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  1. Research

    Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

    Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of th...

    Noelle R. Noyes, Maggie E. Weinroth, Jennifer K. Parker, Chris J. Dean, Steven M. Lakin, Robert A. Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N. Martin, Kenneth L. Jones, Jaime Ruiz, Christina A. Boucher, Keith E. Belk and Paul S. Morley

    Microbiome 2017 5:142

    Published on: 17 October 2017

  2. Research

    Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease

    Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its ...

    Veronika B. Dubinkina, Alexander V. Tyakht, Vera Y. Odintsova, Konstantin S. Yarygin, Boris A. Kovarsky, Alexander V. Pavlenko, Dmitry S. Ischenko, Anna S. Popenko, Dmitry G. Alexeev, Anastasiya Y. Taraskina, Regina F. Nasyrova, Evgeny M. Krupitsky, Nino V. Shalikiani, Igor G. Bakulin, Petr L. Shcherbakov, Lyubov O. Skorodumova…

    Microbiome 2017 5:141

    Published on: 17 October 2017

  3. Short report

    Towards a balanced view of the bacterial tree of life

    The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a sn...

    Frederik Schulz, Emiley A. Eloe-Fadrosh, Robert M. Bowers, Jessica Jarett, Torben Nielsen, Natalia N. Ivanova, Nikos C. Kyrpides and Tanja Woyke

    Microbiome 2017 5:140

    Published on: 17 October 2017

  4. Research

    Individual signatures and environmental factors shape skin microbiota in healthy dogs

    The individual, together with its environment, has been reported as the main force driving composition and structure of skin microbiota in healthy dogs. Therefore, one of the major concerns when analyzing cani...

    Anna Cuscó, Janelle M. Belanger, Liza Gershony, Alma Islas-Trejo, Kerinne Levy, Juan F. Medrano, Armand Sánchez, Anita M. Oberbauer and Olga Francino

    Microbiome 2017 5:139

    Published on: 13 October 2017

  5. Research

    Indoor microbiota in severely moisture damaged homes and the impact of interventions

    The limited understanding of microbial characteristics in moisture-damaged buildings impedes efforts to clarify which adverse health effects in the occupants are associated with the damage and to develop effec...

    Balamuralikrishna Jayaprakash, Rachel I. Adams, Pirkka Kirjavainen, Anne Karvonen, Asko Vepsäläinen, Maria Valkonen, Kati Järvi, Michael Sulyok, Juha Pekkanen, Anne Hyvärinen and Martin Täubel

    Microbiome 2017 5:138

    Published on: 13 October 2017

  6. Research

    Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

    Metallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with thei...

    Fanny Berglund, Nachiket P. Marathe, Tobias Österlund, Johan Bengtsson-Palme, Stathis Kotsakis, Carl-Fredrik Flach, D G Joakim Larsson and Erik Kristiansson

    Microbiome 2017 5:134

    Published on: 12 October 2017

  7. Research

    Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota

    Prebiotics are non-digestible food ingredients that enhance the growth of certain microbes within the gut microbiota. Prebiotic consumption generates immune-modulatory effects that are traditionally thought to...

    Richard Y. Wu, Pekka Määttänen, Scott Napper, Erin Scruten, Bo Li, Yuhki Koike, Kathene C. Johnson-Henry, Agostino Pierro, Laura Rossi, Steven R. Botts, Michael G. Surette and Philip M. Sherman

    Microbiome 2017 5:135

    Published on: 10 October 2017

  8. Research

    City-scale distribution and dispersal routes of mycobiome in residences

    Pathogenic and allergenic bacteria and fungi within the indoors can bring detrimental health effects on the occupants. We previously studied the bacterial communities found in households located throughout Hon...

    Xinzhao Tong, Marcus H. Y. Leung, David Wilkins and Patrick K. H. Lee

    Microbiome 2017 5:131

    Published on: 4 October 2017

  9. Research

    Interactive effects of temperature, organic carbon, and pipe material on microbiota composition and Legionella pneumophila in hot water plumbing systems

    Several biotic and abiotic factors have been reported to influence the proliferation of microbes, including Legionella pneumophila, in hot water premise plumbing systems, but their combined effects have not been ...

    Caitlin R. Proctor, Dongjuan Dai, Marc A. Edwards and Amy Pruden

    Microbiome 2017 5:130

    Published on: 4 October 2017

  10. Short report

    Laboratory colonization stabilizes the naturally dynamic microbiome composition of field collected Dermacentor andersoni ticks

    Nearly a quarter of emerging infectious diseases identified in the last century are arthropod-borne. Although ticks and insects can carry pathogenic microorganisms, non-pathogenic microbes make up the majority...

    Cory A. Gall, Glen A. Scoles, Krisztian Magori, Kathleen L. Mason and Kelly A. Brayton

    Microbiome 2017 5:133

    Published on: 4 October 2017

  11. Research

    Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing

    The Mars500 project was conceived as the first full duration simulation of a crewed return flight to Mars. For 520 days, six crew members lived confined in a specifically designed spacecraft mock-up. The herei...

    Petra Schwendner, Alexander Mahnert, Kaisa Koskinen, Christine Moissl-Eichinger, Simon Barczyk, Reinhard Wirth, Gabriele Berg and Petra Rettberg

    Microbiome 2017 5:129

    Published on: 4 October 2017

  12. Research

    Microbes and associated soluble and volatile chemicals on periodically wet household surfaces

    Microorganisms influence the chemical milieu of their environment, and chemical metabolites can affect ecological processes. In built environments, where people spend the majority of their time, very little is...

    Rachel I. Adams, Despoina S. Lymperopoulou, Pawel K. Misztal, Rita De Cassia Pessotti, Scott W. Behie, Yilin Tian, Allen H. Goldstein, Steven E. Lindow, William W. Nazaroff, John W. Taylor, Matt F. Traxler and Thomas D. Bruns

    Microbiome 2017 5:128

    Published on: 26 September 2017

  13. Research

    Metagenomic characterization of ambulances across the USA

    Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some hea...

    Niamh B. O’Hara, Harry J. Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler and Christopher E. Mason

    Microbiome 2017 5:125

    Published on: 22 September 2017

  14. Research

    Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters

    Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota a...

    Celine C. Lesaulnier, Craig W. Herbold, Claus Pelikan, David Berry, Cédric Gérard, Xavier Le Coz, Sophie Gagnot, Jutta Niggemann, Thorsten Dittmar, Gabriel A. Singer and Alexander Loy

    Microbiome 2017 5:126

    Published on: 22 September 2017

  15. Research

    Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats

    Diet-derived short-chain fatty acids (SCFAs) in the rumen have broad effects on the health and growth of ruminants. The microbe-G-protein-coupled receptor (GPR) and microbe-histone deacetylase (HDAC) axes migh...

    Hong Shen, Zhongyan Lu, Zhihui Xu, Zhan Chen and Zanming Shen

    Microbiome 2017 5:123

    Published on: 19 September 2017

  16. Research

    Feed in summer, rest in winter: microbial carbon utilization in forest topsoil

    Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to se...

    Lucia Žifčáková, Tomáš Větrovský, Vincent Lombard, Bernard Henrissat, Adina Howe and Petr Baldrian

    Microbiome 2017 5:122

    Published on: 18 September 2017

  17. Research

    Profiling bacterial communities by MinION sequencing of ribosomal operons

    An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domai...

    Lee J. Kerkhof, Kevin P. Dillon, Max M. Häggblom and Lora R. McGuinness

    Microbiome 2017 5:116

    Published on: 15 September 2017

  18. Research

    Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

    Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition ...

    Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z. Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A. Fodor and Penny Gordon-Larsen

    Microbiome 2017 5:121

    Published on: 15 September 2017

  19. Research

    Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis

    Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually transmitted infections and complications like...

    Cornelia Gottschick, Zhi-Luo Deng, Marius Vital, Clarissa Masur, Christoph Abels, Dietmar H. Pieper, Manfred Rohde, Werner Mendling and Irene Wagner-Döbler

    Microbiome 2017 5:119

    Published on: 13 September 2017

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