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  1. The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from ...

    Authors: Marcela Zozaya, Michael J. Ferris, Julia D. Siren, Rebecca Lillis, Leann Myers, M. Jacques Nsuami, A. Murat Eren, Jonathan Brown, Christopher M. Taylor and David H. Martin
    Citation: Microbiome 2016 4:16
  2. Chronic granulomatous disease (CGD) is caused by defects in nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) complex subunits (gp91 phox (a.k.a. Nox2), p47 ...

    Authors: E. Liana Falcone, Loreto Abusleme, Muthulekha Swamydas, Michail S. Lionakis, Li Ding, Amy P. Hsu, Adrian M. Zelazny, Niki M. Moutsopoulos, Douglas B. Kuhns, Clay Deming, Mariam Quiñones, Julia A. Segre, Clare E. Bryant and Steven M. Holland
    Citation: Microbiome 2016 4:13
  3. The Neolithic revolution—the transition of our species from hunter and gatherer to cultivator—began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Ne...

    Authors: David S. Thaler
    Citation: Microbiome 2016 4:14
  4. Since 1982, specific serotypes of Shiga toxin-producing Escherichia coli (STEC) have been recognized as significant foodborne pathogens acquired from contaminated beef and, more recently, other food products. Cat...

    Authors: Jessica Chopyk, Ryan M. Moore, Zachary DiSpirito, Zachary R. Stromberg, Gentry L. Lewis, David G. Renter, Natalia Cernicchiaro, Rodney A. Moxley and K. Eric Wommack
    Citation: Microbiome 2016 4:9
  5. Clostridium difficile infection (CDI) is the leading infectious cause of nosocomial diarrhea. Hospitalized patients are at increased risk of developing CDI because they are exposed to

    Authors: Caroline Vincent, Mark A. Miller, Thaddeus J. Edens, Sudeep Mehrotra, Ken Dewar and Amee R. Manges
    Citation: Microbiome 2016 4:12
  6. Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fung...

    Authors: Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J Gregory Caporaso and Scott T. Kelley
    Citation: Microbiome 2016 4:11
  7. Architects are enthusiastic about “bioinformed design” as occupant well-being is a primary measure of architectural success. However, architects are also under mounting pressure to create more sustainable buil...

    Authors: G. Z. Brown, Jeff Kline, Gwynne Mhuireach, Dale Northcutt and Jason Stenson
    Citation: Microbiome 2016 4:6
  8. Lower respiratory tract infection (LRTI) is a major contributor to respiratory failure requiring intubation and mechanical ventilation. LRTI also occurs during mechanical ventilation, increasing the morbidity ...

    Authors: Brendan J. Kelly, Ize Imai, Kyle Bittinger, Alice Laughlin, Barry D. Fuchs, Frederic D. Bushman and Ronald G. Collman
    Citation: Microbiome 2016 4:7
  9. While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung’s bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information...

    Authors: Sushma K. Cribbs, Karan Uppal, Shuzhao Li, Dean P. Jones, Laurence Huang, Laura Tipton, Adam Fitch, Ruth M. Greenblatt, Lawrence Kingsley, David M. Guidot, Elodie Ghedin and Alison Morris
    Citation: Microbiome 2016 4:3
  10. Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composi...

    Authors: Yue Jiang, Xuejian Xiong, Jayne Danska and John Parkinson
    Citation: Microbiome 2016 4:2
  11. A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we eva...

    Authors: Julian Gordon, Prasanthi Gandhi, Gajendra Shekhawat, Angel Frazier, Jarrad Hampton-Marcell and Jack A. Gilbert
    Citation: Microbiome 2015 3:79
  12. Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the ...

    Authors: Aaron J. Prussin II and Linsey C. Marr
    Citation: Microbiome 2015 3:78
  13. Authors: W. Florian Fricke, Yang Song, An-Jiang Wang, Allen Smith, Viktoriya Grinchuk, Chenlin Pei, Bing Ma, Nonghua Lu, Joseph F. Urban Jr., Terez Shea-Donohue and Aiping Zhao
    Citation: Microbiome 2015 3:77

    The original article was published in Microbiome 2015 3:40

  14. The Tasmanian devil, the world’s largest carnivorous marsupial, is at risk of extinction due to devil facial tumour disease (DFTD), a fatal contagious cancer. The Save the Tasmanian Devil Program has establish...

    Authors: Yuanyuan Cheng, Samantha Fox, David Pemberton, Carolyn Hogg, Anthony T. Papenfuss and Katherine Belov
    Citation: Microbiome 2015 3:76
  15. Westernized lifestyle and hygienic behavior have contributed to dramatic changes in the human-associated microbiota. This particularly relates to indoor activities such as house cleaning. We therefore investig...

    Authors: Ekaterina Avershina, Anuradha Ravi, Ola Storrø, Torbjørn Øien, Roar Johnsen and Knut Rudi
    Citation: Microbiome 2015 3:65
  16. The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recen...

    Authors: Joel D. Rudney, Pratik D. Jagtap, Cavan S. Reilly, Ruoqiong Chen, Todd W. Markowski, LeeAnn Higgins, James E. Johnson and Timothy J. Griffin
    Citation: Microbiome 2015 3:69
  17. Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these a...

    Authors: Abbas Kazerouni, James Burgess, Laura J. Burns and Lawrence M. Wein
    Citation: Microbiome 2015 3:75
  18. The microbiome of the built environment (MoBE) is a relatively new area of study. While some knowledge has been gained regarding impacts of the MoBE on the human microbiome and disease vulnerability, there is ...

    Authors: Andrew J. Hoisington, Lisa A. Brenner, Kerry A. Kinney, Teodor T. Postolache and Christopher A. Lowry
    Citation: Microbiome 2015 3:60
  19. Viral infections such as influenza have been shown to predispose hosts to increased colonization of the respiratory tract by pathogenic bacteria and secondary bacterial pneumonia. To examine how viral infectio...

    Authors: Y. Tarabichi, K. Li, S. Hu, C. Nguyen, X. Wang, D. Elashoff, K. Saira, Bryan Frank, Monika Bihan, E. Ghedin, Barbara A. Methé and Jane C. Deng
    Citation: Microbiome 2015 3:74
  20. Aphids are known to live in symbiosis with specific bacteria, called endosymbionts which can be classified as obligate or accessory. Buchnera aphidicola is generally the only obligatory symbiont present in aphids...

    Authors: Caroline De Clerck, Akiko Fujiwara, Pauline Joncour, Simon Léonard, Marie-Line Félix, Frédéric Francis, M. Haissam Jijakli, Tsutomu Tsuchida and Sébastien Massart
    Citation: Microbiome 2015 3:63
  21. The quantified self community brings together enthusiasts who are using technological devices to monitor their health and social media to share their personal data with others online. In light of the growing p...

    Authors: Carine Gimbert and François-Joseph Lapointe
    Citation: Microbiome 2015 3:70
  22. We previously showed that stool samples of pre-adolescent and adolescent US children diagnosed with diarrhea-predominant IBS (IBS-D) had different compositions of microbiota and metabolites compared to healthy...

    Authors: Vijay Shankar, Nicholas V. Reo and Oleg Paliy
    Citation: Microbiome 2015 3:73
  23. A wide variety of specialty textiles are used in health care settings for bedding, clothing, and privacy. The ability of textiles to host or otherwise sequester microbes has been well documented; however, thei...

    Authors: Alina Handorean, Charles E. Robertson, J. Kirk Harris, Daniel Frank, Natalie Hull, Cassandra Kotter, Mark J. Stevens, Darrel Baumgardner, Norman R. Pace and Mark Hernandez
    Citation: Microbiome 2015 3:72
  24. Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microo...

    Authors: Thomas Weinmaier, Alexander J. Probst, Myron T. La Duc, Doina Ciobanu, Jan-Fang Cheng, Natalia Ivanova, Thomas Rattei and Parag Vaishampayan
    Citation: Microbiome 2015 3:62
  25. The Sloan Symposium, “Microbiology of the Indoor Environment,” was held to facilitate dialog on biological research between scientists and practitioners in the field which was complementary to the adjoining ac...

    Authors: Hal Levin, Martin Täubel and Mark Hernandez
    Citation: Microbiome 2015 3:68
  26. Lowering water heater temperature set points and using less drinking water are common approaches to conserving water and energy; yet, there are discrepancies in past literature regarding the effects of water h...

    Authors: William J. Rhoads, Pan Ji, Amy Pruden and Marc A. Edwards
    Citation: Microbiome 2015 3:67
  27. Microorganisms are distributed on surfaces within homes, workplaces, and schools, with the potential to impact human health and disease. University campuses represent a unique opportunity to explore the distri...

    Authors: Ashley A. Ross and Josh D. Neufeld
    Citation: Microbiome 2015 3:66
  28. Newborns delivered by C-section acquire human skin microbes just after birth, but the sources remain unknown. We hypothesized that the operating room (OR) environment contains human skin bacteria that could be...

    Authors: Hakdong Shin, Zhiheng Pei, Keith A. Martinez II, Juana I. Rivera-Vinas, Keimari Mendez, Humberto Cavallin and Maria G. Dominguez-Bello
    Citation: Microbiome 2015 3:59

    The Erratum to this article has been published in Microbiome 2016 4:4

  29. The human gastrointestinal tract harbors a diverse microbial community, in which metabolic phenotypes play important roles for the human host. Recent developments in meta-omics attempt to unravel metabolic rol...

    Authors: Eugen Bauer, Cedric Christian Laczny, Stefania Magnusdottir, Paul Wilmes and Ines Thiele
    Citation: Microbiome 2015 3:55

    The Erratum to this article has been published in Microbiome 2016 4:35

  30. Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic micro...

    Authors: Karen Rossmassler, Carsten Dietrich, Claire Thompson, Aram Mikaelyan, James O. Nonoh, Rudolf H. Scheffrahn, David Sillam-Dussès and Andreas Brune
    Citation: Microbiome 2015 3:56
  31. Infant botulism is the most prevalent form of botulism in the USA, representing 68.5 % of cases reported from 2001–2012. Infant botulism results when botulinum toxin-producing clostridia (BTPC) colonize the in...

    Authors: T. Brian Shirey, Janet K. Dykes, Carolina Lúquez, Susan E. Maslanka and Brian H. Raphael
    Citation: Microbiome 2015 3:54
  32. The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportun...

    Authors: Josué L. Castro-Mejía, Musemma K. Muhammed, Witold Kot, Horst Neve, Charles M. A. P. Franz, Lars H. Hansen, Finn K. Vogensen and Dennis S. Nielsen
    Citation: Microbiome 2015 3:64
  33. The human gut microbiota interacts closely with human diet and physiology. To better understand the mechanisms behind this relationship, gut microbiome research relies on complementing human studies with manip...

    Authors: Katherine R. Amato, Carl J. Yeoman, Gabriela Cerda, Christopher A. Schmitt, Jennifer Danzy Cramer, Margret E. Berg Miller, Andres Gomez, Trudy R. Turner, Brenda A. Wilson, Rebecca M. Stumpf, Karen E. Nelson, Bryan A. White, Rob Knight and Steven R. Leigh
    Citation: Microbiome 2015 3:53
  34. Most human microbiota studies focus on bacteria inhabiting body surfaces, but these surfaces also are home to large populations of viruses. Many are bacteriophages, and their role in driving bacterial diversit...

    Authors: Tasha M. Santiago-Rodriguez, Melissa Ly, Michelle C. Daigneault, Ian H. L. Brown, Julie A. K. McDonald, Natasha Bonilla, Emma Allen Vercoe and David T. Pride
    Citation: Microbiome 2015 3:58
  35. Human microbiome reference datasets provide epidemiological context for researchers, enabling them to uncover new insights into their own data through meta-analyses. In addition, large and comprehensive refere...

    Authors: Daniel McDonald, Amanda Birmingham and Rob Knight
    Citation: Microbiome 2015 3:52
  36. The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understandin...

    Authors: Aleksandra Checinska, Alexander J. Probst, Parag Vaishampayan, James R. White, Deepika Kumar, Victor G. Stepanov, George E. Fox, Henrik R. Nilsson, Duane L. Pierson, Jay Perry and Kasthuri Venkateswaran
    Citation: Microbiome 2015 3:50
  37. As modern humans, we spend the majority of our time in indoor environments. Consequently, environmental exposure to microorganisms has important implications for human health, and a better understanding of the...

    Authors: Rachel I. Adams, Ashley C. Bateman, Holly M. Bik and James F. Meadow
    Citation: Microbiome 2015 3:49
  38. Currently, taxonomic interrogation of microbiota is based on amplification of 16S rRNA gene sequences in clinical and scientific settings. Accurate evaluation of the microbiota depends heavily on the primers u...

    Authors: Wei Zheng, Maria Tsompana, Angela Ruscitto, Ashu Sharma, Robert Genco, Yijun Sun and Michael J. Buck
    Citation: Microbiome 2015 3:48

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