Skip to main content

Articles

Page 17 of 21

  1. A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer geno...

    Authors: Kelly M. Robinson, Jonathan Crabtree, John S. A. Mattick, Kathleen E. Anderson and Julie C. Dunning Hotopp

    Citation: Microbiome 2017 5:9

    Content type: Research

    Published on:

  2. Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and ...

    Authors: Dae-Wook Kang, James B. Adams, Ann C. Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L. Pollard, Simon Roux, Michael J. Sadowsky, Karen Schwarzberg Lipson, Matthew B. Sullivan, J. Gregory Caporaso…

    Citation: Microbiome 2017 5:10

    Content type: Research

    Published on:

  3. The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend ...

    Authors: Elizabeth A. Miller, Joshua A. Livermore, Susan C. Alberts, Jenny Tung and Elizabeth A. Archie

    Citation: Microbiome 2017 5:8

    Content type: Research

    Published on:

  4. Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, prima...

    Authors: Jeremy W. Cox, Richard A. Ballweg, Diana H. Taft, Prakash Velayutham, David B. Haslam and Aleksey Porollo

    Citation: Microbiome 2017 5:7

    Content type: Methodology

    Published on:

  5. Preterm birth is the primary cause of infant death worldwide. A short cervix in the second trimester of pregnancy is a risk factor for preterm birth. In specific patient cohorts, vaginal progesterone reduces t...

    Authors: Lindsay M. Kindinger, Phillip R. Bennett, Yun S Lee, Julian R. Marchesi, Ann Smith, Stefano Cacciatore, Elaine Holmes, Jeremy K. Nicholson, T. G. Teoh and David A. MacIntyre

    Citation: Microbiome 2017 5:6

    Content type: Research

    Published on:

  6. Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified human...

    Authors: Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen and Marco Ventura

    Citation: Microbiome 2017 5:5

    Content type: Research

    Published on:

    The Erratum to this article has been published in Microbiome 2017 5:23

  7. The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 wee...

    Authors: Cian J. Hill, Denise B. Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B. Jeffery, Carol Anne O’Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Tuohy, R. Paul Ross, C. Anthony Ryan, Paul W. O’ Toole and Catherine Stanton

    Citation: Microbiome 2017 5:4

    Content type: Research

    Published on:

    The Erratum to this article has been published in Microbiome 2017 5:21

  8. The goal of the study was to investigate whether cigarette smoking alters oral and nasal microbial diversity, composition, and structure. Twenty-three current smokers and 20 never smokers were recruited. From ...

    Authors: Guoqin Yu, Stephen Phillips, Mitchell H. Gail, James J. Goedert, Michael S. Humphrys, Jacques Ravel, Yanfang Ren and Neil E. Caporaso

    Citation: Microbiome 2017 5:3

    Content type: Research

    Published on:

  9. Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes of numerous plant species, but little information is availabl...

    Authors: Kyle Hartman, Marcel GA van der Heijden, Valexia Roussely-Provent, Jean-Claude Walser and Klaus Schlaeppi

    Citation: Microbiome 2017 5:2

    Content type: Research

    Published on:

  10. The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a hea...

    Authors: Martin Steen Mortensen, Asker Daniel Brejnrod, Michael Roggenbuck, Waleed Abu Al-Soud, Christina Balle, Karen Angeliki Krogfelt, Jakob Stokholm, Jonathan Thorsen, Johannes Waage, Morten Arendt Rasmussen, Hans Bisgaard and Søren Johannes Sørensen

    Citation: Microbiome 2016 4:70

    Content type: Research

    Published on:

  11. Colorectal cancer is a heterogeneous disease arising from at least two precursors—the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut ...

    Authors: Brandilyn A. Peters, Christine Dominianni, Jean A. Shapiro, Timothy R. Church, Jing Wu, George Miller, Elizabeth Yuen, Hal Freiman, Ian Lustbader, James Salik, Charles Friedlander, Richard B. Hayes and Jiyoung Ahn

    Citation: Microbiome 2016 4:69

    Content type: Research

    Published on:

    The Erratum to this article has been published in Microbiome 2017 5:29

  12. The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and n...

    Authors: Katherine E. Gregory, Buck S. Samuel, Pearl Houghteling, Guru Shan, Frederick M. Ausubel, Ruslan I. Sadreyev and W. Allan Walker

    Citation: Microbiome 2016 4:68

    Content type: Research

    Published on:

  13. The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <...

    Authors: Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Andrew Nelson, Bashir Abdulkadir, Tom Skeath, Joseph F. Petrosino, John D. Perry, Janet E. Berrington and Stephen P. Cummings

    Citation: Microbiome 2016 4:67

    Content type: Research

    Published on:

  14. Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a ...

    Authors: Matthew B. Rogers, Brian Firek, Min Shi, Andrew Yeh, Rachel Brower-Sinning, Victoria Aveson, Brittany L. Kohl, Anthony Fabio, Joseph A. Carcillo and Michael J. Morowitz

    Citation: Microbiome 2016 4:66

    Content type: Research

    Published on:

  15. The International Space Station (ISS) represents a unique biotope for the human crew but also for introduced microorganisms. Microbes experience selective pressures such as microgravity, desiccation, poor nutr...

    Authors: Maximilian Mora, Alexandra Perras, Tatiana A. Alekhova, Lisa Wink, Robert Krause, Alina Aleksandrova, Tatiana Novozhilova and Christine Moissl-Eichinger

    Citation: Microbiome 2016 4:65

    Content type: Research

    Published on:

  16. Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the...

    Authors: Melissa Ly, Marcus B. Jones, Shira R. Abeles, Tasha M. Santiago-Rodriguez, Jonathan Gao, Ivan C. Chan, Chandrabali Ghose and David T. Pride

    Citation: Microbiome 2016 4:64

    Content type: Research

    Published on:

  17. Staphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient’s risk of...

    Authors: Claire L. McMurray, Katherine J. Hardy, Szymon T. Calus, Nicholas J. Loman and Peter M. Hawkey

    Citation: Microbiome 2016 4:63

    Content type: Research

    Published on:

  18. There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of ...

    Authors: Jonathan Thorsen, Asker Brejnrod, Martin Mortensen, Morten A. Rasmussen, Jakob Stokholm, Waleed Abu Al-Soud, Søren Sørensen, Hans Bisgaard and Johannes Waage

    Citation: Microbiome 2016 4:62

    Content type: Methodology

    Published on:

  19. Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy s...

    Authors: Euan Watt, Matthew R. Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I. Murray, Emad El-Omar and Georgina L. Hold

    Citation: Microbiome 2016 4:61

    Content type: Research

    Published on:

  20. Airway abnormalities and lung tissue citrullination are found in both rheumatoid arthritis (RA) patients and individuals at-risk for disease development. This suggests the possibility that the lung could be a ...

    Authors: Jose U. Scher, Vijay Joshua, Alejandro Artacho, Shahla Abdollahi-Roodsaz, Johan Öckinger, Susanna Kullberg, Magnus Sköld, Anders Eklund, Johan Grunewald, Jose C. Clemente, Carles Ubeda, Leopoldo N. Segal and Anca I. Catrina

    Citation: Microbiome 2016 4:60

    Content type: Research

    Published on:

  21. There is a significant demand for colorectal cancer (CRC) screening methods that are noninvasive, inexpensive, and capable of accurately detecting early stage tumors. It has been shown that models based on the...

    Authors: Nielson T. Baxter, Charles C. Koumpouras, Mary A. M. Rogers, Mack T. Ruffin IV and Patrick D. Schloss

    Citation: Microbiome 2016 4:59

    Content type: Research

    Published on:

  22. The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth...

    Authors: Anita Mitra, David A. MacIntyre, Julian R. Marchesi, Yun S. Lee, Phillip R. Bennett and Maria Kyrgiou

    Citation: Microbiome 2016 4:58

    Content type: Review

    Published on:

  23. Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and pro...

    Authors: Francesca De Filippis, Nicoletta Pellegrini, Luca Laghi, Marco Gobbetti and Danilo Ercolini

    Citation: Microbiome 2016 4:57

    Content type: Short report

    Published on:

  24. Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed ...

    Authors: Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H. Janssen, Weibing Shi, Jeff Froula, Edward M. Rubin and Graeme T. Attwood

    Citation: Microbiome 2016 4:56

    Content type: Research

    Published on:

  25. Although diet is known to have a major modulatory influence on gut microbiota, knowledge of the specific roles of particular vitamins, minerals, and other nutrients is limited.

    Authors: Siddhartha Mandal, Keith M. Godfrey, Daniel McDonald, Will V. Treuren, Jørgen V. Bjørnholt, Tore Midtvedt, Birgitte Moen, Knut Rudi, Rob Knight, Anne Lise Brantsæter, Shyamal D. Peddada and Merete Eggesbø

    Citation: Microbiome 2016 4:55

    Content type: Research

    Published on:

  26. Clostridium difficile is the most common known cause of antibiotic-associated diarrhea. Upon the disturbance of gut microbiota by antibiotics, C. difficile establishes growth and relea...

    Authors: Manli Y. Davis, Husen Zhang, Lera E. Brannan, Robert J. Carman and James H. Boone

    Citation: Microbiome 2016 4:53

    Content type: Research

    Published on:

  27. Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple dis...

    Authors: Maria Hammond, Felix Homa, Helene Andersson-Svahn, Thijs J. G. Ettema and Haakan N. Joensson

    Citation: Microbiome 2016 4:52

    Content type: Methodology

    Published on:

  28. Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein c...

    Authors: Alessandro Tanca, Antonio Palomba, Cristina Fraumene, Daniela Pagnozzi, Valeria Manghina, Massimo Deligios, Thilo Muth, Erdmann Rapp, Lennart Martens, Maria Filippa Addis and Sergio Uzzau

    Citation: Microbiome 2016 4:51

    Content type: Research

    Published on:

  29. End-stage renal disease (ESRD) is associated with uremia and increased systemic inflammation. Alteration of the intestinal microbiota may facilitate translocation of endotoxins into the systemic circulation le...

    Authors: Janice Crespo-Salgado, V. Matti Vehaskari, Tyrus Stewart, Michael Ferris, Qiang Zhang, Guangdi Wang, Eugene E. Blanchard, Christopher M. Taylor, Mahmoud Kallash, Larry A. Greenbaum and Diego H. Aviles

    Citation: Microbiome 2016 4:50

    Content type: Research

    Published on:

  30. Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored.

    Authors: Weipeng Zhang, Jin Sun, Huiluo Cao, Renmao Tian, Lin Cai, Wei Ding and Pei-Yuan Qian

    Citation: Microbiome 2016 4:49

    Content type: Research

    Published on:

  31. Fresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli. However, the high number of commensal bacteria found on sprouted seeds hampers th...

    Authors: Heike Margot, Roger Stephan and Taurai Tasara

    Citation: Microbiome 2016 4:48

    Content type: Research

    Published on:

  32. We investigated whether the carriage of Blastocystis in IBS patients was associated with differences in the faecal microbiota. Forty patients with diarrhoea-predominant IBS (26 Blastocystis-positive and 14 Blasto...

    Authors: Robyn Nagel, Rebecca J. Traub, Richard J. N. Allcock, Marcella M. S. Kwan and Helle Bielefeldt-Ohmann

    Citation: Microbiome 2016 4:47

    Content type: Short report

    Published on:

  33. Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species ma...

    Authors: Jessica J. Eichmiller, Matthew J. Hamilton, Christopher Staley, Michael J. Sadowsky and Peter W. Sorensen

    Citation: Microbiome 2016 4:44

    Content type: Research

    Published on:

  34. The editors of Microbiome would like to thank all our reviewers who have contributed to the journal in 2015.

    Authors: Jacques Ravel and Eric Wommack

    Citation: Microbiome 2016 4:43

    Content type: Reviewer acknowledgement

    Published on:

  35. Reduced microbial diversity in human intestines has been implicated in various conditions such as diabetes, colorectal cancer, and inflammatory bowel disease. The role of physical fitness in the context of hum...

    Authors: Mehrbod Estaki, Jason Pither, Peter Baumeister, Jonathan P. Little, Sandeep K. Gill, Sanjoy Ghosh, Zahra Ahmadi-Vand, Katelyn R. Marsden and Deanna L. Gibson

    Citation: Microbiome 2016 4:42

    Content type: Research

    Published on:

  36. The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by...

    Authors: Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Massimo Pindo, Daniela Renzi, Lisa Rizzetto, Irene Stefanini, Antonio Calabrò and Carlotta De Filippo

    Citation: Microbiome 2016 4:41

    Content type: Research

    Published on:

  37. In this manuscript, we investigate the “stones best left unturned” of sample storage and preparation and their implications for the next-generation sequencing of infant faecal microbial communities by the 16S ...

    Authors: Alexander G. Shaw, Kathleen Sim, Elizabeth Powell, Emma Cornwell, Teresa Cramer, Zoë E. McClure, Ming-Shi Li and J. Simon Kroll

    Citation: Microbiome 2016 4:40

    Content type: Research

    Published on:

  38. Antibiotics are a mainstay of treatment for bacterial infections worldwide, yet the effects of typical antibiotic prescriptions on human indigenous microbiota have not been thoroughly evaluated. We examined th...

    Authors: Shira R. Abeles, Marcus B. Jones, Tasha M. Santiago-Rodriguez, Melissa Ly, Niels Klitgord, Shibu Yooseph, Karen E. Nelson and David T. Pride

    Citation: Microbiome 2016 4:39

    Content type: Research

    Published on:

  39. Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic unde...

    Authors: Miguel I. Uyaguari-Diaz, Michael Chan, Bonnie L. Chaban, Matthew A. Croxen, Jan F. Finke, Janet E. Hill, Michael A. Peabody, Thea Van Rossum, Curtis A. Suttle, Fiona S. L. Brinkman, Judith Isaac-Renton, Natalie A. Prystajecky and Patrick Tang

    Citation: Microbiome 2016 4:20

    Content type: Methodology

    Published on:

  40. Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease ons...

    Authors: Alison Morris, Joseph N. Paulson, Hisham Talukder, Laura Tipton, Heather Kling, Lijia Cui, Adam Fitch, Mihai Pop, Karen A. Norris and Elodie Ghedin

    Citation: Microbiome 2016 4:38

    Content type: Research

    Published on:

  41. Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway mi...

    Authors: R. L. Marsh, M. Kaestli, A. B. Chang, M. J. Binks, C. E. Pope, L. R. Hoffman and H. C. Smith-Vaughan

    Citation: Microbiome 2016 4:37

    Content type: Research

    Published on:

  42. Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys i...

    Authors: Kate L. Ormerod, David L. A. Wood, Nancy Lachner, Shaan L. Gellatly, Joshua N. Daly, Jeremy D. Parsons, Cristiana G. O. Dal’Molin, Robin W. Palfreyman, Lars K. Nielsen, Matthew A. Cooper, Mark Morrison, Philip M. Hansbro and Philip Hugenholtz

    Citation: Microbiome 2016 4:36

    Content type: Research

    Published on:

  43. Upper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications...

    Authors: Clark A. Santee, Nabeetha A. Nagalingam, Ali A. Faruqi, Gregory P. DeMuri, James E. Gern, Ellen R. Wald and Susan V. Lynch

    Citation: Microbiome 2016 4:34

    Content type: Research

    Published on:

  44. The fermentation of dietary fiber to various organic acids is a beneficial function provided by the microbiota in the human large intestine. In particular, butyric acid contributes to host health by facilitati...

    Authors: A. Venkataraman, J. R. Sieber, A. W. Schmidt, C. Waldron, K. R. Theis and T. M. Schmidt

    Citation: Microbiome 2016 4:33

    Content type: Research

    Published on:

  45. The National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health convened a Working Group on the Microbiome in Cardiovascular, Pulmonary and Hematologic Health and Diseases from June ...

    Authors: Shimian Zou, Lis Caler, Sandra Colombini-Hatch, Simone Glynn and Pothur Srinivas

    Citation: Microbiome 2016 4:32

    Content type: Meeting Report

    Published on:

Annual Journal Metrics

\