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  1. Content type: Commentary

    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

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  2. Content type: Methodology

    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

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  3. Content type: Research

    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

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  4. Content type: Research

    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

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  5. Content type: Research

    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

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  6. Content type: Reviewer Acknowledgment

    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

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  7. Content type: Research

    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

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  8. Content type: Research

    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

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  9. Content type: Software

    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

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  10. Content type: Research

    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

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  11. Content type: Methodology

    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

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  12. Content type: Research

    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

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  13. Content type: Research

    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

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

  14. Content type: Research

    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

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  15. Content type: Research

    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

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  16. Content type: Review

    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

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  17. Content type: Research

    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

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  18. Content type: Software

    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

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

  19. Content type: Methodology

    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

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  20. Content type: Research

    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

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  21. Content type: Research

    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

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  22. Content type: Methodology

    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

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  23. Content type: Research

    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

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  24. Content type: Short report

    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

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  25. Content type: Research

    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

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  26. Content type: Microbiome Announcement

    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

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  27. Content type: Methodology

    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

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  28. Content type: Meeting Report

    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

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  29. Content type: Short report

    Human milk is an important source of bacteria for the developing infant and has been shown to influence the bacterial composition of the neonatal gut, which in turn can affect disease risk later in life. Human...

    Authors: Camilla Urbaniak, Amy McMillan, Michelle Angelini, Gregory B Gloor, Mark Sumarah, Jeremy P Burton and Gregor Reid

    Citation: Microbiome 2014 2:24

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  30. Content type: Research

    The vaginal microbial community plays a vital role in maintaining women’s health. Understanding the precise bacterial composition is challenging because of the diverse and difficult-to-culture nature of many b...

    Authors: Bonnie Chaban, Matthew G Links, Teenus Paramel Jayaprakash, Emily C Wagner, Danielle K Bourque, Zoe Lohn, Arianne YK Albert, Julie van Schalkwyk, Gregor Reid, Sean M Hemmingsen, Janet E Hill and Deborah M Money

    Citation: Microbiome 2014 2:23

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  31. Content type: Research

    The bacterial communities of the nasopharynx play an important role in upper respiratory tract infections (URTIs). Our study represents the first survey of the nasopharynx during a known, controlled viral chal...

    Authors: E Kaitlynn Allen, Alex F Koeppel, J Owen Hendley, Stephen D Turner, Birgit Winther and Michèle M Sale

    Citation: Microbiome 2014 2:22

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  32. Content type: Research

    A growing body of evidence indicates that the gut microbiome plays a role in the development of colorectal cancer (CRC). Patients with CRC harbor gut microbiomes that are structurally distinct from those of he...

    Authors: Nielson T Baxter, Joseph P Zackular, Grace Y Chen and Patrick D Schloss

    Citation: Microbiome 2014 2:20

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  33. Content type: Research

    In recent years, studies on the human intestinal microbiota have attracted tremendous attention. Application of next generation sequencing for mapping of bacterial phylogeny and function has opened new doors t...

    Authors: Agata Wesolowska-Andersen, Martin Iain Bahl, Vera Carvalho, Karsten Kristiansen, Thomas Sicheritz-Pontén, Ramneek Gupta and Tine Rask Licht

    Citation: Microbiome 2014 2:19

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  34. Content type: Research

    This study was undertaken to determine whether the vaginal microbiota of pregnant women who subsequently had a spontaneous preterm delivery is different from that of women who had a term delivery.

    Authors: Roberto Romero, Sonia S Hassan, Pawel Gajer, Adi L Tarca, Douglas W Fadrosh, Janine Bieda, Piya Chaemsaithong, Jezid Miranda, Tinnakorn Chaiworapongsa and Jacques Ravel

    Citation: Microbiome 2014 2:18

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  35. Content type: Microbiome Announcement

    The Amazon River is by far the world’s largest in terms of volume and area, generating a fluvial export that accounts for about a fifth of riverine input into the world’s oceans. Marine microbial communities o...

    Authors: Brandon M Satinsky, Brian L Zielinski, Mary Doherty, Christa B Smith, Shalabh Sharma, John H Paul, Byron C Crump and Mary Ann Moran

    Citation: Microbiome 2014 2:17

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  36. Content type: Methodology

    Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fr...

    Authors: Andrew D Fernandes, Jennifer NS Reid, Jean M Macklaim, Thomas A McMurrough, David R Edgell and Gregory B Gloor

    Citation: Microbiome 2014 2:15

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  37. Content type: Short report

    Cystic fibrosis (CF) is caused by mutations in the CFTR gene that predispose the airway to infection. Chronic infection by pathogens such as Pseudomonas aeruginosa leads to inflammation that gradually degrades lu...

    Authors: Thomas H Hampton, Deanna M Green, Garry R Cutting, Hilary G Morrison, Mitchell L Sogin, Alex H Gifford, Bruce A Stanton and George A O’Toole

    Citation: Microbiome 2014 2:14

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  38. Content type: Research

    Clostridium difficile is an opportunistic human intestinal pathogen, and C. difficile infection (CDI) is one of the main causes of antibiotic-induced diarrhea and colitis. One successful approach to combat CDI, p...

    Authors: Vijay Shankar, Matthew J Hamilton, Alexander Khoruts, Amanda Kilburn, Tatsuya Unno, Oleg Paliy and Michael J Sadowsky

    Citation: Microbiome 2014 2:13

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  39. Content type: Meeting Report

    To augment capacity-building for microbiome and probiotic research in Africa, a workshop was held in Nairobi, Kenya, at which researchers discussed human, animal, insect, and agricultural microbiome and probio...

    Authors: Gregor Reid, Nicholas Nduti, Wilbert Sybesma, Remco Kort, Tobias R Kollmann, Rod Adam, Hamadi Boga, Eric M Brown, Alexandra Einerhand, Hani El-Nezami, Gregory B Gloor, Irene I Kavere, Johanna Lindahl, Amee Manges, Wondu Mamo, Rocio Martin…

    Citation: Microbiome 2014 2:12

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  40. Content type: Erratum

    Authors: Roberto Romero, Sonia S Hassan, Pawel Gajer, Adi L Tarca, Douglas W Fadrosh, Lorraine Nikita, Marisa Galuppi, Ronald F Lamont, Piya Chaemsaithong, Jezid Miranda, Tinnakorn Chaiworapongsa and Jacques Ravel

    Citation: Microbiome 2014 2:10

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    The original article was published in Microbiome 2014 2:4

  41. Content type: Methodology

    Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between spec...

    Authors: Florent E Angly, Paul G Dennis, Adam Skarshewski, Inka Vanwonterghem, Philip Hugenholtz and Gene W Tyson

    Citation: Microbiome 2014 2:11

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  42. Content type: Research

    Humans can spend the majority of their time indoors, but little is known about the interactions between the human and built-environment microbiomes or the forces that drive microbial community assembly in the ...

    Authors: James F Meadow, Adam E Altrichter, Steven W Kembel, Maxwell Moriyama, Timothy K O’Connor, Ann M Womack, G Z Brown, Jessica L Green and Brendan J M Bohannan

    Citation: Microbiome 2014 2:7

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  43. Content type: Methodology

    To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical ...

    Authors: Douglas W Fadrosh, Bing Ma, Pawel Gajer, Naomi Sengamalay, Sandra Ott, Rebecca M Brotman and Jacques Ravel

    Citation: Microbiome 2014 2:6

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