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  1. 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

    Content type: Research

    Published on:

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

  2. 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

    Content type: Research

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  3. 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

    Content type: Research

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  4. 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

    Content type: Research

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

  5. 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

    Content type: Research

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  6. 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

    Content type: Research

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

  7. 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

    Content type: Research

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  8. 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

    Content type: Methodology

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  9. 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

    Content type: Short Report

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  10. 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

    Content type: Methodology

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  11. 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

    Content type: Research

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  12. 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

    Content type: Research

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  13. 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

    Content type: Research

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  14. Recent work indicates that the airways of persons with cystic fibrosis (CF) typically harbor complex bacterial communities. However, the day-to-day stability of these communities is unknown. Further, airway co...

    Authors: Lisa A Carmody, Jiangchao Zhao, Linda M Kalikin, William LeBar, Richard H Simon, Arvind Venkataraman, Thomas M Schmidt, Zaid Abdo, Patrick D Schloss and John J LiPuma

    Citation: Microbiome 2015 3:12

    Content type: Research

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  15. Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, littl...

    Authors: Alexa Weingarden, Antonio González, Yoshiki Vázquez-Baeza, Sophie Weiss, Gregory Humphry, Donna Berg-Lyons, Dan Knights, Tatsuya Unno, Aleh Bobr, Johnthomas Kang, Alexander Khoruts, Rob Knight and Michael J Sadowsky

    Citation: Microbiome 2015 3:10

    Content type: Research

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  16. Necrotizing enterocolitis (NEC) is a devastating neonatal gastrointestinal disease that primarily affects premature infants. It is characterized by bowel inflammation and necrosis. In spite of extensive resear...

    Authors: Valarie E McMurtry, Raegan W Gupta, Lynn Tran, Eugene E Blanchard IV, Duna Penn, Christopher M Taylor and Michael J Ferris

    Citation: Microbiome 2015 3:11

    Content type: Research

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  17. Some metagenomic studies have suggested that less than 10% of the cells that comprise our bodies are Homo sapiens cells. The remaining 90% are bacterial cells. The description of this so-called human microbiome i...

    Authors: Thiago Hutter, Carine Gimbert, Frédéric Bouchard and François-Joseph Lapointe

    Citation: Microbiome 2015 3:9

    Content type: Commentary

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  18. Microbiome samples often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such mixtures are complex, the number of species is huge and abundance inform...

    Authors: Mahdi Shafiei, Katherine A Dunn, Eva Boon, Shelley M MacDonald, David A Walsh, Hong Gu and Joseph P Bielawski

    Citation: Microbiome 2015 3:8

    Content type: Methodology

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  19. Obesity and type 2 diabetes (T2D) are major public health concerns worldwide, and their prevalence has only increased in recent years. Mexican Americans are disproportionately afflicted by obesity and T2D, and...

    Authors: Matthew C Ross, Donna M Muzny, Joseph B McCormick, Richard A Gibbs, Susan P Fisher-Hoch and Joseph F Petrosino

    Citation: Microbiome 2015 3:7

    Content type: Research

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  20. Triclosan is a widely used antimicrobial compound and emerging environmental contaminant. Although the role of the gut microbiome in health and disease is increasingly well established, the interaction between...

    Authors: Adrienne B Narrowe, Munira Albuthi-Lantz, Erin P Smith, Kimberly J Bower, Timberley M Roane, Alan M Vajda and Christopher S Miller

    Citation: Microbiome 2015 3:6

    Content type: Research

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  21. Termites and their microbial gut symbionts are major recyclers of lignocellulosic biomass. This important symbiosis is obligate but relatively open and more complex in comparison to other well-known insect sym...

    Authors: Nurdyana Abdul Rahman, Donovan H Parks, Dana L Willner, Anna L Engelbrektson, Shana K Goffredi, Falk Warnecke, Rudolf H Scheffrahn and Philip Hugenholtz

    Citation: Microbiome 2015 3:5

    Content type: Research

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  22. We are deeply grateful to all of the names listed below, who reviewed manuscripts submitted to Microbiome in 2014. We hope that you all will continue to support the journal as a reviewer or, better yet, as a cont...

    Authors: Jacques Ravel and K Eric Wommack

    Citation: Microbiome 2015 3:4

    Content type: Reviewer Acknowledgment

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  23. Human axillary odour is commonly attributed to the bacterial degradation of precursors in sweat secretions. To assess the role of bacterial communities in the formation of body odours, we used a culture-indepe...

    Authors: Myriam Troccaz, Nadia Gaïa, Sabine Beccucci, Jacques Schrenzel, Isabelle Cayeux, Christian Starkenmann and Vladimir Lazarevic

    Citation: Microbiome 2015 3:3

    Content type: Research

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  24. Staphylococcus aureus and other coagulase-positive staphylococci (CPS) colonize skin and mucous membrane sites and can cause skin and soft tissue infections (SSTIs) in humans and animals. Facto...

    Authors: Ana M Misic, Meghan F Davis, Amanda S Tyldsley, Brendan P Hodkinson, Pam Tolomeo, Baofeng Hu, Irving Nachamkin, Ebbing Lautenbach, Daniel O Morris and Elizabeth A Grice

    Citation: Microbiome 2015 3:2

    Content type: Research

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  25. Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which expl...

    Authors: Cedric C Laczny, Tomasz Sternal, Valentin Plugaru, Piotr Gawron, Arash Atashpendar, Houry Hera Margossian, Sergio Coronado, Laurens van der Maaten, Nikos Vlassis and Paul Wilmes

    Citation: Microbiome 2015 3:1

    Content type: Software

    Published on:

  26. Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we em...

    Authors: Amelieke JH Cremers, Aldert L Zomer, Jenna F Gritzfeld, Gerben Ferwerda, Sacha AFT van Hijum, Daniela M Ferreira, Joshua R Shak, Keith P Klugman, Jos Boekhorst, Harro M Timmerman, Marien I de Jonge, Stephen B Gordon and Peter WM Hermans

    Citation: Microbiome 2014 2:44

    Content type: Research

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  27. The massive characterization of host-associated and environmental microbial communities has represented a real breakthrough in the life sciences in the last years. In this context, metaproteomics specifically ...

    Authors: Alessandro Tanca, Antonio Palomba, Salvatore Pisanu, Massimo Deligios, Cristina Fraumene, Valeria Manghina, Daniela Pagnozzi, Maria Filippa Addis and Sergio Uzzau

    Citation: Microbiome 2014 2:49

    Content type: Methodology

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  28. The changes that occur in the microbiome of aging individuals are unclear, especially in light of the imperfect correlation of frailty with age. Studies in older human subjects have reported subtle effects, bu...

    Authors: Morgan GI Langille, Conor J Meehan, Jeremy E Koenig, Akhilesh S Dhanani, Robert A Rose, Susan E Howlett and Robert G Beiko

    Citation: Microbiome 2014 2:50

    Content type: Research

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  29. The role of the gut microbiome in arresting pathogen colonization and growth is important for protection against Clostridium difficile infection (CDI). Observational studies associate proton pump inhibitor (PPI) ...

    Authors: Charlie T Seto, Patricio Jeraldo, Robert Orenstein, Nicholas Chia and John K DiBaise

    Citation: Microbiome 2014 2:42

    Content type: Research

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    The Erratum to this article has been published in Microbiome 2016 4:10

  30. The variation of microbial communities associated with the human body can be the cause of many factors, including the human genetic makeup, diet, age, surroundings, and sexual behavior. In this study, we inves...

    Authors: Remco Kort, Martien Caspers, Astrid van de Graaf, Wim van Egmond, Bart Keijser and Guus Roeselers

    Citation: Microbiome 2014 2:41

    Content type: Research

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  31. Human-associated microbial communities include fungi, but we understand little about which fungal species are present, their relative and absolute abundances, and how antimicrobial therapy impacts fungal commu...

    Authors: Sven D Willger, Sharon L Grim, Emily L Dolben, Anna Shipunova, Thomas H Hampton, Hilary G Morrison, Laura M Filkins, George A O‘Toole, Lisa A Moulton, Alix Ashare, Mitchell L Sogin and Deborah A Hogan

    Citation: Microbiome 2014 2:40

    Content type: Research

    Published on:

  32. The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt th...

    Authors: Maureen W Groer, Angel A Luciano, Larry J Dishaw, Terri L Ashmeade, Elizabeth Miller and Jack A Gilbert

    Citation: Microbiome 2014 2:38

    Content type: Review

    Published on:

  33. Intestinal microbiota are implicated in risk of necrotizing enterocolitis (NEC) and sepsis, major diseases of preterm infants in neonatal intensive care units (NICUs). Rates of these diseases vary over time an...

    Authors: Diana H Taft, Namasivayam Ambalavanan, Kurt R Schibler, Zhuoteng Yu, David S Newburg, Doyle V Ward and Ardythe L Morrow

    Citation: Microbiome 2014 2:36

    Content type: Research

    Published on:

  34. 16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck i...

    Authors: Falk Hildebrand, Raul Tadeo, Anita Yvonne Voigt, Peer Bork and Jeroen Raes

    Citation: Microbiome 2014 2:30

    Content type: Software

    Published on:

    The Erratum to this article has been published in Microbiome 2014 2:37

  35. Sample storage conditions, extraction methods, PCR primers, and parameters are major factors that affect metagenomics analysis based on microbial 16S rRNA gene sequencing. Most published studies were limited t...

    Authors: Jun Hang, Valmik Desai, Nela Zavaljevski, Yu Yang, Xiaoxu Lin, Ravi Vijaya Satya, Luis J Martinez, Jason M Blaylock, Richard G Jarman, Stephen J Thomas and Robert A Kuschner

    Citation: Microbiome 2014 2:31

    Content type: Methodology

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  36. When diseased intestine (i.e., from colon cancer, diverticulitis) requires resection, its reconnection (termed anastomosis) can be complicated by non-healing of the newly joined intestine resulting in spillage...

    Authors: Benjamin D Shogan, Daniel P Smith, Scott Christley, Jack A Gilbert, Olga Zaborina and John C Alverdy

    Citation: Microbiome 2014 2:35

    Content type: Research

    Published on:

  37. The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to a...

    Authors: Benjamin J Tully, Rohan Sachdeva, Karla B Heidelberg and John F Heidelberg

    Citation: Microbiome 2014 2:34

    Content type: Research

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  38. Recent innovations in sequencing technologies have provided researchers with the ability to rapidly characterize the microbial content of an environmental or clinical sample with unprecedented resolution. Thes...

    Authors: Changjin Hong, Solaiappan Manimaran, Ying Shen, Joseph F Perez-Rogers, Allyson L Byrd, Eduardo Castro-Nallar, Keith A Crandall and William Evan Johnson

    Citation: Microbiome 2014 2:33

    Content type: Methodology

    Published on:

  39. Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) reli...

    Authors: Vaia Galimanas, Michael William Hall, Natasha Singh, Michael David Joseph Lynch, Michael Goldberg, Howard Tenenbaum, Dennis Gerard Cvitkovitch, Josh David Neufeld and Dilani Braziunas Senadheera

    Citation: Microbiome 2014 2:32

    Content type: Research

    Published on:

  40. Changes in respiratory tract microbiota have been associated with diseases such as tuberculosis, a global public health problem that affects millions of people each year. This pilot study was carried out using...

    Authors: Luz Elena Botero, Luisa Delgado-Serrano, Martha Lucía Cepeda, Jose Ricardo Bustos, Juan Manuel Anzola, Patricia Del Portillo, Jaime Robledo and María Mercedes Zambrano

    Citation: Microbiome 2014 2:29

    Content type: Short report

    Published on:

  41. Recent studies have revealed that bronchoalveolar lavage (BAL) fluid contains previously unappreciated communities of bacteria. In vitro and in vivo studies have shown that host inflammatory signals prompt bacter...

    Authors: Robert P Dickson, John R Erb-Downward, Hallie C Prescott, Fernando J Martinez, Jeffrey L Curtis, Vibha N Lama and Gary B Huffnagle

    Citation: Microbiome 2014 2:28

    Content type: Research

    Published on:

  42. The microbiota of the nares has been widely studied. However, relatively few studies have investigated the microbiota of the nasal cavity posterior to the nares. This distinct environment has the potential to ...

    Authors: Christine M Bassis, Alice L Tang, Vincent B Young and Melissa A Pynnonen

    Citation: Microbiome 2014 2:27

    Content type: Microbiome Announcement

    Published on:

  43. Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these ...

    Authors: Yu-Wei Wu, Yung-Hsu Tang, Susannah G Tringe, Blake A Simmons and Steven W Singer

    Citation: Microbiome 2014 2:26

    Content type: Methodology

    Published on:

  44. A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and ...

    Authors: Jacques Ravel, Martin J Blaser, Jonathan Braun, Eric Brown, Frederic D Bushman, Eugene B Chang, Julian Davies, Kathryn G Dewey, Timothy Dinan, Maria Dominguez-Bello, Susan E Erdman, B Brett Finlay, Wendy S Garrett, Gary B Huffnagle, Curtis Huttenhower, Janet Jansson…

    Citation: Microbiome 2014 2:16

    Content type: Meeting Report

    Published on:

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