCH3. The clinical manifestations are influenced...

    Authors: Sheng Liu, Xuejiao Men, Yang Guo, Wei Cai, Ruizhen Wu, Rongsui Gao, Weicong Zhong, Huating Guo, Hengfang Ruan, Shuli Chou, Junrui Mai, Suning Ping, Chao Jiang, Hongwei Zhou, Xiangyu Mou, Wenjing Zhao…
    Citation: Microbiome 2023 11:202

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