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  1. Research

    Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves

    The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchop...

    Isabella Nicola, Francesco Cerutti, Elena Grego, Iride Bertone, Paola Gianella, Antonio D’Angelo, Simone Peletto and Claudio Bellino

    Microbiome 2017 5:152

    Published on: 21 November 2017

  2. Research

    Normalization of the microbiota in patients after treatment for colonic lesions

    Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or ...

    Marc A. Sze, Nielson T. Baxter, Mack T. Ruffin IV, Mary A. M. Rogers and Patrick D. Schloss

    Microbiome 2017 5:150

    Published on: 16 November 2017

  3. Research

    The Inuit gut microbiome is dynamic over time and shaped by traditional foods

    The human gut microbiome represents a diverse microbial community that varies across individuals and populations, and is influenced by factors such as host genetics and lifestyle. Diet is a major force shaping...

    Geneviève Dubois, Catherine Girard, François-Joseph Lapointe and B. Jesse Shapiro

    Microbiome 2017 5:151

    Published on: 16 November 2017

  4. Correction

    Correction to: Towards a balanced view of the bacterial tree of life

    Following publication of the original article [1], the authors pointed out that the figure shown as figure S1 is actually figure S2 and vice versa. Figure S1 should show the barcharts, and figure S2 should sho...

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

    Microbiome 2017 5:149

    Published on: 15 November 2017

    The original article was published in Microbiome 2017 5:140

  5. Research

    Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment

    Colonization by the pathogen Clostridium difficile often occurs in the background of a disrupted microbial community. Identifying specific organisms conferring resistance to invasion by C. difficile is desirable ...

    Sepideh Pakpour, Amit Bhanvadia, Roger Zhu, Abhimanyu Amarnani, Sean M. Gibbons, Thomas Gurry, Eric J. Alm and Laura A. Martello

    Microbiome 2017 5:148

    Published on: 13 November 2017

  6. Research

    Pancreatic cyst fluid harbors a unique microbiome

    It is clear that specific intestinal bacteria are involved in the development of different premalignant conditions along the gastrointestinal tract. An analysis of the microbial constituents in the context of ...

    Shan Li, Gwenny M. Fuhler, Nahush BN, Tony Jose, Marco J. Bruno, Maikel P. Peppelenbosch and Sergey R. Konstantinov

    Microbiome 2017 5:147

    Published on: 9 November 2017

  7. Research

    Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors

    The microbiome provides multiple benefits to animal hosts that can profoundly impact health and behavior. Microbiomes are well-characterized in humans and other animals in controlled settings, yet assessments ...

    Douglas S. Pearce, Brian A. Hoover, Sarah Jennings, Gabrielle A. Nevitt and Kathryn M. Docherty

    Microbiome 2017 5:146

    Published on: 30 October 2017

  8. Research

    Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome—from days to weeks

    The possible impact of changes in diet composition on the intestinal microbiome is mostly studied after some days of adaptation to the diet of interest. The question arises if a few days are enough to reflect ...

    Bruno Tilocca, Katharina Burbach, Charlotte M. E. Heyer, Ludwig E. Hoelzle, Rainer Mosenthin, Volker Stefanski, Amélia Camarinha-Silva and Jana Seifert

    Microbiome 2017 5:144

    Published on: 27 October 2017

  9. Research

    Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission

    The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli ...

    Kaisa Koskinen, Petra Rettberg, Rüdiger Pukall, Anna Auerbach, Lisa Wink, Simon Barczyk, Alexandra Perras, Alexander Mahnert, Diana Margheritis, Gerhard Kminek and Christine Moissl-Eichinger

    Microbiome 2017 5:143

    Published on: 25 October 2017

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. Correction

    Correction to: Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

    Following publication of the original article [1], the authors were alerted by a colleague of a column duplication in Table 1. Since the summary row was correct, though, the interpretation and the conclusion of t...

    Dagmara W. Lewandowska, Osvaldo Zagordi, Fabienne-Desirée Geissberger, Verena Kufner, Stefan Schmutz, Jürg Böni, Karin J. Metzner, Alexandra Trkola and Michael Huber

    Microbiome 2017 5:137

    Published on: 12 October 2017

    The original article was published in Microbiome 2017 5:94

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

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