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  1. Content type: Research

    Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe d...

    Authors: Yiran Liang, Jing Zhan, Donghui Liu, Mai Luo, Jiajun Han, Xueke Liu, Chang Liu, Zheng Cheng, Zhiqiang Zhou and Peng Wang

    Citation: Microbiome 2019 7:19

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  2. Content type: Software

    Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replic...

    Authors: Adrian Fritz, Peter Hofmann, Stephan Majda, Eik Dahms, Johannes Dröge, Jessika Fiedler, Till R. Lesker, Peter Belmann, Matthew Z. DeMaere, Aaron E. Darling, Alexander Sczyrba, Andreas Bremges and Alice C. McHardy

    Citation: Microbiome 2019 7:17

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  3. Content type: Research

    Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. Howe...

    Authors: Ke Yu, Shan Yi, Bing Li, Feng Guo, Xingxing Peng, Zhiping Wang, Yang Wu, Lisa Alvarez-Cohen and Tong Zhang

    Citation: Microbiome 2019 7:16

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  4. Content type: Research

    Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements in crop productivity. Here, we conducted a comprehensive, co...

    Authors: Shuo Jiao, Yiqin Xu, Jie Zhang and Yahai Lu

    Citation: Microbiome 2019 7:15

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  5. Content type: Research

    Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interaction...

    Authors: Wencong Shi, Mingcong Li, Guangshan Wei, Renmao Tian, Cuiping Li, Bing Wang, Rongshan Lin, Chunyu Shi, Xiuli Chi, Bo Zhou and Zheng Gao

    Citation: Microbiome 2019 7:14

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  6. Content type: Research

    Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been ...

    Authors: Tomislav Cernava, Armin Erlacher, Jung Soh, Christoph W. Sensen, Martin Grube and Gabriele Berg

    Citation: Microbiome 2019 7:13

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  7. Content type: Research

    The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on ...

    Authors: Aleksei A. Korzhenkov, Stepan V. Toshchakov, Rafael Bargiela, Huw Gibbard, Manuel Ferrer, Alina V. Teplyuk, David L. Jones, Ilya V. Kublanov, Peter N. Golyshin and Olga V. Golyshina

    Citation: Microbiome 2019 7:11

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  8. Content type: Research

    Helminth parasites represent a significant threat to the health of human and animal populations, and there is a growing need for tools to treat, diagnose, and prevent these infections. Recent work has turned t...

    Authors: Christopher A. Gaulke, Mauricio L. Martins, Virginia G. Watral, Ian R. Humphreys, Sean T. Spagnoli, Michael L. Kent and Thomas J. Sharpton

    Citation: Microbiome 2019 7:10

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  9. Content type: Research

    Bile salt hydrolase plays an important role in bile acid-mediated signaling pathways, which regulate lipid absorption, glucose metabolism, and energy homeostasis. Several reports suggest that changes in the co...

    Authors: Ziwei Song, Yuanyuan Cai, Xingzhen Lao, Xue Wang, Xiaoxuan Lin, Yingyun Cui, Praveen Kumar Kalavagunta, Jun Liao, Liang Jin, Jing Shang and Jing Li

    Citation: Microbiome 2019 7:9

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  10. Content type: Research

    Water springs provide important ecosystem services including drinking water supply, recreation, and balneotherapy, but their microbial communities remain largely unknown. In this study, we characterized the sp...

    Authors: Renato Pedron, Alfonso Esposito, Irene Bianconi, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Mario Cristofolini, Nicola Segata and Olivier Jousson

    Citation: Microbiome 2019 7:8

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  11. Content type: Research

    A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the impl...

    Authors: Vanessa Las Heras, Adam G. Clooney, Feargal J. Ryan, Raul Cabrera-Rubio, Pat G. Casey, Cara M. Hueston, Jorge Pinheiro, Justine K. Rudkin, Silvia Melgar, Paul D. Cotter, Colin Hill and Cormac G. M. Gahan

    Citation: Microbiome 2019 7:7

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  12. Content type: Research

    Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbio...

    Authors: Fuyong Li, Thomas C. A. Hitch, Yanhong Chen, Christopher J. Creevey and Le Luo Guan

    Citation: Microbiome 2019 7:6

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  13. Content type: Commentary

    In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems....

    Authors: Jean-Christophe Simon, Julian R. Marchesi, Christophe Mougel and Marc-André Selosse

    Citation: Microbiome 2019 7:5

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  14. Content type: Research

    Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a...

    Authors: Shan-Hua Yang, Kshitij Tandon, Chih-Ying Lu, Naohisa Wada, Chao-Jen Shih, Silver Sung-Yun Hsiao, Wann-Neng Jane, Tzan-Chain Lee, Chi-Ming Yang, Chi-Te Liu, Vianney Denis, Yu-Ting Wu, Li-Ting Wang, Lina Huang, Der-Chuen Lee, Yu-Wei Wu…

    Citation: Microbiome 2019 7:3

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  15. Content type: Research

    The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understa...

    Authors: Huanzi Zhong, John Penders, Zhun Shi, Huahui Ren, Kaiye Cai, Chao Fang, Qiuxia Ding, Carel Thijs, Ellen E. Blaak, Coen D. A. Stehouwer, Xun Xu, Huanming Yang, Jian Wang, Jun Wang, Daisy M. A. E. Jonkers, Ad A. M. Masclee…

    Citation: Microbiome 2019 7:2

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  16. Content type: Research

    Inflammatory bowel diseases (IBD) are a group of complex and multifactorial disorders with unknown etiology. Chronic intestinal inflammation develops against resident intestinal bacteria in genetically suscept...

    Authors: Heather Armstrong, Misagh Alipour, Rosica Valcheva, Michael Bording-Jorgensen, Juan Jovel, Deenaz Zaidi, Prachi Shah, Yuefei Lou, Cory Ebeling, Andrew L. Mason, Dawson Lafleur, Jeremy Jerasi, Gane K.-S. Wong, Karen Madsen, Matthew W. Carroll, Hien Q. Huynh…

    Citation: Microbiome 2019 7:1

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  17. Content type: Research

    Plant phenology has crucial biological, physical, and chemical effects on the biosphere. Phenological drivers have largely been studied, but the role of plant microbiota, particularly rhizosphere microbiota, h...

    Authors: Tao Lu, Mingjing Ke, Michel Lavoie, Yujian Jin, Xiaoji Fan, Zhenyan Zhang, Zhengwei Fu, Liwei Sun, Michael Gillings, Josep Peñuelas, Haifeng Qian and Yong-Guan Zhu

    Citation: Microbiome 2018 6:231

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  18. Content type: Research

    The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chem...

    Authors: Da-Shuai Mu, Qi-Yun Liang, Xiao-Man Wang, De-Chen Lu, Ming-Jing Shi, Guan-Jun Chen and Zong-Jun Du

    Citation: Microbiome 2018 6:230

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  19. Content type: Research

    In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen ca...

    Authors: Alexander Keller, Annette Brandel, Mira C. Becker, Rebecca Balles, Usama Ramadan Abdelmohsen, Markus J. Ankenbrand and Wiebke Sickel

    Citation: Microbiome 2018 6:229

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  20. Content type: Research

    Due to a lack of systematic diagnostics, our understanding of the diversity and role of eukaryotic microbiota in human health is limited. While studies have shown fungal communities to be significant modulator...

    Authors: Ana Popovic, Celine Bourdon, Pauline W. Wang, David S. Guttman, Wieger Voskuijl, Michael E. Grigg, Robert H. J. Bandsma and John Parkinson

    Citation: Microbiome 2018 6:228

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  21. Content type: Research

    The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the ...

    Authors: Nandan P. Deshpande, Stephen M. Riordan, Natalia Castaño-Rodríguez, Marc R. Wilkins and Nadeem O. Kaakoush

    Citation: Microbiome 2018 6:227

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  22. Content type: Methodology

    The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA sequences not truly present in the sample. Contaminants come from...

    Authors: Nicole M. Davis, Diana M. Proctor, Susan P. Holmes, David A. Relman and Benjamin J. Callahan

    Citation: Microbiome 2018 6:226

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  23. Content type: Research

    Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricular...

    Authors: Dagmara Sirová, Jiří Bárta, Karel Šimek, Thomas Posch, Jiří Pech, James Stone, Jakub Borovec, Lubomír Adamec and Jaroslav Vrba

    Citation: Microbiome 2018 6:225

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    The Correction to this article has been published in Microbiome 2019 7:4

  24. Content type: Research

    Antibiotics are commonly used worldwide, and pesticide is a kind of xenobiotic to which humans are frequently exposed. The interactive impact of antibiotics on pesticides has rarely been studied. We aim to inv...

    Authors: Jing Zhan, Yiran Liang, Donghui Liu, Xiaoran Ma, Peize Li, Chang Liu, Xueke Liu, Peng Wang and Zhiqiang Zhou

    Citation: Microbiome 2018 6:224

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  25. Content type: Research

    It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches ...

    Authors: Samuel Jacquiod, Inês Nunes, Asker Brejnrod, Martin A. Hansen, Peter E. Holm, Anders Johansen, Kristian K. Brandt, Anders Priemé and Søren J. Sørensen

    Citation: Microbiome 2018 6:223

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  26. Content type: Research

    Currently, the effect of the bacterial community on cast iron corrosion process does not reach consensus. Moreover, some studies have produced contrasting results, suggesting that bacteria can either accelerat...

    Authors: Guijuan Zhang, Bing Li, Jie Liu, Mingqiang Luan, Long Yue, Xiao-Tao Jiang, Ke Yu and Yuntao Guan

    Citation: Microbiome 2018 6:222

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  27. Content type: Research

    Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. Wh...

    Authors: Jessica D. Forbes, Chih-yu Chen, Natalie C. Knox, Ruth-Ann Marrie, Hani El-Gabalawy, Teresa de Kievit, Michelle Alfa, Charles N. Bernstein and Gary Van Domselaar

    Citation: Microbiome 2018 6:221

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  28. Content type: Short report

    Faecal microbiota transplantation (FMT) is used in the treatment of recurrent Clostridium difficile infection. Its success is typically attributed to the restoration of a diverse microbiota. Viruses (including ba...

    Authors: L. A. Draper, F. J. Ryan, M. K. Smith, J. Jalanka, E. Mattila, P. A. Arkkila, R. P. Ross, R. Satokari and C. Hill

    Citation: Microbiome 2018 6:220

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  29. Content type: Research

    Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degr...

    Authors: Ornella Carrión, Nasmille L. Larke-Mejía, Lisa Gibson, Muhammad Farhan Ul Haque, Javier Ramiro-García, Terry J. McGenity and J. Colin Murrell

    Citation: Microbiome 2018 6:219

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  30. Content type: Research

    The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adol...

    Authors: Jesse R. Willis, Pedro González-Torres, Alexandros A. Pittis, Luis A. Bejarano, Luca Cozzuto, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Antonia Valentín, Ewa Ksiezopolska, Carlos Company, Harris Onywera, Magda Montfort, Antonio Hermoso, Susana Iraola-Guzmán, Ester Saus, Annick Labeeuw…

    Citation: Microbiome 2018 6:218

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  31. Content type: Research

    Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional ca...

    Authors: Anna Edlund, Youngik Yang, Shibu Yooseph, Xuesong He, Wenyuan Shi and Jeffrey S. McLean

    Citation: Microbiome 2018 6:217

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  32. Content type: Research

    The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have ...

    Authors: Lise Alonso, Charline Creuzé-des-Châtelliers, Théo Trabac, Audrey Dubost, Yvan Moënne-Loccoz and Thomas Pommier

    Citation: Microbiome 2018 6:216

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  33. Content type: Research

    The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts’ polyextreme conditions, plants interact with ed...

    Authors: Ramona Marasco, María J. Mosqueira, Marco Fusi, Jean-Baptiste Ramond, Giuseppe Merlino, Jenny M. Booth, Gillian Maggs-Kölling, Don A. Cowan and Daniele Daffonchio

    Citation: Microbiome 2018 6:215

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  34. Content type: Correction

    Following publication of the original article [1], the authors reported a typographic error in scientific notation in the number of reads, the text should read as:

    Authors: Nitin Kumar Singh, Jason M. Wood, Fathi Karouia and Kasthuri Venkateswaran

    Citation: Microbiome 2018 6:214

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    The original article was published in Microbiome 2018 6:204

  35. Content type: Research

    Even though human sweat is odorless, bacterial growth and decomposition of specific odor precursors in it is believed to give rise to body odor in humans. While mechanisms of odor generation have been widely s...

    Authors: Tze Hau Lam, Davide Verzotto, Purbita Brahma, Amanda Hui Qi Ng, Ping Hu, Dan Schnell, Jay Tiesman, Rong Kong, Thi My Uyen Ton, Jianjun Li, May Ong, Yang Lu, David Swaile, Ping Liu, Jiquan Liu and Niranjan Nagarajan

    Citation: Microbiome 2018 6:213

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  36. Content type: Research

    Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata ext...

    Authors: Peng Huang, Yan Zhang, Kangpeng Xiao, Fan Jiang, Hengchao Wang, Dazhi Tang, Dan Liu, Bo Liu, Yisong Liu, Xi He, Hua Liu, Xiubin Liu, Zhixing Qing, Conghui Liu, Jialu Huang, Yuwei Ren…

    Citation: Microbiome 2018 6:211

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  37. Content type: Meeting Report

    The National Cancer Institute (NCI) sponsored a 2-day workshop, “Next Steps in Studying the Human Microbiome and Health in Prospective Studies,” in Bethesda, Maryland, May 16–17, 2017. The workshop brought tog...

    Authors: Rashmi Sinha, Habibul Ahsan, Martin Blaser, J. Gregory Caporaso, Joseph Russell Carmical, Andrew T. Chan, Anthony Fodor, Mitchell H. Gail, Curtis C. Harris, Kathy Helzlsouer, Curtis Huttenhower, Rob Knight, Heidi H. Kong, Gabriel Y. Lai, Diane Leigh Smith Hutchinson, Loic Le Marchand…

    Citation: Microbiome 2018 6:210

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  38. Content type: Research

    The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many org...

    Authors: Celso Martins, Adélia Varela, Céline C. Leclercq, Oscar Núñez, Tomáš Větrovský, Jenny Renaut, Petr Baldrian and Cristina Silva Pereira

    Citation: Microbiome 2018 6:208

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  39. Content type: Research

    Microbiome composition is linked to host functional traits including metabolism and immune function. Drivers of microbiome composition are increasingly well-characterised; however, evidence of group-level micr...

    Authors: Rachael E. Antwis, Jessica M. D. Lea, Bryony Unwin and Susanne Shultz

    Citation: Microbiome 2018 6:207

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  40. Content type: Correction

    Following publication of the original article, the authors recognized that the left and right panels in Fig. 6b had been inadvertently switched during reformatting.

    Authors: Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen and Eugene J. Leys

    Citation: Microbiome 2018 6:206

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    The original article was published in Microbiome 2018 6:153

  41. Content type: Research

    Understanding the mechanism of the sexual dimorphism in susceptibility to obesity and metabolic syndrome (MS) is important for the development of effective interventions for MS.

    Authors: Kanakaraju Kaliannan, Ruairi C. Robertson, Kiera Murphy, Catherine Stanton, Chao Kang, Bin Wang, Lei Hao, Atul K. Bhan and Jing X. Kang

    Citation: Microbiome 2018 6:205

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  42. Content type: Research

    The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-ba...

    Authors: Nitin Kumar Singh, Jason M. Wood, Fathi Karouia and Kasthuri Venkateswaran

    Citation: Microbiome 2018 6:204

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    The Correction to this article has been published in Microbiome 2018 6:214

  43. Content type: Research

    The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility compl...

    Authors: Hooman Derakhshani, Jan C. Plaizier, Jeroen De Buck, Herman W. Barkema and Ehsan Khafipour

    Citation: Microbiome 2018 6:203

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  44. Content type: Research

    Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models’ fundamental biology include the timescales on which microbiota vary and the fact...

    Authors: Justin D. Silverman, Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee and Lawrence A. David

    Citation: Microbiome 2018 6:202

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    The Correction to this article has been published in Microbiome 2018 6:212

  45. Content type: Research

    Travelers’ diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods...

    Authors: Qiyun Zhu, Christopher L. Dupont, Marcus B. Jones, Kevin M. Pham, Zhi-Dong Jiang, Herbert L. DuPont and Sarah K. Highlander

    Citation: Microbiome 2018 6:201

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  46. Content type: Research

    Mastitis, which affects nearly all lactating mammals including human, is generally thought to be caused by local infection of the mammary glands. For treatment, antibiotics are commonly prescribed, which howev...

    Authors: Chen Ma, Zheng Sun, Benhua Zeng, Shi Huang, Jie Zhao, Yong Zhang, Xiaoquan Su, Jian Xu, Hong Wei and Heping Zhang

    Citation: Microbiome 2018 6:200

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