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  1. Content type: Research

    Multistate foodborne disease outbreaks and recalls of apples and apple products contaminated with Listeria monocytogenes demonstrate the need for improved pathogen control in the apple supply chain. Apple process...

    Authors: Xiaoqing Tan, Taejung Chung, Yi Chen, Dumitru Macarisin, Luke LaBorde and Jasna Kovac

    Citation: Microbiome 2019 7:115

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  2. Content type: Research

    Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not ...

    Authors: Juan E. Pérez-Jaramillo, Mattias de Hollander, Camilo A. Ramírez, Rodrigo Mendes, Jos M. Raaijmakers and Víctor J. Carrión

    Citation: Microbiome 2019 7:114

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  3. Content type: Research

    Space environment imposes a range of challenges to mammalian physiology and the gut microbiota, and interactions between the two are thought to be important in mammalian health in space. While previous finding...

    Authors: Peng Jiang, Stefan J. Green, George E. Chlipala, Fred W. Turek and Martha Hotz Vitaterna

    Citation: Microbiome 2019 7:113

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  4. Content type: Research

    Sugar loss due to storage rot has a substantial economic impact on the sugar industry. The gradual spread of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps is an ongoing cha...

    Authors: Peter Kusstatscher, Christin Zachow, Karsten Harms, Johann Maier, Herbert Eigner, Gabriele Berg and Tomislav Cernava

    Citation: Microbiome 2019 7:112

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  5. Content type: Research

    Normal mammalian development and homeostasis are dependent upon the gut microbiota. Antibiotics, essential for the treatment and prophylaxis of bacterial infections, can have collateral effects on the gut micr...

    Authors: Aonghus Lavelle, Thomas Walter Hoffmann, Hang-Phuong Pham, Philippe Langella, Eric Guédon and Harry Sokol

    Citation: Microbiome 2019 7:111

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  6. Content type: Research

    Whole-genome “shotgun” (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be ch...

    Authors: Samuel S. Minot and Amy D. Willis

    Citation: Microbiome 2019 7:110

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  7. Content type: Research

    Despite recent advances in the understanding of the swine gut microbiome at different growth stages, a comprehensive longitudinal study of the lifetime (birth to market) dynamics of the swine gut microbiome is...

    Authors: Xiaofan Wang, Tsungcheng Tsai, Feilong Deng, Xiaoyuan Wei, Jianmin Chai, Joshua Knapp, Jason Apple, Charles V. Maxwell, Jung Ae Lee, Ying Li and Jiangchao Zhao

    Citation: Microbiome 2019 7:109

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  8. Content type: Research

    The plant microbiota is crucial for plant health and growth. Recently, vertical transmission of a beneficial core microbiota was identified for crop seeds, but for native plants, complementary mechanisms are a...

    Authors: Birgit Wassermann, Tomislav Cernava, Henry Müller, Christian Berg and Gabriele Berg

    Citation: Microbiome 2019 7:108

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  9. Content type: Research

    Early treatment is key for optimizing the therapeutic success of drugs, and the current initiating treatment that blocks the progression of bone destruction during the pre-arthritic stages remains unsatisfacto...

    Authors: Hudan Pan, Ruijin Guo, Yanmei Ju, Qi Wang, Jie Zhu, Ying Xie, Yanfang Zheng, Ting Li, Zhongqiu Liu, Linlin Lu, Fei Li, Bin Tong, Liang Xiao, Xun Xu, Elaine Lai-Han Leung, Runze Li…

    Citation: Microbiome 2019 7:107

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  10. Content type: Research

    Streptococcus pneumoniae is a significant global pathogen that colonises the nasopharynx of healthy children. Pneumococcal conjugate vaccines, which reduce nasopharyngeal colonisation of vaccine-type S. pneumonia...

    Authors: Laura K. Boelsen, Eileen M. Dunne, Moana Mika, Stefanie Eggers, Cattram D. Nguyen, F. Tupou Ratu, Fiona M. Russell, E. Kim Mulholland, Markus Hilty and Catherine Satzke

    Citation: Microbiome 2019 7:106

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  11. Content type: Research

    Dysbiosis of gut microbiota exists in the pathogenesis of many autoimmune diseases, including systemic lupus erythematosus (lupus). Lupus patients who experienced pregnancy usually had more severe disease flar...

    Authors: Qinghui Mu, Xavier Cabana-Puig, Jiangdi Mao, Brianna Swartwout, Leila Abdelhamid, Thomas E. Cecere, Haifeng Wang, Christopher M. Reilly and Xin M. Luo

    Citation: Microbiome 2019 7:105

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  12. Content type: Research

    Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in mi...

    Authors: Jiarui Chen, Shelby E. McIlroy, Anand Archana, David M. Baker and Gianni Panagiotou

    Citation: Microbiome 2019 7:104

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  13. Content type: Research

    Accumulating evidence is supporting the protective effect of whole grains against several chronic diseases. Simultaneously, our knowledge is increasing on the impact of gut microbiota on our health and on how ...

    Authors: Ville M. Koistinen, Olli Kärkkäinen, Klaudyna Borewicz, Iman Zarei, Jenna Jokkala, Valérie Micard, Natalia Rosa-Sibakov, Seppo Auriola, Anna-Marja Aura, Hauke Smidt and Kati Hanhineva

    Citation: Microbiome 2019 7:103

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  14. Content type: Research

    Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumul...

    Authors: Irina M. Velsko, James A. Fellows Yates, Franziska Aron, Richard W. Hagan, Laurent A. F. Frantz, Louise Loe, Juan Bautista Rodriguez Martinez, Eros Chaves, Chris Gosden, Greger Larson and Christina Warinner

    Citation: Microbiome 2019 7:102

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  15. Content type: Research

    The past decade of microbiome research has concentrated on cataloging the diversity of taxa in different environments. The next decade is poised to focus on microbial traits and function. Most existing methods...

    Authors: Sharon Bewick, Eliezer Gurarie, Jake L. Weissman, Jess Beattie, Cyrus Davati, Rachel Flint, Peter Thielen, Florian Breitwieser, David Karig and William F. Fagan

    Citation: Microbiome 2019 7:101

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  16. Content type: Research

    The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbi...

    Authors: Natalia Molinero, Lorena Ruiz, Christian Milani, Isabel Gutiérrez-Díaz, Borja Sánchez, Marta Mangifesta, José Segura, Isabel Cambero, Ana Belén Campelo, Carmen María García-Bernardo, Ana Cabrera, José Ignacio Rodríguez, Sonia González, Juan Miguel Rodríguez, Marco Ventura, Susana Delgado…

    Citation: Microbiome 2019 7:100

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  17. Content type: Research

    Eukaryotes are ubiquitous in natural environments such as soil and freshwater. Little is known of their presence in drinking water distribution systems (DWDSs) or of the environmental conditions that affect th...

    Authors: Jenni Inkinen, Balamuralikrishna Jayaprakash, Sallamaari Siponen, Anna-Maria Hokajärvi, Anna Pursiainen, Jenni Ikonen, Ivan Ryzhikov, Martin Täubel, Ari Kauppinen, Jussi Paananen, Ilkka T. Miettinen, Eila Torvinen, Mikko Kolehmainen and Tarja Pitkänen

    Citation: Microbiome 2019 7:99

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  18. Content type: Research

    Western-style diets arouse neuroinflammation and impair emotional and cognitive behavior in humans and animals. Our previous study showed that a high-fructose diet caused the hippocampal neuroinflammatory resp...

    Authors: Jian-Mei Li, Rong Yu, Li-Ping Zhang, Shi-Yu Wen, Shui-Juan Wang, Xiao-Yang Zhang, Qiang Xu and Ling-Dong Kong

    Citation: Microbiome 2019 7:98

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  19. Content type: Short report

    Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to ...

    Authors: Nachiket P. Marathe, Fanny Berglund, Mohammad Razavi, Chandan Pal, Johannes Dröge, Sharvari Samant, Erik Kristiansson and D. G. Joakim Larsson

    Citation: Microbiome 2019 7:97

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  20. Content type: Short report

    The skin is colonized by a large number of microorganisms, most of which are beneficial or harmless. However, disease states of skin have specific microbiome compositions that are different from those of healt...

    Authors: Bernhard Paetzold, Jesse R. Willis, João Pereira de Lima, Nastassia Knödlseder, Holger Brüggemann, Sven R. Quist, Toni Gabaldón and Marc Güell

    Citation: Microbiome 2019 7:95

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  21. Content type: Research

    Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Altho...

    Authors: Bettina Glasl, David G. Bourne, Pedro R. Frade, Torsten Thomas, Britta Schaffelke and Nicole S. Webster

    Citation: Microbiome 2019 7:94

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  22. Content type: Research

    Marine bacteria form complex relationships with eukaryotic hosts, from obligate symbioses to pathogenic interactions. These interactions can be tightly regulated by bioactive molecules, creating a complex syst...

    Authors: Kristen E. Whalen, Jamie W. Becker, Anna M. Schrecengost, Yongjie Gao, Nicole Giannetti and Elizabeth L. Harvey

    Citation: Microbiome 2019 7:93

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  23. Content type: Research

    The symbiotic rumen microbiota is essential for the digestion of plant fibers and contributes to the variation of production and health traits in ruminants. However, to date, the heritability of rumen microbia...

    Authors: Fuyong Li, Changxi Li, Yanhong Chen, Junhong Liu, Chunyan Zhang, Barry Irving, Carolyn Fitzsimmons, Graham Plastow and Le Luo Guan

    Citation: Microbiome 2019 7:92

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  24. Content type: Software

    Microbiomes are complex aggregates of organisms, each of which has its own extensive metabolic network. A variety of metabolites are exchanged between the microbes. The challenge we address is understanding th...

    Authors: Markus Krummenacker, Mario Latendresse and Peter D Karp

    Citation: Microbiome 2019 7:89

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  25. Content type: Software

    Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effe...

    Authors: G. A. Arango-Argoty, D. Dai, A. Pruden, P. Vikesland, L. S. Heath and L. Zhang

    Citation: Microbiome 2019 7:88

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  26. Content type: Research

    Residual disinfection is often used to suppress biological growth in drinking water distribution systems (DWDSs), but not without undesirable side effects. In this study, water-main biofilms, drinking water, a...

    Authors: Michael B. Waak, Raymond M. Hozalski, Cynthia Hallé and Timothy M. LaPara

    Citation: Microbiome 2019 7:87

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  27. Content type: Research

    Beef cattle in North America frequently receive an antibiotic injection after feedlot placement to control and manage bovine respiratory disease. The potential collateral effect of these antibiotics on the bov...

    Authors: Devin B. Holman, Wenzhu Yang and Trevor W. Alexander

    Citation: Microbiome 2019 7:86

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  28. Content type: Software

    Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods ...

    Authors: Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas and Peer Bork

    Citation: Microbiome 2019 7:84

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  29. Content type: Research

    The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ...

    Authors: Limei Lin, Fei Xie, Daming Sun, Junhua Liu, Weiyun Zhu and Shengyong Mao

    Citation: Microbiome 2019 7:83

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  30. Content type: Research

    The particulate and biological components of indoor air have a substantial impact on human health, especially immune respiratory conditions such as asthma. To better explore the relationship between allergens,...

    Authors: Miles Richardson, Neil Gottel, Jack A. Gilbert, Julian Gordon, Prasanthi Gandhi, Rachel Reboulet and Jarrad T. Hampton-Marcell

    Citation: Microbiome 2019 7:82

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  31. Content type: Correction

    Following publication of the original article [1], the authors reported an error in Fig. 2. The correct figure is shown below.

    Authors: Junhyung Kim, Jae-Ho Guk, Seung-Hyun Mun, Jae-Uk An, Hyokeun Song, Jinshil Kim, Sangryeol Ryu, Byeonghwa Jeon and Seongbeom Cho

    Citation: Microbiome 2019 7:81

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    The original article was published in Microbiome 2019 7:67

  32. Content type: Research

    Staphylococcus epidermidis is one of the most abundant colonizers of healthy human mucosa including that in the respiratory tract. As the respiratory microbiome has been linked to host immune responses, this stud...

    Authors: Hyun Jik Kim, Ara Jo, Yung Jin Jeon, Sujin An, Kang-Mu Lee, Sang Sun Yoon and Jae Young Choi

    Citation: Microbiome 2019 7:80

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  33. Content type: Review

    The skin constitutes the primary physical barrier between vertebrates and their external environment. Characterization of skin microorganisms is essential for understanding how a host evolves in association wi...

    Authors: Ashley A. Ross, Aline Rodrigues Hoffmann and Josh D. Neufeld

    Citation: Microbiome 2019 7:79

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  34. Content type: Research

    The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natu...

    Authors: Chiara Borsetto, Gregory C. A. Amos, Ulisses Nunes da Rocha, Alex L. Mitchell, Robert D. Finn, Rabah Forar Laidi, Carlos Vallin, David A. Pearce, Kevin K. Newsham and Elizabeth M. H. Wellington

    Citation: Microbiome 2019 7:78

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  35. Content type: Research

    Biochar amendments have been widely proposed as a conventional and efficient strategy to promote soil organic carbon (SOC) sequestration via negative priming. Unfortunately, the extent and biological mechanism...

    Authors: Lijun Chen, Yuji Jiang, Chao Liang, Yu Luo, Qinsong Xu, Cheng Han, Qiguo Zhao and Bo Sun

    Citation: Microbiome 2019 7:77

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  36. Content type: Research

    Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid,...

    Authors: Allison M. Veach, Reese Morris, Daniel Z. Yip, Zamin K. Yang, Nancy L. Engle, Melissa A. Cregger, Timothy J. Tschaplinski and Christopher W. Schadt

    Citation: Microbiome 2019 7:76

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  37. Content type: Methodology

    The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconju...

    Authors: Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming and Ines Thiele

    Citation: Microbiome 2019 7:75

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  38. Content type: Research

    In rhesus macaques, simian immunodeficiency virus infection is followed by expansion of enteric viruses but has a limited impact on the gut bacteriome. To understand the longitudinal effects of HIV-1 infection...

    Authors: Muntsa Rocafort, Marc Noguera-Julian, Javier Rivera, Lucía Pastor, Yolanda Guillén, Jost Langhorst, Mariona Parera, Inacio Mandomando, Jorge Carrillo, Víctor Urrea, Cristina Rodríguez, Maria Casadellà, Maria Luz Calle, Bonaventura Clotet, Julià Blanco, Denise Naniche…

    Citation: Microbiome 2019 7:73

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  39. Content type: Research

    The World Health Organization classified processed and red meat consumption as “carcinogenic” and “probably carcinogenic”, respectively, to humans. Haem iron from meat plays a role in the promotion of colorect...

    Authors: Océane C. B. Martin, Maïwenn Olier, Sandrine Ellero-Simatos, Nathalie Naud, Jacques Dupuy, Laurence Huc, Sylviane Taché, Vanessa Graillot, Mathilde Levêque, Valérie Bézirard, Cécile Héliès-Toussaint, Florence Blas Y. Estrada, Valérie Tondereau, Yannick Lippi, Claire Naylies, Lindsey Peyriga…

    Citation: Microbiome 2019 7:72

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  40. Content type: Research

    Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Con...

    Authors: Huayu Qin, Shang Wang, Kai Feng, Zhili He, Marko P. J. Virta, Weiguo Hou, Hailiang Dong and Ye Deng

    Citation: Microbiome 2019 7:71

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  41. Content type: Research

    The microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, arc...

    Authors: Anukriti Sharma, Miles Richardson, Lauren Cralle, Christopher E. Stamper, Juan P. Maestre, Kelly A. Stearns-Yoder, Teodor T. Postolache, Katherine L. Bates, Kerry A. Kinney, Lisa A. Brenner, Christopher A. Lowry, Jack A. Gilbert and Andrew J. Hoisington

    Citation: Microbiome 2019 7:70

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  42. Content type: Research

    In biogas plants, complex microbial communities produce methane and carbon dioxide by anaerobic digestion of biomass. For the characterization of the microbial functional networks, samples of 11 reactors were ...

    Authors: R. Heyer, K. Schallert, C. Siewert, F. Kohrs, J. Greve, I. Maus, J. Klang, M. Klocke, M. Heiermann, M. Hoffmann, S. Püttker, M. Calusinska, R. Zoun, G. Saake, D. Benndorf and U. Reichl

    Citation: Microbiome 2019 7:69

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  43. Content type: Research

    Coronary artery disease (CAD) is associated with gut microbiota alterations in different populations. Gut microbe-derived metabolites have been proposed as markers of major adverse cardiac events. However, the...

    Authors: Honghong Liu, Xi Chen, Xiaomin Hu, Haitao Niu, Ran Tian, Hui Wang, Haiyu Pang, Lingjuan Jiang, Bintao Qiu, Xiuting Chen, Yang Zhang, Yiyangzi Ma, Si Tang, Hanyu Li, Siqin Feng, Shuyang Zhang…

    Citation: Microbiome 2019 7:68

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  44. Content type: Research

    Originating from poultry, particularly chickens, Campylobacter jejuni is the leading foodborne pathogen worldwide and a major cause of campylobacteriosis. Isolating C. jejuni is difficult due to its specific grow...

    Authors: Junhyung Kim, Jae-Ho Guk, Seung-Hyun Mun, Jae-Uk An, Hyokeun Song, Jinshil Kim, Sangryeol Ryu, Byeonghwa Jeon and Seongbeom Cho

    Citation: Microbiome 2019 7:67

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    The Correction to this article has been published in Microbiome 2019 7:81

  45. Content type: Research

    Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicit...

    Authors: Bo-Young Hong, Takanori Sobue, Linda Choquette, Amanda K. Dupuy, Angela Thompson, Joseph A. Burleson, Andrew L. Salner, Peter K. Schauer, Pujan Joshi, Evan Fox, Dong-Guk Shin, George M. Weinstock, Linda D. Strausbaugh, Anna Dongari-Bagtzoglou, Douglas E. Peterson and Patricia I. Diaz

    Citation: Microbiome 2019 7:66

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