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  1. Content type: Research

    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

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  2. Content type: Research

    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

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  3. Content type: Research

    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

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

  4. Content type: Research

    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

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

  5. Content type: Microbiome Announcement

    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

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  6. Content type: Research

    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

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  7. Content type: Methodology

    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

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  8. Content type: Research

    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

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  9. Content type: Research

    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

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  10. Content type: Review

    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

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  11. Content type: Research

    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

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  12. Content type: Research

    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

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  13. Content type: Methodology

    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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  14. Content type: Research

    Settled airborne dust is used as a surrogate for airborne exposure in studies that explore indoor microbes. In order to determine whether detecting differences in dust environments would depend on the sampler ...

    Authors: Rachel I. Adams, Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyvärinen and Martin Täubel

    Citation: Microbiome 2015 3:46

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  15. Content type: Methodology

    High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rR...

    Authors: Oscar Franzén, Jianzhong Hu, Xiuliang Bao, Steven H. Itzkowitz, Inga Peter and Ali Bashir

    Citation: Microbiome 2015 3:43

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    The Erratum to this article has been published in Microbiome 2015 3:57

  16. Content type: Research

    Continuous-flow culture models are one tool for studying complex interactions between members of human fecal microbiotas because they allow studies to be completed during an extended period of time under condi...

    Authors: Jennifer M. Auchtung, Catherine D. Robinson and Robert A. Britton

    Citation: Microbiome 2015 3:42

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  17. Content type: Research

    The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota...

    Authors: Paurush Praveen, Ferenc Jordan, Corrado Priami and Melissa J. Morine

    Citation: Microbiome 2015 3:41

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  18. Content type: Research

    The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Studies that examine differences in intestinal microbial communities acr...

    Authors: Pallavi Singh, Tracy K. Teal, Terence L. Marsh, James M. Tiedje, Rebekah Mosci, Katherine Jernigan, Angela Zell, Duane W. Newton, Hossein Salimnia, Paul Lephart, Daniel Sundin, Walid Khalife, Robert A. Britton, James T. Rudrik and Shannon D. Manning

    Citation: Microbiome 2015 3:45

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  19. Content type: Research

    Dynamic interactions between the host and gastrointestinal microbiota play an important role for local and systemic immune homeostasis. Helminthic parasites modulate the host immune response, resulting in prot...

    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 3:40

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    The Erratum to this article has been published in Microbiome 2015 3:77

  20. Content type: Microbiome Announcement

    The Amazon River runs nearly 6500 km across the South American continent before emptying into the western tropical North Atlantic Ocean. In terms of both volume and watershed area, it is the world’s largest ri...

    Authors: Brandon M. Satinsky, Caroline S. Fortunato, Mary Doherty, Christa B. Smith, Shalabh Sharma, Nicholas D. Ward, Alex V. Krusche, Patricia L. Yager, Jeffrey E. Richey, Mary Ann Moran and Byron C. Crump

    Citation: Microbiome 2015 3:39

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  21. Content type: Research

    Through several observational and mechanistic studies, microbial infection is known to promote cardiovascular disease. Direct infection of the vessel wall, along with the cardiovascular risk factors, is hypoth...

    Authors: Suparna Mitra, Daniela I. Drautz-Moses, Morten Alhede, Myat T. Maw, Yang Liu, Rikky W. Purbojati, Zhei H. Yap, Kavita K. Kushwaha, Alexandra G. Gheorghe, Thomas Bjarnsholt, Gorm M. Hansen, Henrik H. Sillesen, Hans P. Hougen, Peter R. Hansen, Liang Yang, Tim Tolker-Nielsen…

    Citation: Microbiome 2015 3:38

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  22. Content type: Research

    Resistant starch (RS) decreases intestinal inflammation in some settings. We tested the hypothesis that gut inflammation will be reduced with dietary supplementation with RS in rural Malawian children. Eightee...

    Authors: M. Isabel Ordiz, Thaddaeus D. May, Kathie Mihindukulasuriya, John Martin, Jan Crowley, Phillip I. Tarr, Kelsey Ryan, Elissa Mortimer, Geetha Gopalsamy, Ken Maleta, Makedonka Mitreva, Graeme Young and Mark J. Manary

    Citation: Microbiome 2015 3:37

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  23. Content type: Research

    The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, inform...

    Authors: Emily B. Hollister, Kevin Riehle, Ruth Ann Luna, Erica M. Weidler, Michelle Rubio-Gonzales, Toni-Ann Mistretta, Sabeen Raza, Harsha V. Doddapaneni, Ginger A. Metcalf, Donna M. Muzny, Richard A. Gibbs, Joseph F. Petrosino, Robert J. Shulman and James Versalovic

    Citation: Microbiome 2015 3:36

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  24. Content type: Methodology

    Different bacteria in stool have markedly varied growth and survival when stored at ambient temperature. It is paramount to develop optimal biostabilization of stool samples during collection and assess long-t...

    Authors: Roberto Flores, Jianxin Shi, Guoqin Yu, Bing Ma, Jacques Ravel, James J. Goedert and Rashmi Sinha

    Citation: Microbiome 2015 3:33

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  25. Content type: Software

    Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented part...

    Authors: Qiong Wang, Jordan A. Fish, Mariah Gilman, Yanni Sun, C. Titus Brown, James M. Tiedje and James R. Cole

    Citation: Microbiome 2015 3:32

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  26. Content type: Editorial

    The advancement of DNA/RNA, proteins, and metabolite analytical platforms, combined with increased computing technologies, has transformed the field of microbial community analysis. This transformation is evid...

    Authors: Julian R. Marchesi and Jacques Ravel

    Citation: Microbiome 2015 3:31

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  27. Content type: Methodology

    Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nut...

    Authors: Paulo de Boer, Martien Caspers, Jan-Willem Sanders, Robèr Kemperman, Janneke Wijman, Gijs Lommerse, Guus Roeselers, Roy Montijn, Tjakko Abee and Remco Kort

    Citation: Microbiome 2015 3:30

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  28. Content type: Research

    The newborn mammal is rapidly colonized by a complex microbial community, whose importance for host health is becoming increasingly clear. Understanding the forces that shape the early community, especially du...

    Authors: Steven A. Frese, Kent Parker, C. Chris Calvert and David A. Mills

    Citation: Microbiome 2015 3:28

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  29. Content type: Research

    The early life of the human host marks a critically important time for establishment of the gut microbial community, yet the developmental trajectory of gut community-encoded resistance genes (resistome) is un...

    Authors: Aimee M. Moore, Sara Ahmadi, Sanket Patel, Molly K. Gibson, Bin Wang, I. Malick Ndao, Elena Deych, William Shannon, Phillip I. Tarr, Barbara B. Warner and Gautam Dantas

    Citation: Microbiome 2015 3:27

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    The Erratum to this article has been published in Microbiome 2015 3:29

  30. Content type: Research

    Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thu...

    Authors: Alan W. Walker, Jennifer C. Martin, Paul Scott, Julian Parkhill, Harry J. Flint and Karen P. Scott

    Citation: Microbiome 2015 3:26

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  31. Content type: Research

    Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems ...

    Authors: Mariah Wood, Sean M. Gibbons, Simon Lax, Tifani W. Eshoo-Anton, Sarah M. Owens, Suzanne Kennedy, Jack A. Gilbert and Jarrad T. Hampton-Marcell

    Citation: Microbiome 2015 3:25

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  32. Content type: Research

    Chronic malnutrition, termed stunting, is defined as suboptimal linear growth, affects one third of children in developing countries, and leads to increased mortality and poor developmental outcomes. The cause...

    Authors: Ethan K. Gough, David A. Stephens, Erica E.M. Moodie, Andrew J. Prendergast, Rebecca J. Stoltzfus, Jean H. Humphrey and Amee R. Manges

    Citation: Microbiome 2015 3:24

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    The Erratum to this article has been published in Microbiome 2016 4:5

  33. Content type: Research

    Eosinophilic esophagitis (EoE) is an allergic disorder characterized by eosinophil-predominant esophageal inflammation, which can be ameliorated by food antigen restriction. Though recent studies suggest that ...

    Authors: Alain J Benitez, Christian Hoffmann, Amanda B. Muir, Kara K. Dods, Jonathan M. Spergel, Frederic D. Bushman and Mei-Lun Wang

    Citation: Microbiome 2015 3:23

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  34. Content type: Research

    The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses.

    Authors: Yan He, J Gregory Caporaso, Xiao-Tao Jiang, Hua-Fang Sheng, Susan M Huse, Jai Ram Rideout, Robert C Edgar, Evguenia Kopylova, William A Walters, Rob Knight and Hong-Wei Zhou

    Citation: Microbiome 2015 3:20

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    The Erratum to this article has been published in Microbiome 2015 3:34

  35. Content type: Research

    Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space ...

    Authors: Simon Lax, Jarrad T Hampton-Marcell, Sean M Gibbons, Geórgia Barguil Colares, Daniel Smith, Jonathan A Eisen and Jack A Gilbert

    Citation: Microbiome 2015 3:21

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  36. Content type: Methodology

    The rapid expansion of 16S rRNA gene sequencing in challenging clinical contexts has resulted in a growing body of literature of variable quality. To a large extent, this is due to a failure to address spuriou...

    Authors: Jake Jervis-Bardy, Lex E X Leong, Shashikanth Marri, Renee J Smith, Jocelyn M Choo, Heidi C Smith-Vaughan, Elizabeth Nosworthy, Peter S Morris, Stephen O’Leary, Geraint B Rogers and Robyn L Marsh

    Citation: Microbiome 2015 3:19

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  37. Content type: Short Report

    The composition of the intestinal microbiota seems to be an important factor in determining the clinical outcome in children with short bowel syndrome (SBS). Alterations in the microbiota may result in serious...

    Authors: Helene Engstrand Lilja, Hugo Wefer, Niklas Nyström, Yigael Finkel and Lars Engstrand

    Citation: Microbiome 2015 3:18

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  38. Content type: Methodology

    Current research has led to the appreciation that there are differences in the commensal microbiota between healthy individuals and individuals that are predisposed to disease. Treatments to reverse disease pa...

    Authors: Joseph G Daft, Travis Ptacek, Ranjit Kumar, Casey Morrow and Robin G Lorenz

    Citation: Microbiome 2015 3:17

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  39. Content type: Research

    Dietary fibers contribute to health and physiology primarily via the fermentative actions of the host’s gut microbiome. Physicochemical properties such as solubility, fermentability, viscosity, and gel-forming...

    Authors: Özgün C O Umu, Jeremy A Frank, Jonatan U Fangel, Marije Oostindjer, Carol Souza da Silva, Elizabeth J Bolhuis, Guido Bosch, William G T Willats, Phillip B Pope and Dzung B Diep

    Citation: Microbiome 2015 3:16

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  40. Content type: Research

    Estuaries are among the most productive habitats on the planet. Bacteria in estuary sediments control the turnover of organic carbon and the cycling of nitrogen and sulfur. These communities are complex and pr...

    Authors: Brett J Baker, Cassandre Sara Lazar, Andreas P Teske and Gregory J Dick

    Citation: Microbiome 2015 3:14

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  41. Content type: Research

    Individuals with inactive alleles of the fucosyltransferase 2 gene (FUT2; termed the ‘secretor’ gene) are common in many populations. Some members of the genus Bifidobacterium, common infant gut commensals, are k...

    Authors: Zachery T Lewis, Sarah M Totten, Jennifer T Smilowitz, Mina Popovic, Evan Parker, Danielle G Lemay, Maxwell L Van Tassell, Michael J Miller, Yong-Su Jin, J Bruce German, Carlito B Lebrilla and David A Mills

    Citation: Microbiome 2015 3:13

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