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  2. 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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  3. 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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  4. 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

  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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

  19. 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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  20. Content type: Research

    Ubiquitous in natural and engineered ecosystems, microbial immigration is one of the mechanisms shaping community assemblage. However, quantifying immigration impact remains challenging especially at individua...

    Authors: Ran Mei, Jinha Kim, Fernanda P. Wilson, Benjamin T. W. Bocher and Wen-Tso Liu

    Citation: Microbiome 2019 7:65

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  21. Content type: Research

    The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to t...

    Authors: Typhaine Le Doujet, Concetta De Santi, Terje Klemetsen, Erik Hjerde, Nils-Peder Willassen and Peik Haugen

    Citation: Microbiome 2019 7:64

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  22. Content type: Research

    Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is more sustainable than most other cropping systems. Diazotrop...

    Authors: Hazem Sharaf, Richard R. Rodrigues, Jinyoung Moon, Bo Zhang, Kerri Mills and Mark A. Williams

    Citation: Microbiome 2019 7:63

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  23. Content type: Letter to the Editor

    Metagenomic next-generation sequencing (mNGS) experiments involving small amounts of nucleic acid input are highly susceptible to erroneous conclusions resulting from unintentional sequencing of occult contami...

    Authors: M. S. Zinter, M. Y. Mayday, K. K. Ryckman, L. L. Jelliffe-Pawlowski and J. L. DeRisi

    Citation: Microbiome 2019 7:62

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  24. Content type: Short report

    Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly...

    Authors: Krithika Arumugam, Caner Bağcı, Irina Bessarab, Sina Beier, Benjamin Buchfink, Anna Górska, Guanglei Qiu, Daniel H. Huson and Rohan B. H. Williams

    Citation: Microbiome 2019 7:61

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  25. Content type: Research

    Current knowledge of the urinary tract microbiome is limited to urine analysis and analysis of biofilms formed on Foley catheters. Bacterial biofilms on ureteral stents have rarely been investigated, and no cu...

    Authors: Matthias T. Buhmann, Dominik Abt, Oliver Nolte, Thomas R. Neu, Sebastian Strempel, Werner C. Albrich, Patrick Betschart, Valentin Zumstein, Antonia Neels, Katharina Maniura-Weber and Qun Ren

    Citation: Microbiome 2019 7:60

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  26. Content type: Research

    The Mariana Trench is the deepest known site in the Earth’s oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic commun...

    Authors: Jiwen Liu, Yanfen Zheng, Heyu Lin, Xuchen Wang, Meng Li, Yang Liu, Meng Yu, Meixun Zhao, Nikolai Pedentchouk, David J. Lea-Smith, Jonathan D. Todd, Clayton R. Magill, Wei-Jia Zhang, Shun Zhou, Delei Song, Haohui Zhong…

    Citation: Microbiome 2019 7:47

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  27. Content type: Research

    Plants actively shape their associated microbial communities by synthesizing bio-active substances. Plant secondary metabolites are known for their signaling and plant defense functions, yet little is known ab...

    Authors: Enoch Narh Kudjordjie, Rumakanta Sapkota, Stine K. Steffensen, Inge S. Fomsgaard and Mogens Nicolaisen

    Citation: Microbiome 2019 7:59

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  29. Content type: Research

    Revealing the relationship between plants and fungi is very important in understanding biodiversity maintenance, community stability, and ecosystem functioning. However, differences in the community and networ...

    Authors: Hui Yao, Xiang Sun, Chao He, Pulak Maitra, Xing-Chun Li and Liang-Dong Guo

    Citation: Microbiome 2019 7:57

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  30. Content type: Research

    The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. ...

    Authors: Aleksandra Checinska Sielaff, Camilla Urbaniak, Ganesh Babu Malli Mohan, Victor G. Stepanov, Quyen Tran, Jason M. Wood, Jeremiah Minich, Daniel McDonald, Teresa Mayer, Rob Knight, Fathi Karouia, George E. Fox and Kasthuri Venkateswaran

    Citation: Microbiome 2019 7:50

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  31. Content type: Research

    Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing...

    Authors: Frédéric Raymond, Maurice Boissinot, Amin Ahmed Ouameur, Maxime Déraspe, Pier-Luc Plante, Sewagnouin Rogia Kpanou, Ève Bérubé, Ann Huletsky, Paul H. Roy, Marc Ouellette, Michel G. Bergeron and Jacques Corbeil

    Citation: Microbiome 2019 7:56

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  32. Content type: Research

    Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentou...

    Authors: Estelle Couradeau, Ana Giraldo-Silva, Francesca De Martini and Ferran Garcia-Pichel

    Citation: Microbiome 2019 7:55

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  34. Content type: Research

    Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiom...

    Authors: Aaron J. Prussin II, Pedro J. Torres, John Shimashita, Steven R. Head, Kyle J. Bibby, Scott T. Kelley and Linsey C. Marr

    Citation: Microbiome 2019 7:53

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  35. Content type: Software

    Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables...

    Authors: Fanny Berglund, Tobias Österlund, Fredrik Boulund, Nachiket P. Marathe, D. G. Joakim Larsson and Erik Kristiansson

    Citation: Microbiome 2019 7:52

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  37. Content type: Research

    A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we...

    Authors: Charlotte van der Veer, Rosanne Y. Hertzberger, Sylvia M. Bruisten, Hanne L. P. Tytgat, Jorne Swanenburg, Alie de Kat Angelino-Bart, Frank Schuren, Douwe Molenaar, Gregor Reid, Henry de Vries and Remco Kort

    Citation: Microbiome 2019 7:49

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  39. Content type: Software

    Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical s...

    Authors: Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Connell, Jung-Jin Lee, Bryton Fett, Frederic D. Bushman and Kyle Bittinger

    Citation: Microbiome 2019 7:46

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  40. Content type: Research

    Evidence from preclinical and clinical studies suggests that interactions among the brain, gut, and microbiota may affect the pathophysiology of irritable bowel syndrome (IBS). As disruptions in central and pe...

    Authors: Jennifer S. Labus, Vadim Osadchiy, Elaine Y. Hsiao, Julien Tap, Muriel Derrien, Arpana Gupta, Kirsten Tillisch, Boris Le Nevé, Cecilia Grinsvall, Maria Ljungberg, Lena Öhman, Hans Törnblom, Magnus Simren and Emeran A. Mayer

    Citation: Microbiome 2019 7:45

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  42. Content type: Research

    Species-specific differences in tolerance to infection are exemplified by the high susceptibility of humans to enterohemorrhagic Escherichia coli (EHEC) infection, whereas mice are relatively resistant to this pa...

    Authors: Alessio Tovaglieri, Alexandra Sontheimer-Phelps, Annelies Geirnaert, Rachelle Prantil-Baun, Diogo M. Camacho, David B. Chou, Sasan Jalili-Firoozinezhad, Tomás de Wouters, Magdalena Kasendra, Michael Super, Mark J. Cartwright, Camilla A. Richmond, David T. Breault, Christophe Lacroix and Donald E. Ingber

    Citation: Microbiome 2019 7:43

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  43. Content type: Methodology

    Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagen...

    Authors: Tingting Zheng, Jun Li, Yueqiong Ni, Kang Kang, Maria-Anna Misiakou, Lejla Imamovic, Billy K. C. Chow, Anne A. Rode, Peter Bytzer, Morten Sommer and Gianni Panagiotou

    Citation: Microbiome 2019 7:42

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  44. Content type: Research

    Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely ...

    Authors: Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Ian Korf and Danielle G. Lemay

    Citation: Microbiome 2019 7:41

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  45. Content type: Methodology

    The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis...

    Authors: Will PM Rowe, Anna Paola Carrieri, Cristina Alcon-Giner, Shabhonam Caim, Alex Shaw, Kathleen Sim, J. Simon Kroll, Lindsay J. Hall, Edward O. Pyzer-Knapp and Martyn D. Winn

    Citation: Microbiome 2019 7:40

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  46. Content type: Research

    There are complex interactions between aging, frailty, diet, and the gut microbiota; modulation of the gut microbiota by diet could lead to healthier aging. The purpose of this study was to test the effect of ...

    Authors: Tam T. T. Tran, Fabien J. Cousin, Denise B. Lynch, Ravi Menon, Jennifer Brulc, Jillian R.-M. Brown, Eileen O’Herlihy, Ludovica F. Butto, Katie Power, Ian B. Jeffery, Eibhlís M. O’Connor and Paul W. O’Toole

    Citation: Microbiome 2019 7:39

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  47. Content type: Correction

    Following publication of the original article [1], the authors identified wrong citations in the maintext.

    Authors: So-Jeong Kim, Jong-Geol Kim, Sang-Hoon Lee, Soo-Je Park, Joo-Han Gwak, Man-Young Jung, Won-Hyung Chung, Eun-Jin Yang, Jisoo Park, Jinyoung Jung, Yoonsoo Hahn, Jang-Cheon Cho, Eugene L. Madsen, Francisco Rodriguez-Valera, Jung-Ho Hyun and Sung-Keun Rhee

    Citation: Microbiome 2019 7:38

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    The original article was published in Microbiome 2019 7:29

  48. Content type: Research

    Pneumonia is common and frequently fatal in HIV-infected patients, due to rampant, systemic inflammation and failure to control microbial infection. While airway microbiota composition is related to local infl...

    Authors: Meera K. Shenoy, Douglas W. Fadrosh, Din L. Lin, William Worodria, Patrick Byanyima, Emmanuel Musisi, Sylvia Kaswabuli, Josephine Zawedde, Ingvar Sanyu, Emily Chang, Serena Fong, Kathryn McCauley, J. Lucian Davis, Laurence Huang and Susan V. Lynch

    Citation: Microbiome 2019 7:37

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  49. Content type: Research

    Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of norm...

    Authors: John Anthony Yason, Yi Ran Liang, Chin Wen Png, Yongliang Zhang and Kevin Shyong Wei Tan

    Citation: Microbiome 2019 7:30

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  50. Content type: Methodology

    Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets o...

    Authors: Weizhi Song, Bernd Wemheuer, Shan Zhang, Kerrin Steensen and Torsten Thomas

    Citation: Microbiome 2019 7:36

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